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Course Objective:
The course aims to provide an understanding of the principles and application of
proteins, secondary metabolites and enzyme biochemistry in therapeutic
applications and clinical diagnosis. The theoretical understanding of biochemical
systems would certainly help to interpret the results of laboratory experiments.
Course Contents:
Module I
Enzymes: Introduction and scope, Nomenclature, Mechanism of Catalysis.
Module II
Specificity of enzyme action, monomeric and oligomeric enzymes, Enzyme inhibition.
Module III
Enzyme Kinetics: Single substrate steady state kinetics; Michaelis Menten
equation, Linear plots, King-Altman’s method; Inhibitors and activators;
Multisubstrate systems; ping-pong mechanism, Alberty equation, Sigmoidal kinetics
and Allosteric enzymes
Module IV
Extraction & purification of enzymes.
Module V
Immobilization of Enzymes; Advantages, Carriers, adsorption, covalent coupling,
cross-linking and entrapment methods, Micro-environmental effects.
Module VI
Biotechnological applications of enzymes: Large scale production and purification
of enzymes, enzyme utilization in industry, enzymes and recombinant DNA technology
Examination Scheme:
References
• Enzymes Biochemistry, Biotechnology, Clinical Chemistry, Trevor Palner
Dr. S. M. Bhatt smbhatt@amity.edu , smbhatt_bhu@rediffmail.com phone 9313993840
Amity University Uttar Pradesh
•
• Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady State
Enzyme Systems, I.H. Segel, Wiley-Interscience
• Industrial Enzymes & their applications, H. Uhlig, John Wiley and Sons Inc.
Course Objective:
The laboratory will help the students to isolate enzymes from different sources,
enzyme assays and studying their kinetic parameters which have immense importance
in industrial processes.
Course Contents:
Module I
Isolation of enzymes from plant and microbial sources.
Module II
Enzyme assay; activity and specific activity – determination of amylase, nitrate
reductase, cellulase, protease
Module III
Purification of Enzyme by ammonium sulphate fractionation
Module IV
Enzyme Kinetics: Effect of varying substrate concentration on enzyme activity,
determination of Michaelis-Menten constant (Km) and Maximum Velocity (Vmax.) using
Lineweaver-Burk plot.
Module V
Effect of Temperature and pH on enzyme activity
Module VI
Enzyme immobilization
Examination Scheme:
Major Experiments: 40
Minor Experiments: 20
Spotting: 10
Viva: 20
Records: 10
Total: 100
Definition
Introduction
Historical aspects in enzyme discovery
Classification of Enzymes.
application of enzymes
Module I
Enzymes: Introduction and scope, Nomenclature, Mechanism of Catalysis.
Chapter- 1
Enzymes an introduction
Definition
Kinetics: Field of study that deals with determining the rates of biological,
chemical, and physical processes (e.g., how quickly reactants are converted into
products) under various conditions.
Metalloprotein: Protein that incorporates one or more metals into its molecular
structure by binding individual metal ions [e.g., iron (Fe2+ or Fe3+), zinc
(Zn2+), or magnesium (Mg2+)] or nonprotein organic compounds containing metals.
Metalloprotein are important components of electron transport chains.
Steady State: Growth state in which the concentration of bacterial cells is in
equilibrium with the concentration of nutrients or substrates (i.e., the
concentrations remain constant over time).
Introduction
Enzymes are the wonderful creations of the biological system. Various biological
reactions go on smoothly without single mistakes. Enzymes have specificity not
only toward the substrate but also recovered in the end of the reactions. They are
also regulated very precisely. Normal monomeric enzyme like trypsin and pepsin are
regulated by removing or adding a small piece of peptide that make them inactive
or active while the complex enzymes are regulated by end product , or by
allosteric mechanism. Homones in several cases also play important role in
regulations like in formation of lactose by progestron and prolactin before and
after the birth of baby. The system (complex enzymes are termed as system)
specifically and precisely binds to the substrate and convert them into the
required product that sometimes becomes the substrate for next reaction for next
enzyme to act on. Total activity of enzyme depends on several factors like acid
base, structural orientations and strain, electrostatic interactions (by metal
ions) and formation of covalent bond. In several cases certain organic molecule or
metals termed as co-enzyme or cofactor that either or electron or proton acceptor
or by electrostatic mechanism are needed to convert a substrate to product.
Actually enzymes activity depends on the precise function of a small part called
as the active site that is a small pocket like structure that contains various
helper amino acid residues that by electron or proton transport make bond of the
substrate molecule weaker and rearrange them into a stable product at normal
temperature and pressure. Any deficiency in the formation of these pockets like
structure may render the whole enzyme to become inactive that leads to certain
deficiency diseases. Modern techniques like MOLDI-TOF, x-ray crystallography along
with sequencer helped a lot to scientist in deciphering the mechanism of enzyme
activity. Knowledge of enzyme activity and its detailed mechanism made it possible
to design artificial enzyme in the lab to cop up with many enzyme related
metabolic problems or complex viral enzyme like AIDS.
Historical aspects in enzyme discovery
1860 Bertholate disrupted yeast cell and isolated extract that catalyzed
conversion of sucrose to glucose and fructose.
1894 Fisher proposed lock and key hypothesis to explain the mechanism of
1920 Sumner crystallized Urease first time that hydrolyze the urea into CO2 and
NH3.
1958 Koshland proposed induced fit model to account for enzyme catalytic power
and specificity.
1986 RNase was found to work as catalyst by Cech. They were called as
Classification of Enzymes.
The I.U.B. system also specifies a textual name for each enzyme. The enzyme's name
is comprised of the names of the substrate(s), the product(s) and the enzyme's
functional class. Because many enzymes, such as alcohol dehydrogenase, are widely
known in the scientific community by their common names, the change to I.U.B.-
approved nomenclature has been slow. In everyday usage, most enzymes are still
called by their common name.
In 1955 International Union of Biochemistry classified the enzyme on the basis of
kind of reaction they performed, substrate they act, position of group or
functional group and number of amino acid. Therefore they divided the enzyme into
six major classes. Suffix added in the enzyme is –ase to the name of substrate or
to word. Urea hydrolysis is done by the Urease. There are major 6 classes and
each with the subclass. Each enzyme has assigned 4 digit classification number and
a systematic name. For e.g. EC 2.7.1.1 means first digit indicates the class
transferases, and the second digit denotes the subclass, third and four digits is
the group transfer or accepted as shown in figure.
Classes of enzyme: there are six classes of enzyme according to reaction type they
performed
D-hexose-6-phosphotransferase (hexokinase)
D hexose + ATP------------------------------------ D hexose-6-
phosphate + ADP
4. Lyases- These enzymes catalyze the removal of groups and create double bond
in non-aqueous media. An example would be the decarboxylases. Its second digit
denotes the bond broken and third digit denotes type of group removed like 1 for
carboxyl group and 2 for aldehyde group and 3 for ketoacid group.
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligase
Electron transfer
Group transfer
Hydrolysis
Formation of C-C,C-S,C-O,C-N.
Cytochrome oxidase
Carbonic anhydrase
Alcohol dehydrogenase
Hexokinase
Glucose -6-phosphate
Pyruvate kinase.
Arginase
Ribonucleotide reductase
Pyruvate kinase.
Urease
Dinitrogenase
Glutathione peroxidase
Fe+2 or Fe+3
Cu+2
Zn+2
Mg+2
Mn+2
K+
Ni+2
Mo
Se
Chapter-2
Types of Enzymes
A. Simple enzymes
They are composed solely of protein, single or multiple subunits. If they consist
of single polypeptide unit they are termed as monomeric enzyme ( sometime like in
chymotrypsinogen they are of three polypeptide and are inctive zymogen form and
after cleavage from pie to delta and finally to alpha trypsinogen they become
active and consist of two polypepide and still they are termed as monomeic enzyme
since they are read in continous sequences). Monomeric enzymes are of few 200-300
amino acid and molecular weight ranges from 15,000 kd to 35,000 kd (kilodalton)
like trypsin , elastases, that are termed as serine proteases because of an active
serine residue. Serine residue become active due to relay mechanism of electron
transfer (adjacent amino acid can transfer electron in series of pathway and make
the serine active sufficient to active at electron deficient or carbocation center
of substrate making breaking of bond possible. Thus a slight decrease in entropy
make free energy negative that is essential for stabilization of intermediate
transition state). Other enzyme consisting of two or more polypeptide are termed
as oligomeric enzyme. Like alcohol dehydrogenase (contains two polypeptide and
Zn+2 and act by electrostatic meechansim) and lactate dehydrogenase that requires
cofactor NAD+ or NADP+ for its activity and occurs in multiple unit like H4, H3M,
H2M2, HM3, and M4. Thus they contain four subunit and substrate can bind to each
of four subunit and they are termed as isozyme. Actually Ogstien considered three
sites on enzyme one or two binding site along with one catalytic subunit. Lactate
is formed from pyruvate in aneorbic condition and thus pyruvate accumulation are
avoided. Lactate arev then transported to other organs.
B. Complex enzymes Complex enzymes
They involve protein plus small organic molecule(s) or metal. Entire complex
called “holoenzyme”. Protein part called “apoenzyme”. Non-protein part called
“coenzyme” or “prosthetic Group”. They form the integral part of the enzyme and
remain adjacent to the catalytic center to provide coordination for interacting
with substrate functional group. Therefore multiple substrates can interact with
enzyme and react with them. The detailed mechanism will be discussed in next topic
under the head of enzyme specificities. These rules give each enzyme a unique
number.
Enzymes are also classified on the basis of their composition. Enzymes composed
completely of protein are known as simple enzymes in contrast to complex enzymes,
which are composed of protein plus a relatively small organic molecule. Complex
enzymes are also known as holoenzymes. In this terminology the protein component
is known as the apoenzyme, while the non-protein component is known as the
coenzyme or prosthetic group where prosthetic group describes a complex in which
the small organic molecule is bound to the apoenzyme by covalent bonds; when the
binding between the apoenzyme and non-protein components is non-covalent, the
small organic molecule is called a coenzyme. Many prosthetic groups and coenzymes
are water-soluble derivatives of vitamins. It should be noted that the main
clinical symptoms of dietary vitamin insufficiency generally arise from the
malfunction of enzymes, which lack sufficient cofactors derived from vitamins to
maintain homeostasis.
The non-protein component of an enzyme may be as simple as a metal
ion or as complex as a small non-protein organic molecule. Enzymes that require a
metal in their composition are known as metalloenzymes if they bind and retain
their metal atom(s) under all conditions that is with very high affinity. Those
have a lower affinity for metal ion, but still require the metal ion for activity,
are known as metal-activated enzymes.
Role of Coenzymes
A. Catalysts
Catalysts are substances that increase product formation by lowering the energy
barrier (activation energy) for the product to form and increase the favorable
orientation of colliding reactant molecules for product formation to be
successful.
There are two types of catalysts:
1. Heterogeneous Catalysts
2. Homogeneous Catalysts
Heterogeneous catalysts are those that provide a surface for the reaction to
proceed upon. The catalyst and the reactant molecules are not in the same phase.
This is sometimes referred to as surface catalysts. Certain transition state
metals like Palladium, Platinum, Nickel, and Iron serve as industrial catalysts
that catalyze a wide variety of reactions such as Hydrogenation.
Homogeneous catalysts are catalysts that exist in the same phase as the reactant
molecules usually in a solution. Acids and Bases in solution serve as catalysts in
a wide variety of Organic reactions. Most industrial catalysts are responsible for
more than one catalysis among reactants and are considered relatively non-specific
in what they catalyze. Enzymes are very different. All current research suggests
that enzymes are extremely specific in what a given enzyme catalyzes. Indeed, most
enzyme molecules catalyze only one specific reaction but it does so in a
phenomenally efficient manner. One enzyme molecule might be responsible for
converting thousands of reactant molecules called substrate molecules into
product.
B. Biocatalyst or Enzymes
ES
Free energy G
E
Enzyme lowers the activation energy.
Reaction coordinate
R= reactant
P = product
∆G = ∆H – T ∆S this is the thermodynamical term used to explain the stability
of reactions. A negative free energy stabilizes the system and makes the reaction
possible. ∆H denotes the enthalpy and ∆S denotes the entropy. In unstabilized or
uncatalysed system ∆S is positive and formation of transition complex renders
them lowering of entropy leading to make overall free energy negative. A more
ordered system also has lower entropy for example free amino acid has more entropy
than the amino acid linked with the peptide bond.
In cells and organisms most reactions are catalyzed by enzymes, which are
regenerated during the course of a reaction. These biological catalysts are
physiologically important because they speed up the rates of reactions many folds
(up to 10 6 to 10 15 times than normal one) that would otherwise be too slow to
support life. Enzymes increase reaction rates--- sometimes by as much as one
millionfold, but more typically by about one thousand fold. Catalysts speed up the
forward and reverse reactions proportionately so that, although the magnitude of
the rate constants of the forward and reverse reactions is are increased, the
ratio of the rate constants remains the same in the presence or absence of enzyme.
Since the equilibrium constant is equal to a ratio of rate constants, it is
apparent that enzymes and other catalysts have no effect on the equilibrium
constant of the reactions they catalyze. Enzymes increase reaction rates by
decreasing the amount of energy required to form a complex of reactants that is
competent to produce reaction products. This complex is known as the activated
state or transition state complex for the reaction. Enzymes and other catalysts
accelerate reactions by lowering the energy of the transition state. The free
energy required to form an activated complex is much lower in the catalyzed
reaction. The amount of energy required to achieve the transition state is
lowered; consequently, at any instant a greater proportion of the molecules in the
population can achieve the transition state. The result is that the reaction rate
is increased.
Unit of activity
Micromole substrate consumed or product formed per minute is referred as IU
international unit. SI unit is ‘katal’ that is defined as Micromole substrate
consumed or product formed per second.
Chapter 3
Enzyme Specificity
Although enzymes are highly specific for the kind of reaction they catalyze, the
same is not always true of substrates they attack. For example, while succinic
dehydrogenase (SDH) always catalyzes an oxidation-reduction reaction and its
substrate is invariably succinic acid, alcohol dehydrogenase (ADH) always
catalyzes oxidation-reduction reactions but attacks a number of different
alcohols, ranging from methanol to butanol. Generally, enzymes having broad
substrate specificity are most active against one particular substrate. In the
case of ADH, ethanol is the preferred substrate.
Enzymes also are generally specific for a particular steric configuration (optical
isomer) of a substrate. Enzymes that attack D sugars will not attack the
corresponding L isomer. Enzymes that act on L amino acids will not employ the
corresponding D optical isomer as a substrate. The enzymes known as racemases
provide a striking exception to these generalities; in fact, the role of racemases
is to convert D isomers to L isomers and vice versa. Thus racemases attack both D
and L forms of their substrate.
As enzymes have a more or less broad range of substrate specificity, it follows
that a given substrate may be acted on by a number of different enzymes, each of
which uses the same substrate(s) and produces the same product(s). The individual
members of a set of enzymes sharing such characteristics are known as isozymes.
These are the products of genes that vary only slightly; often, various isozymes
of a group are expressed in different tissues of the body. The best studied set of
isozymes is the lactate dehydrogenase (LDH) system. LDH is a tetrameric enzyme
composed of all possible arrangements of two different protein subunits; the
subunits are known as H (for heart) and M (for skeletal muscle). These subunits
combine in various combinations leading to 5 distinct isozymes. The all H isozymes
is characteristic of that from heart tissue, and the all M isozymes is typically
found in skeletal muscle and liver. These isozymes all catalyze the same chemical
reaction, but they exhibit differing degrees of efficiency. The detection of
specific LDH isozymes in the blood is highly diagnostic of tissue damage such as
occurs during cardiac infarct.
Thus enzyme may be group specific if they act over on several closely related
substrate for example alcohol dehydrogenase on which several alcohol are
substrate, or act over by specific substrate like glucokinase that transfer
phosphate from ATP to glucose. They exhibit absolute specificity. They may be of
product specific or substrate specific or stereospecific act on specific stereo
molecules like alanine recemase acts on only L–alanine to convert them into D-
alanine.
Specificity is actually decided by amino acid residue present in the active site
of enzyme that is capable of binding to the substrate molecule. The amino acids
that are not involved in binding to the substrate do not have any contribution
towards the specificity. Therefore both the subunit of enzyme like binding and
catalytic site is the active center of the enzymes. They are only small part of
the total enzyme and they must be accessible to the substrate. For example
chymotrypisn are inactive because their zymogen form don’t have accessible
catalytic center. Therefore further cleavage occurs to make them active exposing
the catalytic center. For proper catalytic activity their side chains must be of
suitable size, shape, and character and must not block the substrate from binding.
For example of several seine proteases like chymostrypsinogen, trypsin and
elastases having almost similar structure but differ in specificity due to
variations in the side chain amino acids. In Elastases substrate are blocked from
binding due to presence of two bulky side chain valine and threonine while
chymostrypsin and trypsin have no bulky group but instead contains glycine amino
acid that facilitates the substrate to approach easily. Replacement of glycine by
alanine make the enzyme more active. Active site most often contains both polar as
well as non-polar amino acid thus facilitates the interaction with both
hydrophilic and hydrophobic amino acid. This is the reason why sometime in
presence of non-polar solvent like DMSO dimethylsulphoxide some enzyme are more
reactive. Other examples include chymotrypsin, alcohol dehydrogenase, etc., ie. a
variety of enzymes from different classes have been shown to function in non-
aqueous media. Specificity May Be Very Strict Or Relatively Broad
Broad specificity is shown by many degradative enzymes e.g. alkaline phosphatase,
which removes phosphates from a wide range of molecules, or carboxypeptidase which
snips the C-terminal amino-acid off many polypeptide chains.
Intermediate specificity is most common e.g. alcohol (ethanol) dehydrogenase of E.
coli will act on C2, C3, and C4 alcohols; pyruvate dehydrogenase will also use the
C4 homolog of pyruvate etc.Some enzymes are absolutely specific. Aspartase
catalyses the interconversion of aspartate and fumarate:
L-Aspartate ↔ Fumarate + NH3
Fig . showing asymmetric binding site in the enzymes. The model of enzyme
structure was proposed by fisher as three point one catalytic site and others are
binding site. Sometime enzymes have both catalytic as well as binding site as same
site. Such enzymes follows michaelis behaviour while others having complex and
separate site behave in more complex way as allosteric site.
It will only use aspartate (not similar amino acids such as glutamate) and only
the L-isomer. Nor will it add NH3 to maleate, the cis isomer of fumarate.
Three theory were proposed to explain the specificity of enzyme but all of them
are correct and none of them are alone operative in the enzyme specificity.
1- Lock and key hypothesis
2- Induced fit hypothesis.
3- Transition state stabilization
Chapter 4
Enzyme-Substrate Interactions
The favored model of enzyme substrate interaction is known as the induced fit
model. This model proposes that the initial interaction between enzyme and
substrate is relatively weak, but that these weak interactions rapidly induce
conformational changes in the enzyme that strengthen binding and bring catalytic
sites close to substrate bonds to be altered. After binding takes place, one or
more mechanisms of catalysis generate transition- state complexes and reaction
products. The possible mechanisms of catalysis are five in number:
1. Catalysis by approximation
2. General acid, general base catalysis
3. Catalysis by electrostatic effects
4. Covalent catalyis (nucleophilic or electrophilic)
5. Catalysis by strain or distortion
d. Covalent Catalysis:
• In catalysis that takes place by covalent mechanisms, the substrate is
oriented to active sites on the enzymes in such a way that a covalent intermediate
forms between the enzyme or coenzyme and the substrate. One of the best-known
examples of this mechanism is that involving proteolysis by serine proteases,
which include both digestive enzymes (trypsin, chymotrypsin, and elastase) and
several enzymes of the blood clotting cascade. These proteases contain an active
site serine whose R group hydroxyl forms a covalent bond with a carbonyl carbon of
a peptide bond, thereby causing hydrolysis of the peptide bond. Biologically
important nucleophiles are negatively charged or contain unshared electrons
• Biologically important electrophiles generally are either positively
charged, or contain unfilled valence electron shells, or contain an
electronegative atom
Covalent Intermediates
Here the strategy is to lower the transition state energy "hump" by taking an
alternative reaction pathway therefore sometime it is also called as alternative
pathway catalysis. Sometime nucleophilic catalyst form intermediate more rapidly
than normal catalysis.
In covalent catalysis, a covalent bond is transiently formed between the substrate
and the enzyme (or coenzyme). This reaction usually involves a nucleophilic group
on the enzyme and an electrophilic group on the substrate
Uncatalysed: BX + Y BY + X
Catalysed: BX + Enz Enz-B + X
Enz-B + Y Enz + BY
Where, B is usually some chemical group such as a phosphate group, acyl group or
glycosyl group. Phosphoenzymes usually attach the phosphate to serine or
histidine. Serine type - phosphoglucomutase, alkaline phosphatase. Histidine type
- glucose 6 phosphatase, phosphotransferase system. Acyl enzymes usually attach
the acyl group at an active serine or cysteine residue. Most proteases (eg
trypsin, elastase, subtilisin are serine enzymes. Cysteine enzymes include papain
(a protease), glyceraldehyde phosphate dehydrogenase and most enzymes using acyl
CoA derivatives.
The proteases are globular, water soluble proteins that function as enzymes. They
catalyze the hydrolyses of peptide bonds in proteins. Being enzymes, proteases can
be characterized by their substrate affinity and the catalytic rate of the
reaction. Using proteases to study the effects of single amino acid substitutions
(mutations) on catalytic rate and substrate affinity demonstrated that these two
properties are linked and that this linkage can be explained by analyzing the
conformation of the catalytic or active site of the enzyme. This analysis showed
that four major functional groups are found in the catalytic site of proteases and
based on this functional groups, 4 families of proteases have been defined:
a. Serine proteases
b. Cystein proteases
c. Aspartate proteases
d. Metallo proteases
This classification uses the functional group within the enzyme, and does not
relate to the substrate specificity of the proteases themselves. The name of the
protease family refers to an amino acid (e.g. aspartate) or a metal as co-enzyme
at the active site of the enzyme.
• The serine proteases are a class of enzymes that degrade proteins in which a
serine in the active site plays an important role in catalysis.
• The family includes among many others, Chymotrypsin and trypsin, which we’ve
talked about, and Elastase.
• All three enzymes are similar in structure, and they all have three
important conserved residues–a histidine, an aspartate, and a serine.
Lysozyme
SUMMARY
The maximum binding energy between an enzyme and a substrate will occur when there
is
maximal complementarity between the structure of the binding site and the
structure of the
substrate.
• The structure of the substrate changes during the reaction, becoming first
the transition state and then products.
• The structure of the enzyme can only be complementary to one form of the
substrate.
• If the structure of the active site is complementary to the transition
state, then binding increases as the reaction proceeds, which lowers the
activation energy.
• Having the active site bind the transition most strongly also means that
products are bound weakly, which favors dissociation of the products from the
enzyme once the reaction is complete.
• When the active site is complementary to the transition state the full
substrate binding energy is only realized as the reaction reaches the transition
state, which lowers the activation energy of the reaction by the magnitude of the
binding energy.
• It is possible that the substrate and enzyme interact unfavorably and this
unfavorable interaction is relived in the transition state.
• We might think that the substrate is under stress meaning that it is
subjected to forces but not distorted by them.
• It is more likely that the enzyme is strained, as for example in induced
fit.
Catalytic Power
Enzymes lower the energy of the transition state by stabilizing the original
reaction intermediate or by providing an alternative reaction pathway. Rate
increases by enzymes range from 108 to 1020 relative to the uncatalysed,
spontaneous reaction (e.g. 109 for alcohol dehydrogenase; 1016 for alkaline
phosphatase). Factors involved in enzyme rate increases: a) Proximity - up to 106
fold; b)Orientation - up to 100 fold c) Covalent enzyme-substrate intermediates -
around 1010 fold d) General acid-base catalysis - around 1010 fold ;e) Metal ion
catalysis - around 1010 fold; f) Distortion of the substrate - up to 108 fold (but
largely hypothetical)
a) Proximity
The enzyme binds the substrate so that the susceptible bond is very close to the
catalytic group in the active site or in close proximity in the active site. It
increases their concentration and and reduces entropy loss for subsequent
formation of a transition state. This has been called as proximation effect or
approximation effect. Therefore it appears that enzyme bound transition state is
the single most in determining whether the reaction should proceed. Calculations
indicate that the local concentration of substrate in the active site may be as
much as 50M whereas its concentration in the cytoplasm may be less than 1mM. Since
chemical reaction rates are proportional to the concentrations of the reactants a
rate enhancement of up to 106 may be generated by local concentration effects.
This effect is counteracted to some extent by the fact that the concentration of
enzyme active sites is low (the active site is a small portion of a very large
molecule; the total protein concentration in cytoplasm is 1 to 10mM at most).
b) Orientation
Proximity alone is insufficient. The reacting groups must be properly oriented.
Orbital steering hypothesis - binding of the substrate(s) to the enzyme aligns the
reactive groups so that the relevant molecular orbitals overlap. This increases
the probability of forming the transition state. For a typical bimolecular
reaction in free solution about 1/100 collisions between molecules of sufficient
energy actually leads to a reaction. Thus the maximum effect of orientation would
be 100-fold.
Consider the attack on an aryl ester by a carboxylic acid.
Now let's put both reacting groups on the same molecule - i.e. we will link R1 and
R2 together. As the five examples show, the relative rate gets greater as the
reacting groups are brought closer together. In addition, holding them in the
correct orientation also helps. (Ar = methoxyphenyl group.)
Enzymes are biological catalysts. With the exception of ribozymes, enzymes are
mainly proteins in nature, and may also possess lipid or sugar moieties. Their
main task is to decrease the activation energy (Eact) of a chemical reaction. The
whole biotechnology field depends on the activities of enzymes, either acting
alone or in concert.
Exploitation of enzymes is not a recent development. They have been used
throughout the ages in leather tanning, in cheese-making, in the preparation of
malted barley for beer brewing & the leavening of bread. These processes use
enzymes in the form of whole cells. Conceptually, it is easy to decide whether one
should use whole cells or isolated enzymes in a biotechnological process to
produce or transform compounds. Some processes require multi-step transformations,
eg. the synthesis of antibiotics, interferons, monoclonal antibodies, or ethanol
production from glucose. These transformations involve a number of enzymes acting
sequentially, along with the requirement for co-factor regeneration in several
steps. They are clearly candidates for using whole cells.
There may be some drawbacks to using whole cells in catalysis. These include
1. Competing side reactions from other enzymes.
2. Sterility problems often arise when one deals with whole cells.
3. Some conditions may lead to cell lysis, and this can result in loss of
biocatalysts or severely decrease reaction rate depending on the nature and type
of enzyme reaction.
4. Formation of by-products.
5. On the other hand, with one-step or two-step stereospecific transformations,
enzymes can be superior because their use will eliminate some of the potential
problems with using whole cells. The advantages of using enzymes include:
6. High catalytic rate possible.
7. Functions in moderate conditions.
8. Non-polluting catalysis.
9. Less by-products formed.
10. Less problem with sterility.
11. Optimizing 1 or 2 enzyme catalyzed reactions is easier than optimizing the
whole pathway in a whole cell.
12. Enzymes catalyze a wide range of reactions, some with high
stereospecificity, such as oxidation, reduction, dehydrogenation, dehalogenation,
hydration, dehydration, etc. Therefore, the scope of enzyme technology is very
broad.
13. Despite all these striking characteristics, enzyme have not been used widely
as compared to chemical catalysis. This is because the use of enzymes also suffers
from some serious drawbacks:
14. Most isolated enzymes are not stable enough for use under industrial
conditions. This may include poor stability with respect to temperature, pH, the
presence of metal ions, etc. This is not surprising considering that most enzymes
have evolved to function in a biological milieu where the conditions may differ
from those used in industry.
15. In cells, all enzymes are subject to turnover, ie. old ones are replaced by
new ones. This is difficult to do with isolated enzymes in vitro.
16. Most enzymes are water-soluble, and therefore, may be difficult to separate
from reactants or products.
17. Many useful enzymes are intracellular, and hence are difficult to isolate.
Abzymes
Catalytic antibodies are also known as abzymes, are capable of catalyzing specific
chemical reactions. They are able to perform this task because they have been
elicited against antigen known as transition state analogues, these are molecules
that closely resemble in shape and charge the reaction transition state (the
highest energy spices in reaction pathway known as activated complex). Enzyme
observed to bind transition complex but not the substrate, and the product. Enzyme
by forming the active site similar to the transition state, enzyme stabilizes or
lowers down the energy of this species. The effect is to accelerate the reaction
because the activation barrier is more easily overcome. This complementarity in
shape and charge to the transition state is readily demonstrated by the
effectiveness of transition state analogue is a phosphonate containing molecule
that mimics the transition state of the hydrolysis of the corresponding acyl
derivative. When an ester is hydrolysed the central carbonyl group changes from
planer sp2 structure to tetrahedral sp3. the phosphonate containing molecule
analogue is able to reproduce the shape of the transition state as well as the
partially negative charged oxygen. In addition, it is chemically stable, where as
the actual transition state exists only fleetingly. In this example, an enzyme
that catalysed the hydrolysis of this ester would also bind tightly to phosphonate
analogue. The general strategies behind the production of catalytic antibody is to
(i) design and synthesize a molecule whose shape is closely resemble to that of
transition state of the reaction one wishes to catalyze, (2) tether this molecule
to larger molecule, (3) elicit an immune response to this conjugate, (4) screen
the resultant monoclonal antibodies for catalytic activity of the type desired.
Antibodies that are elicited against transition state analogue and therefore have
the ability to bind them will be chemically and sterically complementary to the
transition state and will therefore be potentially capable of catalyzing the
reaction.
Table 7. 1
Exercises
LONG TYPE
1. Describe the six classes of enzyme with examples?
2. Define Biocatalyst ? Describe how biocatalyst lower down the activation
energy?
3. Define Enzyme ? Classify the Enzyme on the basis of enzyme commission?
4. Define holoenzyme ? write the role of apoenzyme, cofactor, and
metalloenzymes on enzyme activity.
5. Define enzyme specific activity? Write the different method of enzyme
substrate interaction in brief?
Short type
1. write short notes on following
a. Enzyme activity
b. Enzyme specificity
c. Enzyme commission.
d. Holoenzyme.
e. Cofactor
f. Metalloenzymes.
g. Coenzyme.
Module II
Specificity of enzyme action, monomeric and oligomeric enzymes, Enzyme inhibition.
Chapter-5
ENZYME KINETICS & INHIBITION
TERMS
Enzymes are protein catalysts of biological origin that, like all catalysts, speed
up the rate of a chemical reaction without being used up in the process. They
achieve their effect by temporarily binding to the substrate.
Competitive inhibition, when the substrate and inhibitor compete for binding to
the same active site.
Noncompetitive inhibition, when the inhibitor binds somewhere else on the enzyme
molecule reducing its efficiency.
Enzyme kinetics The study of the rate at which an enzyme works is called enzyme
kinetics.
Alloenzymes. If a gene exists in a heterozygous state, two different polypeptide
chains will be generated. They may be separated by gel electrophoresis under
favourable conditions. They may also differ in their rate of substrate turnover.
The gene product a, for example, may be inactive while that of A is fully active.
But all states in between are also possible. Furthermore, it was shown in numerous
examples that A may be favourable under certain environmental conditions while a,
is favourable under other conditions (more in the section about evolution).
Polypeptides (enzymes) that are encoded by different alleles are called
alloenzymes.
Isoenzymes. By duplication of the genetic material a gene may be present within a
haploid genome for two or more times. It is not important whether the gene loci
are on one chromosome or distributed over several chromosomes. The gene products
(enzymes) of the different gene loci (pseudoalleles) are called isoenzymes.
Competitive inhibitors are molecules that bind to the same site as the substrate -
preventing the substrate from binding as they do so - but are not changed by the
enzyme.
Noncompetitive inhibitors are molecules that bind to some other site on the enzyme
reducing its catalytic power.
INTRODUCTION
A B----------------------------1
-[A] = k[B]-----------------------2
[B] = k[A]--------------------3
In the second equation (of the 3 above) the negative sign signifies a decrease in
concentration of A as the reaction progresses, brackets define concentration in
molarity and the k is known as a rate constant. Rate constants are simply
proportionality constants that provide a quantitative connection between chemical
concentrations and reaction rates. Each chemical reaction has characteristic
values for its rate constants; these in turn directly relate to the equilibrium
constant for that reaction. Thus, reaction can be rewritten as an equilibrium
expression in order to show the relationship between reaction rates, rate
constants and the equilibrium constant for this simple case. The rate constant for
the forward reaction is defined as k+1 and the reverse as k-1.
At equilibrium the rate (v) of the forward reaction (A B) is by
definition is equal to that of the reverse or back reaction (B A), a
relationship which is algebraically symbolized as:
V forward = v reverse---------------4
V forward = k+1[A]---------------5
V reverse = k-1[B]----------------6
In the above equations, k+1 and k-1 represent rate constants for the forward and
reverse reactions, respectively. The negative subscript refers only to a reverse
reaction, not to an actual negative value for the constant. To put the
relationships of the two equations into words, we state that the rate of the
forward reaction [v forward] is equal to the product of the forward rate constant
k+1 and the molar concentration of A. The rate of the reverse reaction is equal to
the product of the reverse rate constant k-1 and the molar concentration of B.
At equilibrium, the rate of the forward reaction is equal to the rate of the
reverse reaction leading to the equilibrium constant of the reaction and is
expressed by:
This equation demonstrates that the equilibrium constant for a chemical reaction
is not only equal to the equilibrium ratio of product and reactant concentrations,
but is also equal to the ratio of the characteristic rate constants of the
reaction.
FIGURE 10. 1
FIGURE 10. 2
For this reaction the forward reaction rate would be written as:
V forward = k1 [ADP][H2PO4]---------------9
L. Michaelis and M. Menten in 1913 postulated that enzyme first combine reversibly
with the substrate to form an enzyme substrate complex in a relatively fast
reversible step and then product is released along with free enzyme.
Initial velocity
Michaelis-Menton constant
E + S ES ES* EP E +
P-------------------10
and
K1
E+S ES ………. 11
k-1
The ES complex then breaks down in a slower second step to
yield the free enzyme and the reaction product P: k2
ES -------- E+P ……………..(12)
Since the second step is slower and therefore it limits the rate of overall
reaction. It means that, overall rate of enzyme-catalyzed reaction must be
proportional to the concentration of species that reacts in the second step, which
is ES.
At any time the enzyme-catalyzed reaction, the enzyme exists in the combined form
E or uncombined form ES. At low [S], most of the enzyme will be in uncombined form
E. here the rate will be proportional to the [s] because the equilibrium of
equation will shift for the formation of more ES as S is increased. The maximum
initial rate is observed when the entire enzyme E0 is present as ES complex and
the concentration of E is very small. Under these state the enzyme is “saturated”
with its substrate, so that further increase in [S] have no effect on rate. This
is the condition when [S] is sufficiently high that essentially all the free
enzyme is converted into the ES form. After the ES complex breaks down to yield
product P the enzyme is free to catalyze another reaction.
a. Pre-steady state:--
The duration in which ES formation takes place is called as pre-steady
state. It is too difficult to observe because of very short time.
b. Steady state:--
Here ES complex is constant over a period of time.
Derivation:
To Simplify the equation add the term k1[E] [S] to both side, we finally get
K1[Et][S]
[ES] = ------------------
--------------------------------(20)
k1[S] + k-1+ k2
or
[Et][S]
[ES] = ------------------
--------------------------------(21)
[S] +( k-1+ k2)/ k1
The term ( k-1+ k2)/ k1 is called as Michaelis—Menten equation, the rate equation
of one substrate, enzyme catalyzed reaction and is denoted by the Km. this defines
the rate of initial velocity and maximum velocity. Putting value of ES in equation
21 from equation 13 gives new final equation that is
What will happen if the initial velocity is exactly one-half of maximum velocity?
So if V0 = Vmax/2, then
--------------------24
This represent that Km is equivalent to the substrate concentration at which Vo is
one half Vmax. Note that Km has unit of molarity. This shows that the Michaelis-
Menten constant equals the substrate concentration at half-maximal reaction
velocity. Consequently, the dimension of kM is Mol. The smaller the value of kM ,
the higher is the enzyme's affinity for its substrate. See figure 10.3. Km is
(roughly) an inverse measure of the affinity or strength of binding between the
enzyme and its substrate. The lower the Km, the greater the affinity (so the lower
the concentration of substrate needed to achieve a given rate).
Note :for the Michaelis-Menten reaction, k2 is the rate limiting ; thus
k2<<k-1
So Km reduces to
Km=k-1/k1, and it is defined as dissociation constant,
Ks for the ES complex.
Figure 10. 4 Graphical method to find the value of Km by plotting the graph
between the 1/Vo verses 1/[S]
10.4 Catalytic efficiency and Turnover number.
Catalytic efficiency is denoted by the ratio of Kcat/ Km. K cat is the turn over
number of enzyme . See from the table below the enzyme having very high value of
Kcat have high capacity to convert substrate into the product The turnover number
is a measure of catalytic activity. The kcat is a direct measure of the catalytic
production of product under saturating substrate conditions.l kcat, the turnover
number, is the maximum number of substrate molecules converted to product per
enzyme molecule per unit of time. According to M-M model, k cat = Vmax /Et.
Values of k cat range from less than 1/sec to many millions per sec. in multistep
enzymatic reaction, one step may be rate limiting that rate limiting step is
equivalent to Kcat. Equation 22 can be written as by placing the value of Vmax =
Kcat x Et
-------------------26
figure 10. 5 showing turn over number of different enzyme. Note that high the TON
of an enzyme, best is the enzyme for maximum conversion of substrate into the
product.
FIGURE 10. 6
The constant Kcat has unit S-1, reciprocal of time. Note that two enzymes
catalyzing different reaction may have the same Kcat value (turnover number) yet
the rate may be different. It also denotes about the reaction between the enzyme
and substrate since at low K cat, Km value will also be unsatisfactory. From
equation 26, Vo depends on both Et and S, therefore K cat /Km is a second order
rate constant. Therefore Kcat /Km is the best way to compare the catalytic
efficiency of the enzyme. Many enzymes have K cat /Km value in the range 108 to
109 .
FIGURE 10. 7
The kinetics of simple reactions like that above was first characterized by
biochemists Michaelis and Menten. The concepts underlying their analysis of enzyme
kinetics continue to provide the cornerstone for understanding metabolism today,
and for the development and clinical use of drugs aimed at selectively altering
rate constants and interfering with the progress of disease states.
ENZYME KINETICS
It is also useful to write down two other definitions and assumptions before we
continue:
1. The first thing we need to realize is that the total concentration of enzyme in
all of its forms
should be equal to the original free enzyme concentration:
2. The second point is that the rate of the reaction should be equal to formation
of products, so
the initial velocity, vo, and maximum possible velocity, or Vmax, obtained when
all the enzyme
is substrate-bound, can be written as
Now, before making the steady-state approximation, we can look at the kinetic
scheme above
and deduce that the rate of change in the concentration of the enzyme-substrate
complex should
be equal to the rate of formation of the complex minus the rate of decay of the
complex. The rate
of formation is dependent upon the rate constant k+2 and the enzyme and substrate
complexes.
The rate of decay involves two possible pathways. One is to form products, and the
other is to
reform the reactants. Therefore the rate of decay of the enzyme-substrate complex
will be the
sum of two rate constants, k+2 and k-1. Therefore we can write
and from the steady-state approximation, this has to equal zero. Before making
this
approximation, that equation is insoluble. Now, however, you can solve it fairly
simply (despite
what I did in class). First, if the steady-state approximation holds, then you can
rearrange the
equation to look like this:
Now group all of the rate constants together
We can define this collection of rate constants as something called the Michaelis
Constant, or
Km. Note that this is not an equilibrium constant.
Now we have an even simpler expression:
We are almost done. However, we want an expression in terms of constants and
measurable quantities such as the substrate concentration, [S], and the initial
velocity, vo. To get the equation into that form, we need two things from above.
The first is our statement that the total enzyme concentration is equal to the
concentration of enzyme in all of its forms, which in turn is the same as the
starting concentration of enzyme, i.e.,E total = Eo = [E] + [ES] or conveniently
[E] = [Eo] – [ES] more, . Then we can substitute that into our previously
simplified equation to obtain
Solve for ES
Chapter-6
Factor affecting the rate of catalysis.
1- Substrate concentration.
2- Temperature
3- pH
4- Inhibitors
3. The presence of inhibitors. The study of the rate at which an enzyme works
is called enzyme kinetics. Many toxic substances owe their toxic properties to
their ability to act as inhibitors (slow down the rate of reactions by different
mechanism) to important enzymes responsible for catalyzing important biochemical
processes. Once the enzyme is inhibited the process cannot take place, and a
toxicological symptom occurs that often leads to paralysis, coma or even death of
the organism. For example, cyanide poisoning is due to the cyanide ion
competitively inhibiting the active site of the cytochromases enzymes responsible
for catalyzing the Oxidation and Reduction processes of the Electron Transport
System which is responsible for cellular respiration.
Competitive Inhibition occurs when a molecule that is close enough to the shape of
the true substrate will fit into the active site. Once locked into position, the
blocker molecule prevents the true substrate molecule from getting into position.
This effectively blocks the active site. The molecule competes for the active site
with the true substrate molecule which is concentration dependent. If the
concentration of substrate becomes more than the inhibitor they may replace the
inhibitor later on. This is the reason why ethyl alcohol is given to person that
has consumed the toxic alcohol (methyl alcohol) so that methyl alcohol can be
competitively replaced by ethyl alcohol.
Other inhibitors latch themselves not to the active site itself but to some
portion of the enzyme molecule close to the active site which results in the
changing of the shape of the active site. This is referred to as non-competitive
inhibition or mixed inhibition. Many heavy metals like Lead, Mercury, and Chromium
will function as non-competitive inhibitors. Toxicology is the study of how
toxicological substances can interfere with life sustaining enzymes via
inhibition.
The pesticide and herbicide industries make use of competitive and Non-Competitive
Inhibitors. Biological warfare owes its success to enzyme inhibition but so does
the life giving chemotherapeutic treatment of cancerous tumor growths with agents
that inhibit important cancel cell enzymes. All in all the use of inhibitors can
be used for the benefit of mankind or its destruction.
FIGURE 10. 8
FIGURE 10. 9
10.4.2 Effect of temperature and pressure
Every enzyme has a temperature range of optimum activity. Outside that temperature
range the enzyme is rendered inactive and is said to be totally inhibited. This
occurs because as the temperature changes this supplies enough energy to break
some of the intramolecular attractions between polar groups (Hydrogen bonding,
dipole-dipole attractions) as well as the Hydrophobic forces between non-polar
groups within the protein structure. When these forces are disturbed and changed,
this causes a change in the secondary and tertiary levels of protein structure,
and the active site is altered in its conformation beyond its ability to
accommodate the substrate molecules it was intended to catalyze. Most enzymes (and
there are hundreds within the human organism) within the human cells will shut
down at a body temperature below a certain value which varies according to each
individual. This can happen if body temperature gets too low (hypothermia) or too
high (hyperthermia).
Temperature is an important factor in the regulation of enzyme activity. At some
temperature activity becomes zero and at some temperature enzyme efficiency of
conversion of substrate into product becomes high. Of all most important factor is
the active site, because active site contains amino acid residues inside the
pocket, and the ability of these residue to interact with the substrate functional
group and capacity to breaking and making bonds is certainly going to be effected
by the .
Rates of all reactions, including those catalyzed by enzymes, rise with increase
in temperature in accordance with the Arrhenius equation.
K = A e –ΔG*/RT --------------27
OR
log K = log A –EA /2.3 RT
where k is the kinetic rate constant for the reaction, A is the Arrhenius
constant, also known as the frequency factor, ΔG* =EA is the standard free energy
of activation (kJ M-1) which depends on entropic and enthalpy factors, R is the
gas law constant and T is the absolute temperature. Typical standard free energies
of activation (15 - 70 kJ M-1) give rise to increases in rate by factors between
1.2 and 2.5 for every 10°C rise in temperature. This factor for the increase in
the rate of reaction for every 10°C rise in temperature is commonly denoted by the
term Q10 (i.e. in this case, Q10 is within the range 1.2 - 2.5). All the rate
constants contributing to the catalytic mechanism will vary independently, causing
changes in both Km and Vmax. It follows that, in an exothermic reaction, the
reverse reaction (having higher activation energy) increases more rapidly with
temperature than the forward reaction. This, not only alters the equilibrium
constant, but also reduces the optimum temperature for maximum conversion as the
reaction progresses. The reverse holds for endothermic reactions such as that of
glucose isomerase where the ratio of fructose to glucose, at equilibrium,
increases from 1.00 at 55°C to 1.17 at 80°C.
In general, it would be preferable to use enzymes at high temperatures in order to
make use of this increased rate of reaction plus the protection it affords against
microbial contamination. Enzymes, however, are proteins and undergo essentially
irreversible denaturation (i.e.. conformational alteration entailing a loss of
biological activity) at temperatures above those to which they are ordinarily
exposed in their natural environment. These denaturing reactions have standard
free energies of activation of about 200 - 300 kJ mole-1 (Q10 in the range 6 - 36)
which means that, above a critical temperature, there is a rapid rate of loss of
activity (Figure 8.5). The actual loss of activity is the product of this rate and
the duration of incubation (Figure 8.6). It may be due to covalent changes such as
the deamination of asparagine residues or non-covalent changes such as the
rearrangement of the protein chain. Inactivation by heat denaturation has a
profound effect on the enzymes productivity (Figure 8.7).
________________________________________
FIGURE 10. 10
FIGURE 10. 11
A schematic diagram showing the effect of the temperature on the activity of an
enzyme catalyzed reaction. —— short incubation period; ----- long incubation
period. Note that the temperature at which there appears to be maximum activity
varies with the incubation time.
________________________________________
________________________________________
FIGURE 10. 12
A schematic diagram showing the effect of the temperature on the productivity of
an enzyme catalyzed reaction. —— 55°C; —— 60°C; —— 65°C. The optimum productivity
is seen to vary with the process time, which may be determined by other additional
factors (e.g. overhead costs). It is often difficult to get precise control of the
temperature of an enzyme catalyzed process and, under these circumstances, it may
be seen that it is prudent to err on the low temperature side.
Chapter-7
Enzyme inhibition
A number of substances may cause a reduction in the rate of an enzyme catalysed
reaction. Some of these (e.g. urea) are non-specific protein denaturants. Others,
which generally act in a fairly specific manner, are known as inhibitors. Loss of
activity may be either reversible, where activity may be restored by the removal
of the inhibitor, or irreversible, where the loss of activity is time dependent
and cannot be recovered during the timescale of interest. If the inhibited enzyme
is totally inactive, irreversible inhibition behaves as a time-dependent loss of
enzyme concentration (i.e.. lower Vmax), in other cases, involving incomplete
inactivation.There may be time-dependent changes in both Km and Vmax. Heavy metal
ions (e.g. mercury and lead) should generally be prevented from coming into
contact with enzymes as they usually cause such irreversible inhibition by binding
strongly to the amino acid backbone.
More important for most enzyme-catalysed processes is the effect of reversible
inhibitors. These are generally discussed in terms of a simple extension to the
Michaelis-Menten reaction scheme.
--------------------42
where I represents the reversible inhibitor and the inhibitory (dissociation)
constants Ki and Ki' are given by
--------------------43
and,
--------------------------44
For the present purposes, it is assumed that neither EI nor ESI may react to form
product. Equilibrium between EI and ESI is allowed, but makes no net contribution
to the rate equation as it must be equivalent to the equilibrium established
through:
------45
Binding of inhibitors may change with the pH of the solution, as discussed earlier
for substrate binding, and result in the independent variation of both Ki and Ki'
with pH.
In order to simplify the analysis substantially, it is necessary that the rate of
product formation (k+2) is slow relative to the establishment of the equilibria
between the species.
Therefore:
-----------46
also
----------------------------47
where:
-----------48
therefore
---------------49
Substituting from equations (43), ( 44) and (46), followed by simplification,
gives:
--------------50
therefore
--------------51
If the total enzyme concentration is much less than the total inhibitor
concentration (i.e. [E]0<< [I]0), then:
--------------------52
This is the equation used generally for mixed inhibition involving both EI and ESI
complexes (Figure 10.19a). A number of simplified cases exist that are reversible.
1. Competitive inhibition.
2. Noncompetitive inhibition
3. Uncompetitive inhibition.
Figure 11. 2 figure showing competitive inhibition 1/Vo (1/ M/min) verses 1/[S]
(1/ mM). note that on increasing inhibitor concentration 1/Vmax remain unchanged
while Km value changes.
Figure 11. 4
figure 11.6 A schematic diagram showing the effect of reversible inhibitors on the
rate of enzyme-catalysed reactions. —— no inhibition, (a) —— mixed inhibition
([I] = Ki = 0.5 Ki'); lower Vmaxapp (= 0.67 Vmax), higher Kmapp (= 2 Km). (b) ——
competitive inhibition ([I] = Ki); Vmaxapp unchanged (= Vmax), higher Kmapp (= 2
Km). (c) —— uncompetitive inhibition ([I] = Ki'); lower Vmaxapp (= 0.5 Vmax) and
Kmapp (= 0.5 Km). (d) —— noncompetitive inhibition ([I] = Ki = Ki'); lower
Vmaxapp (= 0.5 Vmax), unchanged Kmapp (= Km).
________________________________________
A special case of uncompetitive inhibition is substrate inhibition which occurs at
high substrate concentrations in about 20% of all known enzymes (e.g. invertase is
inhibited by sucrose). It is primarily caused by more than one substrate molecule
binding to an active site meant for just one, often by different parts of the
substrate molecules binding to different sites within the substrate binding site.
If the resultant complex is inactive this type of inhibition causes a reduction in
the rate of reaction, at high substrate concentrations. It may be modeled by the
following scheme
---------------65
where
---------------------66
The assumption is made that ESS may not react to form product. It follows from
equation (52) that:
-------------------------67
Even quite high values for KS lead to a leveling off of the rate of reaction at
high substrate concentrations, and lower KS values cause substantial inhibition
(Figure 10.20).
________________________________________
Figure 11. 9
Figure 11. 7 The direct linear plot. A plot of the initial rate of reaction
against the initial substrate concentration also showing the way estimates can be
directly made of the Km and Vmax. Every pair of data points may be utilised to
give a separate estimate of these parameters (i.e. n(n-1)/2 estimates from n data
points with differing [S]0). These estimates are determined from the intersections
of lines passing through the (x,y) points (-[S]0,0) and (0,v); each intersection
forming a separate estimate of Km and Vmax. The intersections are separately
ranked in order of increasing value of both Km and Vmax and the median values
taken as the best estimates for these parameters. The error in these estimates can
be simply determined from sub-ranges of these estimates, the width of the sub-
range dependent on the accuracy required for the error and the number of data
points in the analysis. In this example there are 7 data points and, therefore, 21
estimates for both Km and Vmax. The ranked list of the estimates for Km (mM) is
0.98,1.65, 1.68, 1.70, 1.85, 1.87, 1.89, 1.91, 1.94, 1.96, 1.98, 1.99, 2.03, 2.06,
1.12, 2.16, 2.21, 2.25, 2.38, 2.40, 2.81, with a median value of 1.98 mM. The Km
must lie between the 4th (1.70 mM) and 18th (2.25 mM) estimate at a confidence
level of 97% (Cornish-Bowden et al., 1978). The list of the estimates for Vmax (
M.min-1) is ranked separately as 3.45, 3.59, 3.80, 3.85, 3.87, 3.89, 3.91, 3.94,
3.96, 3.96, 3.98, 4.01, 4.03, 4.05, 4.13, 4.14, 4.18, 4.26, 4.29, 4.35, with a
median value of 3.98 M.min-1. The Vmax must lie between the 4th (3.85 M.min-1)
and 18th (4.18 M.min-1) estimate at a confidence level of 97%. It can be seen
that outlying estimates have little or no influence on the results. This is a
major advantage over the least-squared statistical procedures where rogue data
points cause heavily biased effects.
________________________________________
Three ways in which the hyperbolic relationship between the initial rate of
reaction and the initial substrate concentration
--------------74
Figure 11. 9 (b) Eadie-Hofstee plot of v against v/[S]0 giving intercepts at Vmax
and Vmax/Km
(75)
Figure 11. 11 FIGURE 10. 15 . A schematic plot showing the amount of product
formed (productivity) against the time of reaction, in a closed system. The
specificity constant may be determined by a weighted least-squared fit of the data
to the relationship given by equation (73).
Table -2
Module III
Enzyme Kinetics: Single substrate steady state kinetics; Michaelis Menten
equation, Linear plots, King-Altman’s method; Inhibitors and activators;
Multisubstrate systems; ping-pong mechanism, Alberty equation, Sigmoidal kinetics
and Allosteric enzymes
Chapter-8
Multisubstrate enzymes
Many Enzymes react with two or more substrates simultaneously (includes cofactors
: ATP, NADPH, NADP, FADH, FAD etc) Michaelis Menten kinetics is observed when only
one substrate is varied with the other(s) held constant (usually the cofactors)
Common observed Mechanisms:
Sequential – All substrates are bound by enzyme before the any products are formed
and released
Ordered : Substrates bind and products released in specific order
Random : no order
Ping Pong – When one or more product(s) are released before all substrates are
bound by enzyme (acyl/phosphoryl enzyme intermediate)
sequential means all substrates on before any products off, while ping pong has
products off before all substrates on - can be ordered or random - e.g.:
________________________________________
DG= refers to the difference in free energy between the transition state and the
substrate
Enzymes work by decreasing DG= to facilitate more rapid formation of P
Think of it as enzymes helping the chemical reaction get over the “hump” in
order to form product (P)
• ES complex demonstrated in a variety of ways including X-ray
crystallography, electron microscopy, and spectrophotometry
• Enzymes derive much of their catalytic power by bringing in a substrate
molecule at a “favorable” orientation (this is how enzymes reduce the free energy
required to convert S into P)
• Leonor Michaelis (1913): noticed that at constant [enzyme] the rate of a
reaction increases with increasing [S] until a “maximal velocity” (Vmax) is
achieved
• This “saturation effect” is an important distinction versus uncatalyzed
reactions
• Interpretation of data: ES complexes formed until substrate saturation
occurs at which point no more substrate binding sites (i.e., enzyme molecules) are
available
• The kinetic mechanism of an enzyme is simply the sequence in which
substrates bind to, and products are released from the enzyme. It should not be
confused with the chemical mechanism which is concerned with the chemical
interactions between the enzyme and its substrate(s) which results in the creation
of product(s). Kinetic mechanisms can be broadly divided into two main types,
sequential and ping-pong (also known as double displacement) mechanisms.
• Sequential mechanisms
• Sequential reactions are ones in which all reactants bind to the enzyme
before the first product is released. They can be further subdivided into ordered
reactions, in which the reactants and products are bound and released in an
obligatory sequence, and random reactions, in which there is no obligatory binding
sequence.
• Ping-pong mechanisms
• Ping-pong reactions are ones in which at least one product is released
before all the substrates have bound.
• To clarify these distinctions we'll look at each of these mechanisms in turn
using a typical bi bi enzyme:
• A + B P + Q
• We'll start by looking at an ordered sequential reaction, which is perhaps
the simplest in kinetic terms.
Types of specificity:
o Geometric specificity: shape
Chiral specificity: most chirally specific enzymes are absolutely
stereospecific.
Prochirality, because of their own chiral nature enzymes can often hold
substrates in such a way that on one chiral product is made, distinguishing
between seemingly identical groups.
o Chemical specificity: functional groups, types of chemical reaction.
Enzyme Catalysis
We will look at catalysis in two types of systems:
• Model systems in organic chemistry to elucidate probable mechanisms of
chemical catalysis.
• Example enzymes to demonstrate these mechanisms in enzyme catalysis.
Mechanisms of Chemical Catalysis
Look at some examples of catalysis in model systems (organic chemistry) and how
they might operate in enzymes.
Types of Catalysis:
• Acid/Base
o Specific (H+ & OH- in water)
o General (Bronsted acid definition: proton donor/acceptor pairs; buffers.)
• Covalent
o nucleophilic
o electrophilic
• Proximity/orientation
• Stabilization of Transition State Conformation (Strain/distortion; Charge
neutralization)
• Metal/Metal ion.
So how does catalysis work? Recall that the slow step of a reaction is reaching
the transition state. Thus if we can find a way to stabilize the transition state
(lower Ea) then the reaction rate will be enhanced. Generally we will be looking
at three ways to increase rates
1. stabilize transition states
2. increase the concentrations of intermediates
3. use a different reaction pathway.
o
First order because rate depends only on the formation of the carbocation, which
in turn depends only on [R3CCl]
• Second order: r = k[A][B] for A + B P; or can have r = k[A]2 ;
o Example - SN2 from organic chemistry: A + B C + D as 2nd order reaction, as
in the hydroxylation of primary alkylchlorides:
Now 2nd order because both RH2CCl and OH- (reverse of figure above) are involved
in slow step.
• Higher order reactions occur, but uncommon.
• Zero order: r = k: Only occurs with catalysts, important in enzyme
catalysis. 0 order also only occurs above a minimum [A].
one-substrate enzymes:
For simple enzyme, S P get rectangular hyperbola type plot for vi vs [S] (text
Figure 6-11), similar to Mb binding curve.
•
•
• Let's look at a mathematical model and attempt to generate curve. This was
first done by Michaelis and Menten for an equilibrium model. Better is the steady
state model of Haldane and Briggs (more general), which we will derive.
• For S P assume
•
• And for initial reaction conditions [P] = 0 & therefore k4 = 0, so have
•
• Now vi = d[P]/dt = k3[ES] (Note that kcat is often used instead of k3);
• Assume steady state (steady state assumption: d[ES]/dt= 0):
• d[ES]/dt= 0; Thus: 0 = d[ES]/dt= k1[E][S] - k2[ES] - k3[ES].
So, Which is known as the Michaelis-Menten Equation.
For simple, one-substrate enzymes then, have Michaelis-Menten Equation as a model
for enzyme activity.
Turnover Number. The rate constant (First order) for the breakdown of the [ES]
complex, kcat (k3), is also known as the turnover number, that is the maximum
number of substrate molecules processed/active site (moles substrate/mole active
site): kcat=Vmax / [E]total. Note that this is best determined under saturating
conditions. (text Table 6-08) At very low concentrations of [S] can find the
second-order rate constant for the conversion of E + S E + P: vo = (kcat /
KM)([E][S].
Linear plots for enzyme kinetic studies
Double Reciprocal or Lineweaver-Burke Plot: Need in form: y = ax + b , so take
reciprocals of both sides and have
. (text Box 6-01 figure 6-1)
Other linear plots are also available, and are better in terms of statistics (L-B
one of worst, best quality points [high concentration] have least influence on
slope, while low precision points [low concentration] are more spread out, and
have a large moment, with a strong influence on the slope and the KM intercept ¬
this is not as much of a concern now with computer statistical packages, but you
still have to understand the statistics). We will see others in the laboratory
discussion.
FYI - The Eadie-Hofstee Plot
One common plot is shown below. Note that the data points are distributed much
more evenly over the plot giving better statistics for the slope. In addition the
value of KM is obtained from the slope, giving better precision.
We can model this inhibition with chemical equations, keeping in mind that S & I
are mutually exclusive, E can bind to one OR the other: (text Figure 6-15a)
•
Multi-substrate Enzymes
Look at three common and easily understood types. We will use Cleland Nomenclature
and "Kinetic mechanism diagrams."
• Ordered Sequential Bi Bi mechanism (two on; two off); Note: A must bind
first, Q is released last.
• Ping Pong Bi Bi (one on, one off; one on, one off); Note: have some sort of
modified enzyme intermediate (often covalent intermediate)
• Random Sequential Bi Bi (two on; two off); Note: A or B may bind first, P or
Q may be released last.
Two-substrate Enzyme Product Inhibition Patterns
(Based on: E. B. Cunningham, Biochemistry: Mechanisms of Metabolism. McGraw-Hill
Book Company, New York (1978), and W. Cleland, "Substrate Inhibition: in
Contemporary Enzyme Kinetics and Mechanism. (Daniel L. Purich, ed.) Academic
Press, New york (1983))
Kinetic Mechanism Variable Substrate Product Type of Inhibition
Ordered Sequential Bi Bi
Ordered Sequential Bi Bi A Q Competitive
B Q Noncompetitive
A P Noncompetitive
B P Noncompetitive
Random Sequential Bi Bi
Random Sequential Bi Bi A Q Noncompetitive
B Q Noncompetitive
A P Noncompetitive
B P Noncompetitive
Ping pong Bi Bi
Ping pong Bi Bi A Q Competitive
B Q Noncompetitive
A P Noncompetitive
B P Competitive
Note that in each case we can predict/explain the pattern of inhibition on the
basis of the substrate and inhibitor binding to the same "enzyme form." Thus for
the Ordered Sequential mechanism only the first substrate and last product bind to
the same form, in this case the free enzyme. Similarly for the Ping pong mechanism
the first substrate and last product should be competitive as the both bind the
free enzyme. In this case we also see a competitive inhibition between the second
substrate and the first product, since they both bind to the E-X complex. The
Random Sequential mechanism is a bit more subtle. Here we see across the board
noncompetitive since in each case the substrates (and products) can each bind to
more than one substrate form, so competitive inhibition will not be possible!
(Think of the product as competing with one order of binding but not the other.)
The ping-pong (double displacement) mechanism
________________________________________
The distinguishing feature of these enzymes is that at least one product is
released from the enzyme before all of the substrates have bound. This might seem
slightly unlikely at a first glance, but it's actually easily explained and quite
a common mechanism. Some very familiar enzymes, for instance the serine proteases
(trypsin, chymotrypsin, etc.) and the amino transferases work in this way.
The process starts by binding of the enzyme to the first substrate in the usual
way:
E + A (EA)
Notice that I've used parentheses around the EA complex to indicate that it is a
central complex. The active site is full as this substrate will be converted to
product before the second substrate can bind. The active site has no room for the
second substrate so it is full.
The next reaction is the key to the whole process:
(EA) (FP)
In this reaction a part of the substrate has been removed from substrate A,
converting it to product P. The removed section has become covalently bound to the
enzyme to create a new form of the enzyme, enzyme F.
The first product of the reaction is now released and the second substrate binds:
(FP) F + P
F + B (FB)
Now the stored section of the first substrate is transferred to the second
substrate to create the second product, which is then released:
(FB) (EQ)
(EQ) E + Q
The animation should help to clarify this.
as the first upward arrow (product P) is to the left of the first down arrow
(substrate B).
Now that we're familiar with the principal types of kinetic mechanism we need to
think about experimental techniques to distinguish between them. To start with
we'll examine the effects of changes in substrate concentration on multisubstrate
reactions.
Effects of Substrate Concentration in Multisubstrate Systems
________________________________________
With a multisubstrate enzyme, let's say a typical bi bi enzyme:
A + B P + Q
we can carry out exactly the same experiment. We simply need to keep one substrate
(the fixed substrate) at a constant concentration in all our assays, while we vary
the concentration of the other substrate (the variable substrate). The results
would be exactly the same as you'd expect in a single substrate system and you
could use any of the methods that we've studied to calculate the kinetic
parameters. What would happen though if you repeated the experiment with an
increased concentration of the fixed substrate. Since you're increasing the
concentration of a substrate you would expect the velocity to rise and in fact the
reaction would be faster at any given concentration of the variable substrate than
it was in the previous experiment. So you'd end up with a second set of data which
you could use in your chosen plot. The kinetic parameters would change to reflect
the change in velocity. If you repeated this at a variety of concentrations of the
fixed substrate you would get a series of lines. A typical Lineweaver-Burk plot
obtained as a result of this type of experiment can be seen below. Substrate A was
used as the variable substrate and substrate B as the fixed substrate.
The actual pattern of lines obtained will vary according to the way in which the
enzyme interacts with the two substrates and, as we'll see in the next couple of
pages, enables us to distinguish between sequential and ping-pong enzymes.
In discussing graphs of this type we'll be considering changes in the Vmax and
slope of the line. A change in Vmax indicates the effect that a change in the
concentration of the fixed substrate on the reaction speed at very high
concentrations of the variable substrate. Remember that Vmax is the velocity of
the reaction under those conditions. A change in slope indicates the effect of a
change in concentration of the fixed substrate on the speed at very low
concentrations of the variable substrate. Remember in our discussion of enzyme
inhibition we found that the slope was the rate constant at low substrate
concentrations.
We'll start by considering the expected results of this experiment when carried
out with a sequential enzyme.
Substrate concentration assays with sequential enzymes
________________________________________
Consider a bi bi ordered sequential reaction:
A + B P + Q
The Cleland plot for such a reaction would be:
We'll discuss the results of a set of enzyme assays in which substrate A is used
as the variable substrate and substrate B as the fixed substrate.
At very low A concentrations the rate limiting step of the reaction would be the
binding of A to the enzyme as the substrate is in very short supply. An increase
in the concentration of B would reduce the concentration of the EA complex in the
reaction mixture by binding to it to form EAB complex. Reducing the concentration
of the product of the E + A EA reaction will pull it to the right by the Law of
Mass Action. So the increase in B has increased the speed of the rate limiting
step, and therefore of the overall reaction. As we're looking at effects at low A
concentrations this would be seen as a change in the slope of the Lineweaver-Burk
plot.
At very high A concentrations the rate limiting step would be the EAB EPQ, which
is the inherently slowest reaction, or EA + B EAB at low B levels. An increase in
B would increase the speed of either of these as a reactant in the second reaction
and by the knock on effect of generating more EAB for the central reacton to
occur. This would be seen as a change in Vmax as we are considering effects at
high A concentration.
In summary then, for an ordered sequential reaction, a change in the concentration
of the fixed substrate would bring about a change in both the slope and intercept
of the Lineweaver-Burk plot and the graph would be similar to that suggested on
the previous page.
A similar result would be obtained if the assay was reversed and B used as the
variable substrate or if the enzyme used a random sequential mechanism. You might
like to demonstrate that yourself as an exercise.
Chapter-9
ISOLATION AND PURIFICATION OF ENZYME
INTRODUCTION
ENZYME is isolated and purified to obtain maximum desired product because they are
not utilized during the product formation. And also isolation of enzyme gives the
maximum understanding of the behavior of the enzyme in complex system, its
regulation mechanism. PURIFIED enzyme is needed for laboratory work and less
purified enzyme is needed for commercial purpose. Purifying enzyme is much labor
intensive process and main aim is to separate other protein that are not the part
of the enzyme. Often during purification enzyme yield is decreases many folds.
Purification of enzyme is aimed to get maximum turn over number that is to
increase the activity of enzyme in other world to increase its efficiency of
conversion of per mole substrate into the product. It helps in increasing the
sensitivity of the diagnosis test in the clinics. Other need of the enzyme
purification is the study of kinetics that is rate of enzyme and its specificity
towards the substrate. Inhibition kinetics helps in functional study of the
enzyme. During the disturbance in the metabolic pathway some enzyme may not form
and it results in the formation of unwanted product like in the phenylketonuria
disease homigenistic acid secretion in the urine results. Therefore for the
diagnostic purpose much pure enzyme is needed.
FIGURE 8. 1
strategies for enzyme purification.
source of enzyme
Method of enzyme isolation (cell lysis by osmotic, enzyme, sonication, or
homogenization method)
Method of separation.
[i] Based on size and mass ( centrifugation, GPC gel permeation chromatography,
Dialysis and ultracentrifugation).
[ii] Based on polarity (Ion –exchange, electrophoresis, isoelectric focusing,
hydrophobic interaction chromatography).
[iii] Based on changes in solubility ( by change of pH, change in ionic strength
(Salting in or salting out).
[iv] Based on change in dielectric strength by adding organic solvent.
[v] Based on specific binding site.
Affinity chromatography.
Affinity elution.
Dye –ligand chromatography.
Immuno-adsorption chromatography.
Covalent chromatography.
(4). Test of purification
a). test of purity
b). Test of catalytic activity
c). Active site titration
Test of purity is done by following method
1. Ultrapurification (for impurities < 5%)
2. Electrophoresis (Examining enzyme composed of non identical subunit)
3. SDS-PAGE ( good method for detecting impurities and for detecting damage of
non-identical subunit.)
4. Capillary Electrophoresis
5. Isoelectric –focusing ( very sensitive method)
6. Mass –spectrometry.( power full method )
Source of enzyme
Biologically active enzymes may be extracted from any living organism. A very wide
range of sources are used for commercial enzyme production from Actinoplanes to
Zymomonas, from spinach to snake venom. Of the hundred or so enzymes being used
industrially, over a half are from fungi and yeast and over a third are from
bacteria with the remainder divided between animal (8%) and plant (4%) sources
(Table 8.1). A very much larger number of enzymes find use in chemical analysis
and clinical diagnosis. Non-microbial sources provide a larger proportion of
these, at the present time. Microbes are preferred to plants and animals as
sources of enzymes because:
1. they are generally cheaper to produce.
2. their enzyme contents are more predictable and controllable,
3. reliable supplies of raw material of constant composition are more easily
arranged, and
4. plant and animal tissues contain more potentially harmful materials than
microbes, including phenolic compounds (from plants), endogenous enzyme inhibitors
and proteases.
5. Attempts are being made to overcome some of these difficulties by the use of
animal and plant cell culture.
________________________________________
Table 2.1. Some important industrial enzymes and their sources.
Enzyme a
EC number b
Source Intra/extra
-cellular c
Scale of production d
Industrial use
Animal enzymes
Catalase 1.11.1.6 Liver I - Food
Chymotrypsin 3.4.21.1 Pancreas E - Leather
Lipasee
3.1.1.3 Pancreas E - Food
Rennetf
3.4.23.4 Abomasum E + Cheese
Trypsin 3.4.21.4 Pancreas E - Leather
Plant enzymes
Actinidin 3.4.22.14 Kiwi fruit E - Food
Amylase 3.2.1.1 Malted barley E +++ Brewing
-Amylase 3.2.1.2 Malted barley E +++ Brewing
Bromelain 3.4.22.4 Pineapple latex E - Brewing
Glucanaseg
3.2.1.6 Malted barley E ++ Brewing
Ficin 3.4.22.3 Fig latex E - Food
Lipoxygenase 1.13.11.12 Soybeans I - Food
Papain 3.4.22.2 Pawpaw latex E ++ Meat
Bacterial enzymes
Amylase 3.2.1.1 Bacillus E +++ Starch
-Amylase 3.2.1.2 Bacillus E + Starch
Asparaginase 3.5.1.1 Escherichia coli I - Health
Glucose isomeraseh
5.3.1.5 Bacillus I ++ Fructose syrup
Penicillin amidase 3.5.1.11 Bacillus I - Pharmaceutical
Proteasei
3.4.21.14 Bacillus E +++ Detergent
Pullulanasej
3.2.1.41 Klebsiella E - Starch
Fungal enzymes
Amylase 3.2.1.1 Aspergillus E ++ Baking
Aminoacylase 3.5.1.14 Aspergillus I - Pharmaceutical
Glucoamylasek
3.2.1.3 Aspergillus E +++ Starch
Catalase 1.11.1.6 Aspergillus I - Food
Cellulase 3.2.1.4 Trichoderma E - Waste
Dextranase 3.2.1.11 Penicillium E - Food
Glucose oxidase 1.1.3.4 Aspergillus I - Food
Lactasel
3.2.1.23 Aspergillus E - Dairy
Lipasee
3.1.1.3 Rhizopus E - Food
Rennetm
3.4.23.6 Mucor miehei E ++ Cheese
Pectinasen
3.2.1.15 Aspergillus E ++ Drinks
Pectin lyase 4.2.2.10 Aspergillus E - Drinks
Proteasem
3.4.23.6 Aspergillus E + Baking
Raffinaseo
3.2.1.22 Mortierella I - Food
Yeast enzymes
Invertasep
3.2.1.26 Saccharomyces I/E - Confectionery
Lactasel
3.2.1.23 Kluyveromyces I/E - Dairy
Lipasee
3.1.1.3 Candida E - Food
Raffinaseo
3.2.1.22 Saccharomyces I - Food
a The names in common usage are given. As most industrial enzymes consist of
mixtures of enzymes, these names may vary from the recommended names of their
principal component. Where appropriate, the recommended names of this principal
component is given below.
b The EC number of the principal component.
c I - intracellular enzyme; E - extracellular enzyme.
d +++ > 100 ton year-1; ++ > 10 ton year-1; + > 1 ton year-1; - < 1 ton year-1.
e triacylglycerol lipase;
f chymosin;
g Endo-1,3(4)- -glucanase;
h xylose isomerase;
i subtilisin;
j dextrin endo-1,6- -glucosidase;
k glucan 1,4- -glucosidase;
l -galactosidase;
m microbial aspartic proteinase;
n polygalacturonase;
o -galactosidase;
p -fructofuranosidase.
In practice, the great majority of microbial enzymes come from a very limited
number of genera, of which Aspergillus species, Bacillus species and Kluyveromyces
(also called Saccharomyces) species predominate. Most of the strains used have
either been employed by the food industry for many years or have been derived from
such strains by mutation and selection. There are very few examples of the
industrial use of enzymes having been developed for one task. Shining examples of
such developments are the production of high fructose syrup using glucose
isomerase and the use of pullulanase in starch hydrolysis.
Media for enzyme production
Detailed description of the development and use of fermentors for the large-scale
cultivation of microorganisms for enzyme production is outside the scope of this
volume but mention of media use is appropriate because this has a bearing on the
cost of the enzyme and because media components often find their way into
commercial enzyme preparations. Details of components used in industrial scale
fermentation broths for enzyme production are not readily obtained. This is not
unexpected as manufacturers have no wish to reveal information that may be of
technical or commercial value to their competitors. Also some components of media
may be changed from batch to batch as availability and cost of, for instance,
carbohydrate feedstock change. Such changes reveal themselves in often quite
profound differences in appearance from batch to batch of a single enzyme from a
single producer. The effects of changing feedstock must be considered in relation
to downstream processing. If such variability is likely to significantly reduce
the efficiency of the standard methodology, it may be economical to use a more
expensive defined medium of easily reproducible composition.
Clearly defined media are usually out of the question for large scale use on cost
grounds but may be perfectly acceptable when enzymes are to be produced for high
value uses, such as analysis or medical therapy where very pure preparations are
essential. Less-defined complex media are composed of ingredients selected on the
basis of cost and availability as well as composition. Waste materials and by-
products from the food and agricultural industries are often major ingredients.
Thus molasses, corn steep liquor, distillers soluble and wheat bran is important
components of fermentation media providing carbohydrate, minerals, nitrogen and
some vitamins. Extra carbohydrate is usually supplied as starch, sometimes refined
but often simply as ground cereal grains. Soybean meal and ammonium salts are
frequently used sources of additional nitrogen. Most of these materials will vary
in quality and composition from batch to batch causing changes in enzyme
productivity.
Often the enzyme may be purified several hundred-fold but the yield of the enzyme
may be very poor, frequently below 10% of the activity of the original material
(Table 2.2). In contrast, industrial enzymes will be purified as little as
possible, only other enzymes and material likely to interfere with the process
which the enzyme is to catalyze, will be removed. Unnecessary purification will be
avoided as each additional stage is costly in terms of equipment, manpower and
loss of enzyme activity. As a result, some commercial enzyme preparations consist
essentially of concentrated fermentation broth, plus additives to stabilize the
enzyme's activity.
The content of the required enzyme should be as high as possible (e.g. 10% w/w of
the protein) in order to ease the downstream processing task. This may be achieved
by developing the fermentation conditions or, often more dramatically, by genetic
engineering. It may well be economically viable to spend some time cloning extra
copies of the required gene together with a powerful promoter back into the
producing organism in order to get 'over-producers' (see Chapter protein
engineering).
It is important that the maximum activity is retained during the preparation of
enzymes. Enzyme inactivation can be caused by heat, proteolysis, sub-optimal pH,
oxidation, denaturants, irreversible inhibitors and loss of cofactors or
coenzymes. Of this heat inactivation, this together with associated pH effects is
probably the most significant. It is likely to occur during enzyme extraction and
purification if insufficient cooling is available, but the problem is less when
preparing thermophilic enzymes. Proteolysis is most likely to occur in the early
stages of extraction and purification when the proteases responsible for protein
turnover in living cells are still present. It is also the major reason for enzyme
inactivation by microbial contamination. In their native conformations, enzymes
have highly structured domains which are resistant to attack by proteases because
many of the peptide bonds are mechanically inaccessible and because many proteases
are highly specific. The chances of a susceptible peptide bond in a structured
domain being available for protease attack are low. Single 'nicks' by proteases in
these circumstances may have little immediate effect on protein conformation and,
therefore, activity. The effect, however, may severely reduce the conformational
stability of the enzyme to heat or pH variation so greatly reducing its
operational stability. If the domain is unfolded under these changed conditions,
the whole polypeptide chain may be available for proteolysis and the same,
specific, protease may destroy it. Clearly the best way of preventing proteolysis
is to rapidly remove, or inhibit, protease activity. Before this can be achieved
it is important to keep enzyme preparations cold to maintain their native
conformation and slow any protease action that may occur.
Some intracellular enzymes are used commercially without isolation and
purification but the majority of commercial enzymes is either produced
extracellularly by the microbe or plant or must be released from the cells into
solution and further processed (Figure 2.1). Solid/liquid separation is generally
required for the initial separation of cell mass, the removal of cell debris after
cell breakage and the collection of precipitates. This can be achieved by
filtration, centrifugation or aqueous biphasic partition. In general, filtration
or aqueous biphasic systems are used to remove unwanted cells or cell debris
whereas centrifugation is the preferred method for the collection of required
solid material.
Figure 2.1. Flow diagram for the preparation of enzymes.
This technique is used to investigate the different parameter of the molecule such
as molecular mass, shape, and density. In this process gravity plays most
important role. Therefore, the basis of centrifugation separation techniques
therefore is to exert the lager force than does the gravitational earth, thus
increasing the rate at which the particle settles.
The technique can be divided into two types:
1 preparative centrifugation: for separation of the whole cells, subcellular
organelles, plasma membranes, polysomes, ribosome, chromatin, nucleic acids,
lipoprotein and viruses
2. Analytical centrifugation: it is devoted to study of pure or virtually pure or
macromolecular or particles. They are related with the study of macromolecular
structure rather than the collection of particle fractions.
Principles:
Rate depends on the centrifugal field G directed radially outward (angular
velocity)
G = ωr 2
ω =2π/60 revolution min-1
This method is based upon the difference in the sedimentation rate of particles of
different size and density. In centrifugation the larger particle are sedimented
first. The particle having the same mass but different density, the denser
particle is sedimented first and less dense will sediment later. Particle having
similar density can be separated by the differential centrifugation or the rate
zonal method.
In differentiated centrifugation, the particle to be separated is divided
centrifugally into a number of fractions by increasing the applied centrifugal
field. After the centrifugation, pellet and supernatant are separated, pellet is
washed several time and again centrifugation is done. The particle moves against
respective sedimentation rates. Centrifugation is continued long enough to pellet
all the largest class of particles, the resulting supernatant then being
centrifuged at higher speed to separate medium sized particle and so on. However,
since particles of varying sizes and densities were distributed homogeneously at
the start of centrifugation, so pellet will not be homogeneous but will contain a
mixture of all the sediment components.
Particle separation by the rate zonal technique is based on differences in the
size, shape, and density of the particle. Most of the biological particles having
same size are having narrower density range. So , separation of similar particle
by the rate zonal technique is based mainly upon differences in their sizes and
can not be separated easily like mitochondria, lysosome, peroxisomes. The
technique has been used for the separation of enzymes hormones and RNA and DNA
hybrids, ribosomal subunits, sub cellular organelles.
There are two type of density gradient centrifugation, --1. The rate zonal
technique and the isopycnic (equal density)
Isopycnic centrifugation depends solely upon the buoyant density of the particles
and not its shape or size and is independent of time the size of the particle
affecting only the rate at which it reaches its isopycnic position in the
gradient. The technique is useful in separating the particle of same size but
differing in density.
1Svedberg = 10-13 second
Centrifugation separates on the basis of the particle size and density difference
between the liquid and solid phases. Sedimentation of material in a centrifugal
field may be described by
(2.11)
where v is the rate of sedimentation, d is the particle diameter, rs is the
particle density, rl is the solution density is the angular velocity in radians s-
1, r is the radius of rotation, η is the kinematic viscosity, Fs is a correction
factor for particle interaction during hindered settling and θ is a shape factor
(=1 for spherical particles). Fs depends on the volume fraction of the solids
present; approximately equaling 1, 0.5, 0.1 and 0.05 for 1%, 3%, 12% and 20%
solids volume fraction respectively. Only material which reaches a surface during
the flow through continuous centrifuges will be removed from the centrifuge
feedstock, the efficiency depending on the residence time within the centrifuge
and the distance necessary for sedimentation (D). This residence time will equal
the volumetric throughput (Ф) divide by the volume of the centrifuge (V). The
maximum throughput of a centrifuge for efficient use is given by
(2.12)
The efficiency of the process is seen to depend on the solids volume fraction, the
effective clarifying surface (V/D) and the acceleration factor (ω2r/g, where g is
the gravitational constant, 921 cm s-2; a rotor of radius 25 cm spinning at 1 rev
s-1 has an acceleration factor of approximately 1 G). Low acceleration factors of
about 1 500 g may be used for harvesting cells whereas much higher acceleration
factors are needed to collect enzyme efficiently. The product of these factors
(ω2rV/gD) is called the sigma factor Σ and is used to compare centrifuges and to
assist scale-up.
Laboratory centrifuges using tubes in swing-out or angle head rotors have high
angular velocity ω and radius of rotation (r) but small capacity (V) and
substantial sedimentation distance (D). This type of design cannot be scaled-up
safely, primarily because the mechanical stress on the centrifuge head increases
with the square of the radius, which must increase with increasing capacity.
For large-scale use, continuous centrifuges of various types are employed (Figure
2.2). These allow the continuous addition of feedstock, the continuous removal of
supernatant and the discontinuous, semicontinuous or continuous removal of solids.
Where discontinuous or semicontinuous removal of precipitate occurs, the
precipitate is flushed out by automatic discharge systems which cause its dilution
with water or medium and may be a problem if the precipitate is required for
further treatment. Centrifugation is the generally preferred method for the
collection of enzyme-containing solids as it does not present a great hazard to
most enzymes so long as foam production, with consequent enzymic inactivation, is
minimised.
centrifuges are long and thin enabling rapid acceleration and deceleration,
minimizing the down-time required for the removal of the sedimented solids. Here
the radius and effective liquid thickness are both small allowing a high angular
velocity and hence high centrifugal force; small models can be used at
acceleration factors up to 50,000 g, accumulating 0.1 Kg of wet deposit whereas
large models, designed to accumulate up to 5 Kg of deposit, are restricted to
16,000 g. The capacities of these centrifuges are only moderate.Multichamber disc-
stack centrifuges, originally designed (by Westfalia and Alpha-Laval) for cream
separation, contain multiple coned discs in a stack which are spun and on which
the precipitate collects. They may be operated either semi-continuously or, by
using a centripetal pressurising pump within the centrifuge bowl which forces the
sludge out through a valve, continuously. The capacity and radius of such devices
are large and the thickness of liquid is very small, due to the large effective
surface area. The angular velocity, however, is restricted giving a maximum
acceleration factor of about 2,000 g. A different design which is rather similar
in principle is the solid bowl scroll centrifuge in which an Archimedes' screw
collects the precipitate so that fluid and solids leave at opposite ends of the
apparatus. These can only be used at low acceleration (about 3,000 g) so they are
suitable only for the collection of comparatively large particles.
Although many types of centrifuge are available, the efficient precipitation of
small particles of cell debris can be difficult, sometimes near-impossible.
Clearly from Equation 2.2, the efficiency of centrifugation can be improved if the
particle diameter (d) is increased. This can be done either by coagulating or
flocculating particles. Coagulation is caused by the removal of electrostatic
charges (e.g. by pH change) and allowing particles to adhere to each other.
Flocculation is achieved by adding small amounts of high-molecular-weight charged
materials which bridge oppositely-charged particles to produce a loose aggregate
which may be readily removed by centrifugation or filtration. Flocculation and
coagulation are cheap and effective aids to precipitating or otherwise harvesting
whole cells, cell debris or soluble proteins but, of course, it is essential that
the agents used must not inhibit the target enzymes. It is important to note that
the choice of flocculants is determined by the pH and ionic strength of the
solution and the nature of the particles. Most flocculants have very definite
optimum concentrations above which further addition may be counter-effective. Some
flocculants can be rapidly ruined by shear.
A comparatively recent introduction designed for the removal of cell debris is a
moderately hydrophobic product in which cellulose is lightly derivatised with
diethylaminoethyl functional groups. This material (Whatman CDR; cell debris
remover) is inexpensive (essential as it is not reusable), binds to unwanted
negatively charged cell constituents, acts as a filter aid and may be incinerated
to dispose of hazardous
Figure 2.3. The basic design of the rotary vacuum filter. The suspension is sucked
through a filter cloth on a rotating drum. This produces a filter cake which is
removed with a blade. The filter cake may be rinsed during its rotation. These
filters are generally rather messy and difficult to contain making them generally
unsuitable for use in the production of toxic or recombinant DNA products. There
have been recent developments that improve their suitability, however, such as the
Disposable Rotary Drum Filter.
________________________________________
A simple and familiar filtration apparatus is the perforate bowl centrifuge or
basket centrifuge, in effect a spin drier. Cell debris is collected on a cloth
with, or without, filter aid and can be skimmed off when necessary using a
suitable blade. Such centrifugal filters have a large radius and effective liquid
depth, allowing high volumes. However, safety decrees that the angular velocity
must be low and so only large particles (e.g. plant material) can be removed
satisfactorily.
________________________________________
Figure 2.4. Principles of (a) dead-end filtration and (b) cross-flow filtration.
In dead-end filtration the flow causes the build-up of the filter cake, which may
prevent efficient operation. This is avoided in cross-flow filtration where the
flow sweeps the membrane surface clean.
________________________________________
Chapter-10
Separation in Aqueous biphasic systems
The 'incompatibility' of certain polymers in aqueous solution was first noted by
Beijerinck in 1296. In this case two phases were formed when agar was mixed with
soluble starch or gelatin. Since then, many two phase aqueous systems have been
found; the most thoroughly investigated being the aqueous dextran-polyethylene
glycol system (e.g. 10% polyethylene glycol 4000/2% dextran T500), where dextran
forms the more hydrophilic, denser, lower phase and polyethylene glycol the more
hydrophobic, less dense, upper phase. Aqueous three phase systems are also known.
Phases form when limiting concentrations of the polymers are exceeded. Both phases
contain mainly water and are enriched in one of the polymers. The limiting
concentrations depend on the type and molecular weight of the polymers and on the
pH, ionic strength and temperature of the solution. Some polymers form the upper
hydrophobic phase in the presence of fairly concentrated solutions of phosphates
or sulphate (e.g. 10% polyethylene glycol 4000/12.5% potassium phosphate buffer).
A drawback to the useful dextran/polyethylene glycol system is the high cost of
the purified Dextran used. This has been alleviated by the use of crude
unfractionated dextran preparations, much cheaper hydroxypropyl starch derivatives
and salt-containing biphasic systems.
Aqueous biphasic systems are of considerable value to biotechnology. They provide
the opportunity for the rapid separation of biological materials with little
probability of denaturation. The interfacial tension between the phases is very
low (i.e. about 400-fold less than that between water and an immiscible organic
solvent), allowing small droplet size, large interfacial areas, efficient mixing
under very gentle stirring and rapid partition. The polymers have a stabilizing
influence on most proteins. A great variety of separations have been achieved, by
far the most important being the separation of enzymes from broken crude cell
material. Separation may be achieved in a few minutes, minimizing the harmful
action of endogenous proteases. The systems have also been used successfully for
the separation of different types of cell membranes and organelles, the
purification of enzymes and for extractive bioconversions. Continuous liquid two-
phase separation is easier than continuous solid/liquid separation using equipment
familiar from immiscible solvent systems, for example disc-stack centrifuges and
counter-current separators. Such systems are readily amenable to scale-up and may
be employed in continuous enzyme extraction processes involving some recycling of
the phases.
Cells, cell debris proteins and other material distribute themselves between the
two phases in a manner described by the partition coefficient (P) defined as.
--------------------- (2.14)
Where Ct and Cb represent the concentrations in the top and bottom phases
respectively. The yield and efficiency of the separation is determined by the
relative amounts of material in the two phases and therefore depends on the volume
ratio (Vt/Vb). The partition coefficient is exponentially related to the surface
area (and hence molecular weight) and surface charge of the particles in addition
to the difference in the electrical potential and hydrophobicity of the phases. It
is not generally very sensitive to temperature changes. This means that proteins
and larger particles are normally partitioned into one phase whereas smaller
molecules are distributed more evenly between phases. A partition coefficient of
greater than 3 is required if usable yields are to be achieved by a single
extraction process. Typical partition coefficients for proteins are 0.01-100
whereas the partition coefficients for cells and cell debris are effectively zero.
The influence of pH and salts on protein partition is complex, particularly when
phosphate buffers are present. A given protein distributes differently between the
phases at different pH's and ionic strength but the presence of phosphate ions
affect the partition coefficient in an anomalous fashion because these ions
distribute themselves unequally resulting in electrostatic potential (and pH)
differences. This means that systems may be 'tuned' to enrich an enzyme in one
phase, ideally the upper phase with cell debris and unwanted enzymes in the lower
phase.
An enzyme may be extracted from the upper (polyethylene glycol) phase by the
addition of salts or further polymer, generating a new biphasic system. This stage
may be used to further purify the enzyme. A powerful modification of this
technique is to combine phase partitioning and affinity partitioning. Affinity
ligand (e.g. triazine dyes) may be coupled to either polymer in an aqueous
biphasic system and thus greatly increase the specificity of the extraction.
Phases form when limiting concentrations of the polymers are exceeded. Both phases
contain mainly water (typically 70-90% w/w water) and are enriched in one of the
polymers. The limiting concentrations depend on the type and molecular weight of
the polymers and on the pH, ionic strength and temperature of the solution. Some
polymers form a two-phase system by themselves; PEG forming the upper more-
hydrophobic phase in the presence of fairly concentrated solutions of citrates,
phosphates or sulfates or at higher temperatures (see below). Such aqueous liquid-
liquid two-phase systems are finding increasing use in the extractive separation
of labile biomolecules such as proteins, offering mild conditions due to the low
interfacial tension between the phases (i.e. about 400-fold less than that between
water and an immiscible organic solvent) allowing small droplet size, large
interfacial areas, efficient mixing under very gentle stirring and rapid
partition. The polymers also have a stabilizing influence on most proteins. A
great variety of separations have been achieved, by far the most important being
the separation of enzymes from broken crude cell material. Separation may be
achieved in a few minutes, minimizing the harmful action of endogenous proteases.
The systems have also been used successfully for the separation of different types
of cell membranes, organelles and actinide ions, the purification of enzymes,
extractive bioconversions. Although sometimes perceived as due to polymer
incompatibilities, the properties of these biphasic systems can be mainly
attributed to incompatibility between aqueous pools of low and higher density
water. Each phase may be considered as a different, although aqueous, solvent with
properties determined by its structuring.
PEG usually has a far higher concentration in the upper (low-density) phase of
such solutions in spite of its inherent density being greater than water. These,
together with the properties of this PEG phase encourage the belief that it
creates a predominantly low-density water environment due to its partially
hydrophobic character, in turn mainly determined by the methylene groups. Further
proof of this may be seen by use of microwave dielectric measurements, which show
the water surrounding PEG to be ordered, whereas that surrounding more hydrophilic
polymers is disordered [332]. Also, the dissolution of PEG is exothermic (and
increasingly exothermic with PEG size), in line with a shift in the ES CS
equilibrium towards the more ordered ES structure. It is interesting and perhaps
not simply fortuitous that the diameter (4.9 Å) of the favored PEG helix (formed
by trans, gauche, trans links across the C-O-C-C, O-C-C-O, C-C-O-C bonds) is the
same as the diameter of the spines of the ES water cluster (4.7 Å) formed by
pentagonal boxes, the ether (O-C-C-O) distances (2.22 Å) are close to the O•••O
distances (2.24 Å) in water and the next ether (O-C-C-O-C-C-O) (5.6 Å) distances
are close to the next vertex distance on opposite sides of the pentagonal boxes
(5.4 Å).a Model building shows that optimum hydrogen bonding would tend to distort
this PEG helix, however. The strongly-held hydration, as determined by viscosity,
increases from two molecules of water per PEG monomer at very low polymerization
(tetramer) to 5 molecules of water per PEG monomer for 45-mer , showing that the
extent of water clustering increases with PEG size. The partitioning of proteins
into the hydrophobic PEG phase shows great sensitivity to the protein's surface
hydrophobicity (partition increasing with surface hydrophobicity) and also depends
on the PEG size; increasing with PEG molecular mass , in line with the extent of
water clustering. Increasing PEG size and concentration both increase the
proteins' effective hydration as the PEG is excluded from the proteins' surface.
However, when the PEG phase becomes too ordered (e.g. at higher PEG size)
partitioned proteins are excluded due to the reduced available water content.
An interesting and revealing phenomenon occurs in PEG solutions as the temperature
is raised; the solution at low temperatures separates into two phases (PEG-rich
and PEG-poor) at higher temperature (separating at the cloud-point) and reverts to
a single phase at even higher temperatures. This may be explained as the PEG
creating a low-density water environment with decreased entropy. At low
temperatures a solution is formed due to the enthalpy of hydrogen bonding between
the PEG and the water more than compensating for the entropy lost in forming the
low-density water. This entropy loss is required, due to the hydrophobicity of the
methylene groups, but is not great as the water is somewhat ordered already at
lower temperatures. At the cloud point, the entropy cost is greater as the water
is no longer naturally as structured, and two phases develop. The stronger
hydrogen bonding in D2O, relative to H2O, is expected to raise this cloudpoint. At
higher temperatures still, the water possesses excess energy and cannot be
structured by the PEG. This reduces the entropic cost, so allowing a solution to
form once more.
Anions have a distinct effect on the cloud point in line with the Hofmeister
Series (cloud point lowering: SCN- < I- < Br- < Cl- < F- < OH- < SO42- < HPO42- <
CO32- < PO43-); the greater lowering of the cloud point is in line with greater
surface charge density , stronger hydration, greater tendency to avoid low-density
water and the greater destruction of the natural structuring of the water. A
oppositely-ordered compensating effect on the cloud point has been recognized due
to binding of the anions to the polymer surface. This tends to raise the
cloudpoint at lower salt concentrations as the bound salt increases the polymer
net charge and, hence, solubility. The relative effect of the ions is the reverse
of the Hofmeister series just given with weakly hydrated ions binding best, i.e.
SCN- having the greatest effect and ionic kosmotropes below Cl- having negligible
effect.
Cations have a lesser but opposite effect to anions with chaotropes (e.g. NH4+)
tending to lower the cloud point but kosmotropes (e.g. Li+) raising it.
Exceptionally, however, some di- and trivalent cations such as Mg2+ and Zn2+ act
counter to their normal Hofmeister behavior, due presumably to their specific
chelation to oxygen atoms in the PEG molecules.
Anions and cations distribute themselves differently between the phases depending
on their affinity for low or higher density water but with the requirements that
the phases be electrically neutral and iso-osmotic, so producing an interfacial
potential difference, which may aid the partitioning of charged biomolecules. Thus
sulfate and phosphate ions prefer the bottom phase and, as a consequence,
negatively charged proteins are partitioned into the upper PEG phase, so allowing
more sulfate or phosphate ions to partition into their preferred lower phase.
Preference for the PEG-rich or PEG-poor phase is related to the Hofmeister Series
for the structuring ability of the salts, particularly the anions (e.g. preference
for PEG-rich phase: I- > Br- > Cl- > F- > SO42-; Cs+ > Na+ > Ba2+ > Ca2+;
preference for PEG-poor phase: SO42- > F- > Cl- > Br- > I-). A similar Hofmeister
Series effect is noticed intensifying the incompatibility between two polymers
such as polyethylenimine-PEG, or dextran-PEG, by increasing the concentration of
strongly hydrated (CS-forming) anions, such as sulfate.
a Note that the polymers formed with either one (-O-C-O-C-O-) or three (-O-C-C-C-
O-C-C-C-O-) methylene groups between the oxygen atoms are both insoluble in water.
The reason however is not so much that the O•••O distances (2.12 Å and 4.79 Å
respectively) fit less well with the water cluster spacing but rather that the
molecules form almost-linear extended (rather than helical) chains with a
pronounced hydrophobic character that have strong intra-molecular attraction.
2.9 Preparation of enzymes from clarified solution; Ultrafiltration
In many cases, especially when extracellular enzymes are being prepared for sale,
the clarified solution is simply concentrated, preservative materials added, and
sold as a solution or as a dried preparation. The concentration process chosen
will be the cheapest which is compatible with the retention of enzyme activity.
For some enzymes rotary evaporation can be considered, followed if necessary by
spray drying. The most popular method, though, is ultrafiltration, whereby water
and low molecular weight materials are removed by passage through a membrane under
pressure, enzyme being retained. Ultrafiltration differs from conventional
filtration and microfiltration with respect to the size of particles being
retained (< 50 nm diameter). It uses asymmetric microporous membranes with a
relatively dense but thin skin, containing pores, supported by a coarse strong
substructure. Membranes possessing molecular weight cut-offs from 1000 to 100,000
and usable at pressure up to 2 MPa are available.
There are number types of apparatus available. Stirred cells represent the
simplest configuration of ultrafiltration cell. The membrane rests on a rigid
support at the base of a cylindrical vessel which is equipped with a magnetic
stirrer to combat concentration polarization. It is not suitable for large scale
use but is useful for preliminary studies and for the concentration of laboratory
column eluates. Various large-scale units are available in which membranes are
formed into wide diameter tubes (1 - 2 cm diameter) and the tubes grouped into
cartridges. These are not as compact as capillary systems (area/volume about 25 m-
1) and are very expensive but are less liable to blockage by stray large particles
in the feedstream. Cheaper thin-channel systems are available (area/volume about
500 m-1) which use flat membrane sandwiches in filter press arrangements of
various designs chosen to produce laminar flow across the membrane and minimise
concentration polarization. Capillary membranes represent a relatively cheap and
increasingly popular type of ultrafiltration system which uses micro-tubular
membranes 0.2 - 1.1 mm diameter and provides large membrane areas within a small
unit volume (area/volume about 1000 m-1). Membranes are usually mounted into
modules for convenient manipulation. This configuration of membranes can be scaled
up with ease. Commercial models are available that give ultrafiltration rates of
up to 600 L hr-1.
The steady improvement in the performance, durability and reliability of membranes
has been a boon to enzyme technologists, encouraging wide use of the various
ultrafiltration configurations. Problems with membrane blockage and fouling can
usually be overcome by treatment of membranes with detergents, proteases or, with
care, acids or alkalis. The initial cost of membranes remains considerable but
modern membranes are durable and cost-effective. Ultrafiltration, done
efficiently, results in little loss of enzyme activity. However, some
configurations of apparatus, particularly in which solutions are recycled, can
produce sufficient shear to damage some enzymes.
Chapter-10
Concentration and purification of enzyme
Concentration by precipitation
Precipitation of enzymes is a useful method of concentration and is ideal as an
initial step in their purification. It can be used on a large scale and is less
affected by the presence of interfering materials than any of the chromatographic
methods described later. There are method of salting in and salting out. Salting
in is the method in which ammonium sulphate is used for dissolving the protein.
Note that protein dissolves least at its isoelectric point. On increasing the
ammonium sulphate concentration further proteins starts precipitating this
phenomenon is called as salting out. All this process must be done in the ice cold
solution so that no protein can denature.
Salting out of proteins is done by use of ammonium sulphate, is one of the best
known and used methods of purifying and concentrating enzymes, particularly at the
laboratory scale. Increases in the ionic strength of the solution cause a
reduction in the repulsive effect of like charges between identical molecules of a
protein. It also reduces the forces holding the salvations shell around the
protein molecules. When these forces are sufficiently reduced, the protein will
precipitate; hydrophobic proteins precipitating at lower salt concentrations than
hydrophilic proteins. Ammonium sulphate is convenient and effective because of its
high solubility, cheapness, lack of toxicity to most enzymes and its stabilizing
effect on some enzymes (see Table 2.4). Its large-scale use, however, is limited
as it is corrosive except with stainless steel, it forms dense solutions
presenting problems to the collection of the precipitate by centrifugation, and it
may release gaseous ammonia, particularly at alkaline pH. The practice of using
ammonium sulphate precipitation is more straightforward than the theory.
Reproducible results can only be obtained provided the protein concentration,
temperature and pH are kept constant. The concentration of the salt needed to
precipitate an enzyme will vary with the concentration of the enzyme. However,
fractionation of protein mixtures by the stepwise increase in the ionic strength
can be a very effective way of partly purifying enzymes.
The solubility of an enzyme can be described by the equation
(2.11)
where S is the enzyme solubility, Kintercept is the intercept constant, Ksalt is
the salting out constant and T is the ionic strength which is proportional to the
concentration of a precipitating salt. Kintercept is independent of the salt used
but depends on the pH, temperature, enzyme and the other components in the
solution. Ksalt depends on both the enzyme required and the salt used but is
largely independent of other factors. This equation (2.11) may also be used to
give the minimum salt concentration necessary before enzyme will start to
precipitate; the concentration change necessary to precipitate the enzyme varying
according to the magnitude of the salting out constant.
Some enzymes do not survive ammonium sulphate precipitation. Other salts may be
substituted but the more favored alternative is to use organic solvents such as
methanol, ethanol, propan-2-ol and acetone. These act by reducing the dielectric
of the medium and consequently reducing the solubility of proteins by favoring
protein-protein rather than protein-solvent interactions. Organic solvents are not
widely used on a large scale because of their cost, their flammability, and the
tendency of proteins to undergo rapid denaturation by these solvents if the
temperature is allowed to raise much above 0°C. On safety grounds when organic
solvents are used, special flameproof laboratory areas are used and temperatures
maintained below their flashpoints.
Except when enzymes are presented for sale as ammonium sulphate precipitates, the
precipitating salt or solvent must be removed. This may be done by dialysis,
Ultrafiltration or by using a desalting column of, for instance, Sephadex G-25.
A. Nucleic acid removal
Intracellular enzyme preparations contain nucleic acids which can give rise to
increased viscosity interfering with enzyme purification procedures, in particular
ultrafiltration. Some organisms contain sufficient nuclease activity to eliminate
this problem but, otherwise, the nucleic acids must be removed by precipitation or
degraded by the addition of exogenous nucleases. Ammonium sulphate precipitation
can be effective in removing nucleic acids but will remove some protein at the
same time. Various more specific precipitants have been used, usually positively-
charged materials which form complexes with the negatively-charged phosphate
residues of the nucleic acids. These include, in order of roughly decreasing
effectiveness, polyethyleneimine, the cationic detergent cetyltrimethyl ammonium
bromide, streptomycin sulphate and protamine sulphate. All of these are expensive
and possibly toxic, particularly streptomycin sulphate. Also, they may complex
undesirably with certain enzymes. They may be necessary, however, where possible
contamination of the enzyme product must be avoided, such as in the preparation of
restriction endonucleases. Otherwise, treatment with bovine pancreatic nucleases
is probably the most cost-effective method of nucleic acid removal.
B. Heat treatment
In many cases, unwanted enzyme activities may be removed by heat treatment.
Different enzymes have differing susceptibility to heat denaturation and
precipitation. Where the enzyme required is relatively heat-stable this allows its
easy and rapid purification in terms of enzymic activity. For such enzymes heat-
treatment is always considered as an option at an early stage in their
purification. This method has been particularly successfully applied to the
production of glucose isomerase, where a short incubation at a relatively high
temperature is used (e.g. 60 - 25°C for 10 min). No interfering activity remains
after this treatment and the heat-treated, and hence leaky, cells may be
immobilised and used directly.
1. Enzyme purification by Chromatography
________________________________________
Low molecular weight polyols (e.g. glycerol, sorbitol and mannitol) are also
useful for stabilizing enzymes, by repressing microbial growth, due to the
reduction in the water activity, and by the formation of protective shells which
prevent unfolding processes. Glycerol may be used to protect enzymes against
denaturation due to ice-crystal formation at sub-zero temperatures. Some
hydrophilic polymers (e.g. polyvinyl alcohol, polyvinylpyrrolidone and
hydroxypropylcelluloses) stabilise enzymes by a process of compartmentalisation
whereby the enzyme-enzyme and enzyme-water interactions are somewhat replaced by
less potentially denaturing enzyme-polymer interactions. They may also act by
stabilizing the hydrophobic effect within the enzymes. Many specific chemical
modifications of amino acid side chains are possible which may (or, more commonly,
may not) result in stabilization. A useful example of this is the derivatisation
of lysine side chains in proteases with N-carboxyamino acid anhydrides. These form
polyaminoacylated enzymes with various degrees of substitution and length of
amide-linked side chains. This derivatisation is sufficient to disguise the
proteinaceous nature of the protease and prevent autolysis.
Important lessons about the molecular basis of thermostability have been learned
by comparison of enzymes from mesophilic and thermophilic organisms. A frequently
found difference is the increase in the proportion of arginine residues at the
expense of lysine and histidine residues. This may be possibly explained by noting
that arginine is bidentate and has a higher pKa than lysine or histidine (see
Table 2.1). Consequently, it forms stronger salt links with bidentate aspartate
and glutamate side chains, resulting in more rigid structures. This observation,
among others, has given hope that site-specific mutagenesis may lead to enzymes
with significantly improved stability . In the meantime it remains possible to
convert lysine residues to arginine-like groups by reaction with activated urea.
It should be noted that enzymes stabilised by making them more rigid usually show
lower activity (i.e. Vmax) than the 'natural' enzyme.
Enzymes are more stable in the dry state than in solution. Solid enzyme
preparations sometimes consist of freeze-dried protein. More usually they are
bulked out with inert materials such as starch, lactose, carboxymethylcellulose
and other poly-electrolytes which protect the enzyme during a cheaper spray-drying
stage. Other materials which are added to enzymes before sale may consist of
substrates, thiols to create a reducing environment, antibiotics, benzoic acid
esters as preservatives for liquid enzyme preparations, inhibitors of
contaminating enzyme activities and chelating agents. Additives of these types
must, of course, be compatible with the final use of the enzyme's product.
Chapter-12
Techniques used in Enzyme characterization
Introduction
After salting in and salting out procedure, enzymes are further purified by two
main common techniques 1- Chromatography; 2- Gel electrophoresis. In this chapter
we will focus mainly on choice of these techniques and their broad details of the
application and principles.
A. Chromatography
Principles of chromatography
Mobile phase: This is chosen according to the nature of the biomolecules. Mobile
phase is used to isolate the biomolecules because most of the biomolecules are
present in the solution. Mobile phase is poured in the gel and get separated due
to attachment with the stationary phase.
The basis of all type of chromatography is the partition or distribution
coefficient (Kd). Two immiscible phases are formed after the distribution of
compound in the matrix and is denoted by Kd= concentration of compound in phase A
/ concentration of compound in phase B.
For two substances of different relative molecular mass and kd value for example
Kd’ and kd’’ is the difference in their elution volumes, Vs, can be derived from
the equation and shown to be:
The resolution depends on the beads. The coarser beads are unable to hold the
fluid, so poorer resolution results. For maximum resolution, superfine beads are
used.
The gel is a three dimensional network whose structure is usually random. The gels
acts as molecular sieves consist of cross linked polymers that are generally
inert, do not bind or react with the material that is being analyzed, and are
uncharged. The space within the gel is filled with liquid occupies most of the gel
volume.
The gels currently in use are of three types: ---dextran, agarose, and
polyacrylamide. They are used in the aqueous solution.Dextran is a polysaccharide
composed of glucose residues. It is commercially available in the trade name
“Sephadex”. They can not be used for molecules that have size more than 600, 000.
the alkyl dextran is called as N, N’- methylene bis acrylamide. They made strong
beads. The product is called as Sephacryl S-300.Agarose is a linear polymer of D-
galactose. It forms a gel held together with crosslink of H-bonds. The pore size
is usually much larger than sephadex. This is the reason why they can be used for
the separation of the large macromolecular substance like protein,
DNA.Polyacrylamide gels are produced by cross-linking acrylamide and N, N’-
methylene-bis acrylamide. It is marketed in the name of Bio-Gel –P. Mixed gel of
polyacrylamide and agarose is known as Ultra-Gel.
Beads can be prepared with defined degrees of porosity, average radii, and mean
radii. In general, the porosity of the beads determines the size range of
molecules that can be effectively separated- the fractionation range. The radii of
the beads are more important for determining the capacity of the column to
separate molecules of similar size. Gel permeation chromatography is normally
considered to be a medium- to high resolution chromatographic (polishing)
technique.
Mechanism of separation by size in gel permeation chromatography
For our discussion of the theory of gel permeation chromatography, we will make
the assumption that many proteins have a roughly spherical shape (often called
globular proteins, as opposed to fiber proteins). Access to included volume
(volume that hydrates the inside of the bed) depends on the size of the sphere
(the hydrodynamic radius) that each protein occupies. The pore size of the bead
will determine whether a protein of s Moreover, since proteins have roughly
constant density (mass per volume), the size of this sphere is directly related to
the mass of the globular protein. Thus, gel permeation chromatography is found to
separate globular proteins according to mass. Note, however, that large deviations
from spherical shape can cause a protein to migrate anomalously during gel
permeation chromatography that is with regard to migration versus mass. Void
volume, etc. For chromatography beads of a given porosity, molecules above a
certain size will be completely excluded from the pore structure of the beads.
These excluded molecules elute in the "void volume" (Vo) of the column and are not
fractionated. In contrast, molecules below a certain size for beads of a given
porosity will completely penetrate the pore structure and will elute with the
"included volume" (Vi). Thus, these molecules are not fractionated either. Only
molecules with masses (hydrodynamic radii) that allow them to penetrate the pore
structure of the beads only partially fall within the fractionation range and are
separated according to their molecular size (approximately, as described
above).The use of a gel permeation column as an analytical tool requires the
determination of Vo, Vi, and the elution volumes (Ve) of the proteins of interest.
By comparing the elution volumes of protein standards of known molecular mass, the
molecular mass of an unknown protein can be estimated. In contrast to denaturing
gel electrophoresis, which gives subunit molecular masses for an oligomeric
protein, gel permeation chromatography provides an estimate of mass for the
oligomeric holoprotein. The combination of denaturing gel electrophoresis and gel
permeation chromatography is thus exceedingly powerful for elucidating basic
features of protein structures.
Use of gel permeation chromatography as part of a purification scheme
Most protein purification schemes involve several steps. These can be
characterized as either bulk or polishing steps. Bulk purification steps are
generally useful for samples of low purity and large volume, both of which are
typical of the starting material to be used in a protein purification, such as a
cellular extract. Common bulk purification methods are centrifugation;
precipitation, such as with salt, solvent, acid, or polyethylene glycol;
filtration; and ion-exchange chromatography. Polishing purification steps are
generally useful for samples of higher quality and smaller volume, typical of
partially purified fractions obtained from bulk purification steps. Common
polishing purification methods are ion exchange, affinity, and gel permeation
chromatography. Gel permeation chromatography is a common and often excellent
polishing step during any protein purification; however, it would not be used as a
first step in purification except in unusual circumstances (e.g., high abundance
of the target protein in the starting material).
Table:1
MATERIAL:
POLYMER TRADE NAME FRACTIONATION RANGE
1.DEXTRAN G 10
< 0.7
SEPHADEX G 25
1.0-5
G 50
1.5—3.0
G 100
4--150
G 200
5---600
SEPHYCRYL S 200
5---250
S 300
10---1500
S 400
20—8000
2. AGAROSE 2 B
10-4000
SEPHAROSE 4B
60---20,000
6B
70—40,000
A 5m
10---5000
BIO-GEL A 15m 40---
15,000
A 50
100---50,000
3. POLYACRYLAMIDE BIO-GEL P2
0.1---1.8
P6
1.0—6
P100 5.0---
100.0
Overview of a typical gel permeation chromatography experiment
In a typical gel permeation experiment, a protein sample (often a partially
purified fraction from a previous purification step, see below) is applied onto
the top of the column packing (beads) and allowed to flow into them. As additional
buffer is applied to the top of the column and allowed to flow through the column,
the protein sample migrates through the column. Due to the differential
partitioning of molecules into the pore structure of the beads (as described
above), the protein molecules are separated. As buffer is eluted from the column,
it is collected in fractions until all the components of the original sample have
passed through the column.
Note that all the large M’s come out at nearly the same volume, Vo. This is
because none of the very large polymers ever enter a pore. So they all elute
together at the void volume, Vo. It is customary to plot log(M), not M. Note
that the independent variable is plotted on the y axis by convention.
With such a curve, you are to select a representative sampling of points. For
example, consider point A, indicated by the cross. Starting at VeA read up until
you hit the M vs. Ve trend and then read left to get MA from the left y-axis.
Obtain DRIA similarly from the right ordinate. Repeat for as many points as you
wish! The DRI response is proportional to the concentration of polymer:
DRI c ( in g/mL)
Mw = =
Mn = = = =
Log M
THE plot is between K verses log M (molecular weight). It yields a straight line
except for very small and very large molecule.
The parameter K = Ve---Vo / Vs, where Ve= elution volume, Vo= void volume, Vs=
volume of stationary phase or = Vt---Vo, Vt is the total volume of the column
PAPER CHROMATOGRAPHY
Cellulose has many hydroxyl groups which are polar and bind H2O. The bound H2O is
the Stationary Phase. H2O run across the cellulose paper due to capillary action.
Mobile Phase is mixture of organic solvents (alcohols, ketone, aldehyde etc.) and
possibly water.
The mobile phase solvent will be less polar than H2O; it is usually a mixture of
Solutes partition between H2O in the stationary phase and the solvent of the
mobile phase. One can change the characteristics of separation by changing the
polarity of the mobile phase (i.e. adjust the composition).
Paper Chromatography is the most common form of cellulose chromatography in which
solute is "spotted" on "dry" paper (still contains H2O) encircle by the pencil at
a line mark and chromatograph is "developed by dipping one end in the mobile
phase. There are two modes of chromatography1: Ascending and 2-Descending.The
solvent moves through the paper, drawn by capillary action Solutes move as spots
with a rate depending upon how much time they spend in the stationary phase vs.
the mobile phase--determined by their partition coefficient--measured as an Rf
value. Maximum distance covered by the solvent is noted and the distance covered
by the solute is noted. The ratio of two gives Rf value. This Rf value is fixed
and is generally less than one.
Ion –exchange chromatography
This type of chromatography is used for many biological materials like amino cid
and proteins, which have ionisable groups, i.e. they have either negative or
positive charge. The name ion exchange is given because of exchanging ions for ion
in aqueous solution.
The principle of ion exchange chromatography is that charged molecule adsorb to
ion exchangers reversibly so that molecule can be bound or eluted by changing the
ionic environment. Separation by ion exchange is usually involving two step. First
–the substances to be separated are bound to the exchanger, using the conditions
that make them more stable and tight binding. Ion exchange separation is carried
out mainly in column packed with an ion –exchangers. The column packing for ion
chromatography consist of ion-exchange resins bonded to inert polymeric particles
(typically 10 µm diameter). For cation separation the cation-exchange resin is
usually a sulfonic or carboxylic acid, and for anion separation the anion-exchange
resin is usually a quaternary ammonium group. For cation-exchange with a sulfonic
acid group the reaction is:
-SO3- H+(s) + Mx+(aq) -SO3- Mx+(s) + H+(aq)
where Mx+ is a cation of charge x, (s) indicates the solid or stationary phase,
and (aq) indicates the aqueous or mobile phase. The equilibrium constant for this
reaction is:
[-SO3- Mx+]s [H+]aq
Keq = ------------------------------------------
[-SO3- H+]s [Mx+]aq
Different cations have different values of Keq and are therefore retained on the
column for different lengths of time. The time at which a given cation elutes from
the column can be controlled by adjusting the pH ([H+]aq). Most ion-chromatography
instruments use two mobile phase reservoirs containing buffers of different pH,
and a programmable pump that can change the pH of the mobile phase during the
separation.
Chromatographic
Separation principle Commercial name Nature of stationary
Phase Type of support
Adsorption Partisil C8
Corasil
Pellumina
Partisil
Micro Pak Al
Bondapak C18
ULTRA pak TSK ODS Octylsilane
Silica
Alumina
Silica
Alumina Porous
Pellicular
Pellicular
Microporous
Microporous
Pellicular
Porous
Ion exchange Partisil-SAX
MicroPak-NH2
Strong base
Weak base Porous
Porous
Exclusion Bio-glass
Styragel
Superpose
Fractogel TSK Glass
Polystyrene-divenyl benzene
Agarose
Polyvinylchloride Rigid solid
Semi-rigid gel
Soft-gel
Semi-rigid gel
Affinity chromatography
Principle
Affinity chromatography is almost exclusively used for the purification of
biological molecules such as proteins and other macromolecules. The technique has
been known for almost a century, but suitable support materials were not available
until much more recently. With new materials and new demands, the technique became
extremely useful in the 1960s, and it has become essential with the growing demand
of the biotech in the 1980s and 1990s.Biotech research has used affinity
chromatography because of its ability to separate one desired species from a host
of other biological molecules. Specificity based on three aspects of affinity—the
matrix, the ligand, and the attachment of the ligand to the matrix—is the hallmark
of this process and the reason for its success. As the name suggests, it utilizes
the property of biological affinity of the substances to be separated. As a
consequence, it is capable of giving absolute purification, even from complex
mixtures, in a single process.
Affinity chromatography operates on the principle that ligand (as stated in the
Table), attached to a matrix made up of an inert substance, bind to the desired
molecule within a solution to be analyzed . Ideally, the ligand will interact only
with the desired molecule and form a permanent bond. All other compounds in the
solution will elude, leaving the desired product in the column. The desired
molecule is then removed from the column by using a wash (typically changing the
pH) that lowers the dissociation constant and allows recovery of a nearly pure
sample.
Choosing the correct ligand is the first hurdle. The ligand must bind strongly
with the molecule that is to be recovered. Biological systems have millions of
ligand (also known as receptors), and most can be affixed to the matrix and used
to isolate the desired molecule.
If the ligand chosen can bind to more than one molecule in the sample in question,
then a technique called negative affinity, which uses ligand to remove everything
but the target molecule from the solution, may be used. For example, if you were
looking for a molecule from a cell, but the only ligand that binds the molecule
also trapped two additional, different molecules, you could run a normal affinity
column and collect these three molecules. Then, if a ligand were found that
attached to the two unwanted molecules, that ligand could be used in the size
exclusion chromatography and affinity column, allowing the desired molecule to
elute while the other two were retained in the column. Matrix materials simply
hold the active ligand and provide a pore structure to increase the surface area
to which the molecules can bind. Ligand attachment requires that the matrix be
activated and then react with the ligand to fix them onto the matrix. During this
process, the ligand must also remain active toward the target molecule, or all
will be for naught. Substituent groups within the matrix, such as amino, hydroxyl,
carbonyl, and thio groups, are easily activated and can serve as the sites to
which the ligand attach. Matrix materials are often polysaccharides, such as
agarose, that have many hydroxyl groups that can be activated. The matrix, in
addition to requiring activation, must also often stand up to decontamination when
purifying pharmaceutical compounds. Decontamination is typically performed by
rinsing the column with sodium hydroxide or urea. Different matrix materials are
stable in different pH ranges, adding the third aspect of selection for affinity
chromatography. The technique was originally developed for the purification of
enzymes, but it has been extended to nucleotides, nucleic acids, immunoglobulin,
and membrane receptors and even to whole cells and cell fragments.
M + L ML
For the success of the experiment following steps must be kept in mind.
1. Matrix should have broad range of thermal and chemical stability. It should
not absorb any chemical or substance to be purified itself.
2. The ligand should be coupled without altering its binding properties.
3. A ligand must bind tightly.
4. During the elution the matrix should not be destroyed.
The most useful material is the Agarose, and polyacrylamide, since they have broad
range of thermal tolerance, exhibit minimum absorption, maintain good flow
property after coupling, and does not denature after application of extreme pH and
ionic strength.
The choice of ligand depends on the specificity of the substance. For example for
an enzyme ligand must be the substrate, a reversible inhibitor, or an allosteric
activator.
METHOD OF LIGAND IMMOBILIZATION
Linking or coupling of the ligand to matrix material is called as immobilization.
1. CNBR activated agarose
CNBr is negatively charged so they can react strongly with the amino group. It
is extremely useful for coupling enzyme, Co-enzyme, inhibitors, antigen, antibody,
nucleic acid and most protein to agarose.
2. 6-AMINO-HEXENOIC ACID & 1,6 DIAMINO HEXANE.
a) Used mainly for small ligand.
b) They can solve the steric problem
c) Only a Spacer can be attached between matrix and ligand.
d) Spacer can be attached by reacting functional group C00H (by using Agarose)
and NH2 (group of 6AHA).
e) Epoxy –activated Agarose.This is useful for linkage of sugars and
carbohydrate or any material containing OH gp, amino gp, thiol gp.
f) Thiopropyl-Agarose.Can be Used or sulpher containing protein. Before using,
it should be treated with the cysteine.
3. Carbomyl diimidazole activated agarose.
Coupling of N-nucleophile to CNBr. This results in isourea linkage that carries
potential charge and thus can act as an ion-exchanger.
Substance Use
Lectin Polysaccharides and glycoprotein present on the RBC membrane.
Con A Sepharose They selectively can binds to the N-acetyl glucosamine residue.
Therefore they can be used for the lymphocyte separation.
Helix pomatia lectin Used for separation of the pure T-cell
Lactose Caster bean, pea nut can be used for separation of lactose.
Maltose Can be separated by the jack bean.
D-glucosamine Can be separated by clam
NADP+ Can be separated by using 2, 5’ ADP.
Protein A Can be used for separation of IgG (using Fc region)
Poly A Can be separated of m-RNA
Boronate polyacrylamide RNA, sugar, catecholamine
Heparin-Agarose Blood protein, DNA polymerase, Ribosome, androgen receptor
Imino-diacetic acid Zn+2, Cu +2 Can be separated
Octyl –agarose Protein Can be separated
Thio-propul Sepharose Can be separated by clam Protein, Urease, and Papain.
Applications
The applications of affinity chromatography have been numerous, but they are
predominantly in the field of biochemistry. Early applications were in the
separation of biomacromolecules from other biological compounds, such as molecules
from an entire cell. This continues to be the primary and extremely important
field for affinity chromatography. For example, S. Loukas and colleagues studied
the existence of one type of suspected opiate receptor in the brain (1994). They
separated the ( -opioid binding protein by using an opioid receptor antagonist
that was specific to the ( -opioid binding protein. These studies may one day lead
to a better understanding of how drugs such as opium affect our brains.
In addition to using small ligand to separate large molecules, researchers have
immobilized large molecules on the matrix and used them to separate the small
molecules that bind to them. In addition to biological separation, affinity
chromatography can be used to determine dissociation constants of ligand and
molecules. The longer a molecule stays on the column, the broader the
chromatographic peak, indicating that the molecule is more tightly bound to the
ligand. This quantitative information can be used in further studies of the ligand
or molecule.
A thin layer of about .25 mm thick slurry is prepared in water is applied to glass
with the help of plate spreader.
CaSO4 is mixed to facilitate adhesion of the adsorbent to the plate.
The plate is dried at 100—1200C. This is also helpful in the activation of the
plate. Sample is applied to the plate 2—2.5 cm from edge by means of micropipette
or microsyringe.
The TLC plate is dipped in the developing phase to depth of about 1.5 cm it is
left for one hour.
Detection is done by the several methods. For e.g. fluorescent dye (this can be
absorbed by the UV light.
For investigating the unsaturated compound I2 vapour can be used. For radiolabel
led compound autoradiography can be used.
Movement of compound can be observed by the specific Rf values.
IT has great resolving power and greater speed of separation. A wider range of
sorbant can be used and also due to easy detection of spot and separation of
chromatogram. Two factor that affect the TLC has, High surface to volume ratio and
the weight ratio, If necessary 2D gels electrophoresis can be used in the TLC
plate this can be used by placing the plate in the buffer at right angle to first
separation. Commonly used separating agent is the Ninhydrin for detection of the
amino acid. Rhodamine B is used for the detection of the lipid; SbCl2 for steroid
and tarpenoid; H2SO4 for organic acid, H2SO4 and KMN03 for hydrocarbon. Br2 vapour
is used for olefins detection.
HPTLC and HPPLC
Thin-layer chromatography (TLC) gets the high-performance (HP) treatment through
several optimization steps leading to improved efficiency and automation. The
layers are made smaller (0.02 mm instead of 0.25 mm), they have smaller mean grain
sizes of the coating particles (down to 7 µm instead of 12–30 µm), and the grain
size is more uniform. Equally if not more important, HPTLC shows better optical
properties than standard TLC, allowing for easy densitometry studies. Better
resolution as well as a 10-fold improvement in detection limits are key to HPTLC’s
increasing popularity.
By using a forced-flow mobile phase and a sealing chamber, researchers can
transform HPTLC into high-pressure planar liquid chromatography (HPPLC), gaining
the added benefits that pressure provides, especially to the speed of the run.
HPTLC can also be used with centrifugation to force the sample outward in what is
known as rotational planar chromatography (RPC). These adaptations are
collectively responsible for what is known as modern TLC, which relies heavily on
instrumental analysis.
Applications of these modern forms are extensive, including routine use in the
pharmaceutical industry and clinical analysis, in food analysis, natural products
analysis (including a variety of botanicals and herbals), and in environmental
analysis for determining such things as pesticides in drinking water.
F= qv/ velocity
q-= charge and V is the potential difference. Electrophoretic mobility (μ) is
defined as ratio of velocity to field strength.
IF this free radical is represented as R’. Oxygen can be used for the removal of
the free radicals. Free radical generation can be done by the photo
polymerization. Low percentage gel can be used for the separation of the DNA. For
protein separation SDS –PAGE can be used the usual percentage lies between the 3
to 30 % of acrylamide. Since protein separation done in the two steps: first it is
separated in the stalking gel, and size exclusion chromatography on it is resolved
by the resolving gel. Stalking gel generally uses lower percentage of the gel that
provides the larger pore size. It allows the free movement of the protein so that
one type of protein either same in the molecular weight or charge can stalk at one
position. After this process the protein is separated in the gel having smaller
pore size. All these process can be done by the vertical slabs.
c. SDS-PAGE
SDS is an anionic detergent (CH3—(CH2)10 –CH2OSO3-Na+). With β mercaptoethanol and
SDS, protein can be denatured into the simple protein. It helps in the better
separation of the protein. And thus protein is analyzed in qualitative way. On
average it has seen that one SDS can binds to the two amino acid. Problem arises
during the electrophoresis is the settling of sample and exact tracking of the
protein position in the gel. For settling problem sucrose solution is used, and
for tracking the protein bromo-phenol blue is used. The protein first of all
loaded in the stalking gel. In this master mix, glycine is added. This is done to
sharpen the protein band. But note that glycinate ion have a lower electrophoretic
mobility than protein –SDS complex, which have lower mobility than chloride ion of
the loading buffer and the stacking gel
Cl- > PROTEIN-SDS > GLYCINATE
So protein SDS band lies in between the Cl- and glycinate ion. PH of the stacking
gel is generally 6.8 and resolving gel has pH about 8.8. The negatively charged
protein is attracted toward the anode. After the protein is reaches the bottom,
the gel is removed and placed in stain more generally the Coomassie blue. The gel
is then placed in the destain solution. Staining of gel is done for 2-3 hrs. And
destaining requires overnight. Generally 15 % polyacrylamide gel is used in the
separating gel. This can allow separation of the protein in the range of 100,000
to 10, 000. For protein of molecular weight more than 150, 000 7.5% gel is used.
Molecular weight of protein Mr can be determined by the comparing its mobility
with those of a number of protein used as standard. By plotting a graph of
distance moved against log Mr for each of standard proteins, a calibration curve
can be
constructed. The distance moved by the protein of unknown Mr is then measured and
its log Mr and hence Mr can be determined from calibration curve. A protein
generally have single band in the protein unless it has two same subunit.
d. Native (buffer) gel
In this method SDS is not used for the separation of the protein subunit prior to
loading. Here protein is separated according to the native charge of protein at pH
of the gel (normally pH 8.7) and according to the different electrophoretic
nobilities and the sieving effect of the gel. The method is generally used for
the enzyme –substrate reaction and total protein content.
e. Gradient gel
The protein is separated according to the gradient formed by the different
concentration of the gel. Generally 5% at the top, while 15% gel is used at the
bottom. The main advantage is that – very similar molecular weight can be
resolved.
f. Iso-electric focusing: IEF gel:
It utilizes the horizontal gels and separates the protein according to the iso-
electric point of the protein. As we know that protein is the ampholytes, it can
be separated easily. Here riboflavin is used for initiation of the polymerization
of the gel. Protein having pH lower than iso-electric point will be positively
charged, and will initially migrate towards the cathode. As they proceed further,
the charge on the protein decreases slowly and at one point protein stops where IP
is equal to the charge. For determining the IP of the protein, a standard IP of
known protein can be determined and with the help of this calibration curve, IP of
unknown protein can be determined. IEF is highly sensitive technique and used for
studying heterogeneity of the protein.
g. Chromatofocussing
Is suitable for the protein separation. This is based on forming a pH gradient.
The ion-exchanger is fixed in the column and set to a particular temperature and
pH. The difference of pH lies between 3-4 unit from upper and bottom. On adding
protein at top of column the protein moves at its isoelectric point. Just beyond
the isoelectric point the protein is bind to the positive charge of the ion-
exchange column. Chromatofocussing gives a good resolution of quit complex mixture
of protein provided that there is close difference in their isoelectric point, it
gives poor resolution of compound having same isoelectric point.
2D-PAGE
This technique utilizes the technique of both IEF and the SDS-PAGE. In the first
dimension –isoelectric focusing is done in polyacrylamide gel in narrow tubes in
the presence of ampholytes, 8M urea and non-ionic detergent. Denatured protein is
separated in the gel according to the isoelectric point. In another step the
protein is run in presence of SDS. Generally the technique is used in the
translational product of the gene or mRNA. It also helps in isolating the extra
protein in the expression. Now a days to reduce so much of the labor, computerized
2D is done.
Figure 6.2. Schematic diagram showing the effect of soluble enzyme concentration
on the activity of enzyme immobilised by adsorption to a suitable matrix. The
amount adsorbed depends on the incubation time, pH, ionic strength, surface area,
porosity, and the physical characteristics of both the enzyme and the support.
________________________________________
Table 6.1 Preparation of immobilised invertase by adsorption (Woodward 1985)
Support type
% bound at DEAE-Sephadex
anion exchanger CM-Sephadex
cation exchanger
pH 2.5 0 100
pH 4.7 100 75
pH 7.0 100 34
________________________________________
Covalent coupling
This involves the formation of a covalent bond between the enzyme and the carrier
material. The bond is normally formed between functional groups on the carrier and
the enzyme. Those on the enzymes are usually amino acid residues such as amino
(NH2) group from Lys or Arg, carboxyl (COOH) group from Asp, Glu, hydroxyl (OH)
group from Ser, Thr, and sulfhydryl (SH) group from Cys. Tests must be run to
ensure the formation of covalent bonds will not inactivate the enzyme. Through
chemical modifications, functional groups on the carriers can be altered to
different forms to accommodate different kinds of covalent bonds to be formed with
the enzyme. For example, chemical modification of -OH group can give rise to AE-
cellulose (aminoethyl), CM- cellulose (carboxymethyl), and DEAE-cellulose
(diethylaminoethyl). This increases the range of immobilization methods that can
be used for a given carrier.
While many supports exist, an important factor for enzyme immobilization appears
to be hydrophilicity, which helps to maintain enzyme activity in a hydrophilic
milieu. Immobilisation of enzymes by their covalent coupling to insoluble matrices
is an extensively researched technique. Only small amounts of enzymes may be
immobilised by this method (about 0.02 gram per gram of matrix) although in
exceptional cases as much as 0.3 gram per gram of matrix has been reported. The
strength of binding is very strong, however, and very little leakage of enzyme
from the support occurs.
Functional groups that affects the covalent coupling
The relative usefulness of various groups, found in enzymes, for covalent link
formation depends upon their availability and reactivity (nucleophilicity), in
addition to the stability of the covalent link, once formed (Table 3.2). The
reactivity of the protein side-chain nucleophiles is determined by their state of
protonation (i.e. charged status) and roughly follows the relationship -S- > -SH >
-O- > -NH2 > -COO- > -OH >> -NH3+where the charges may be estimated from a
knowledge of the pKa values of the ionising groups (Table 1.1) and the pH of the
solution. Lysine residues are found to be the most generally useful groups for
covalent bonding of enzymes to insoluble supports due to their widespread surface
exposure and high reactivity, especially in slightly alkaline solutions. They also
appear to be only very rarely involved in the active sites of enzymes.
________________________________________
Table 6.2 Relative usefulness of enzyme residues for covalent coupling
Residue Content Exposure Reactivity Stability
of couple Use
Aspartate + ++ + + +
Arginine + ++ - ± -
Cysteine - ± ++ - -
Cystine + - ± ± -
Glutamate + ++ + + +
Histidine ± ++ + + +
Lysine ++ ++ ++ ++ ++
Methionine - - ± - -
Serine ++ + ± + ±
Threonine ++ ± ± + ±
Tryptophan - - - ± -
Tyrosine + - + _+ +
C terminus - ++ + + +
N terminus - ++ ++ ++ +
Carbohydrate - ~ ++ ++ + + ±
Others - ~ ++ - - - ~ ++ -
The most commonly used method for immobilising enzymes on the research scale (i.e.
using less than a gram of enzyme) involves Sepharose, activated by cyanogen
bromide. This is a simple, mild and often successful method of wide applicability.
Sepharose is a commercially available beaded polymer which is highly hydrophilic
and generally inert to microbiological attack. Chemically it is an agarose (poly-
{β1,3-D-galactose-α-1,4-(3,6-anhydro)-L-galactose}) gel. The hydroxyl groups of
this polysaccharide combine with cyanogen bromide to give the reactive cyclic
imido-carbonate. This reacts with primary amino groups (i.e. mainly lysine
residues) on the enzyme under mildly basic conditions (pH 9 - 11.5, Figure 3.3a).
The high toxicity of cyanogen bromide has led to the commercial, if rather
expensive, production of ready-activated Sepharose and the investigation of
alternative methods, often involving chloroformates, to produce similar
intermediates (Figure 3.3b).
Carbodiimides (Figure 13.3c) are very useful bifunctional reagents as they allow
the coupling of amines to carboxylic acids. Careful control of the reaction
conditions and choice of carbodiimide allow a great degree of selectivity in this
reaction.
Glutaraldehyde is another bifunctional reagent which may be used to cross-link
enzymes or link them to supports (Figure 13.3d). It is particularly useful for
producing immobilised enzyme membranes, for use in biosensors, by cross-linking
the enzyme plus a non-catalytic diluent protein within a porous sheet (e.g. lens
tissue paper or nylon net fabric). The use of trialkoxysilanes allows even such
apparently inert materials as glass to be coupled to enzymes (Figure 13.3e). There
are numerous other methods available for the covalent attachment of enzymes (e.g.
the attachment of tyrosine groups through diazo-linkages, and lysine groups
through amide formation with acyl chlorides or anhydrides).
________________________________________
A. cyanogen bromide
Figure 6.3. (e) The use of trialkoxysilane to derivatise glass. The reactive glass
may be linked to enzymes by a number of methods including the use thiophosgene, as
shown.
________________________________________
It is clearly important that the immobilised enzyme retains as much catalytic
activity as possible after reaction. This can, in part, be ensured by reducing the
amount of enzyme bound in non-catalytic conformations (Figure 3.4). Immobilisation
of the enzyme in the presence of saturating concentrations of substrate, product
or a competitive inhibitor ensures that the active site remains unreacted during
the covalent coupling and reduces the occurrence of binding in unproductive
conformations. The activity of the immobilised enzyme is then simply restored by
washing the immobilised enzyme to remove these molecules.
________________________________________
Chapter-14
Introduction to Industrial biotechnology
Figure 7.10. Diagram showing the production rate of a seven-column PBR facility on
start -up, assuming exponential decay of reactor activity. The columns are brought
into use one at a time. At any time a maximum of six PBRs are operating in
parallel, whilst the seventh, exhausted, reactor is being refilled with fresh
biocatalyst. ——— PBR activities allowed to decay through three half-lives (to
12.5% initial activity) before replacement. The final average productivity is 2.51
times the initial productivity of one column. - - -- - - - PBR activities
allowed to decay through two half-lives (to 25% initial activity) before
replacement. The final average productivity is 3.23 times the initial productivity
of one column. It may be seen that the final average production rate is higher
when the PBRs are individually operated for shorter periods but this 29% increase
in productivity is achieved at a cost of 50% more enzyme, due to the more rapid
replacement of the biocatalyst in the PBRs. A shorter PBR operating time also
results in a briefer start-up period and a more uniform productivity.
________________________________________
After isomerisation, the pH of the syrup is lowered to 4 - 5 and it is purified by
ion-exchange chromatography and treatment with activated carbon. Then, it is
normally concentrated by evaporation to about 70% dry solids.For many purposes a
42% fructose syrup is perfectly satisfactory for use but it does not match the
exacting criteria of the quality soft drink manufacturers as a replacement for
sucrose in acidic soft drinks. For use in the better colas, 55% fructose is
required. This is produced by using vast chromatographic columns of zeolites or
the calcium salts of cation exchange resins to adsorb and separate the fructose
from the other components. The fractionation process, although basically very
simple, is only economic if run continuously. The fructose stream (90% (w/w)
fructose, 9% glucose) is blended with 42% fructose syrups to give the 55% fructose
(42% glucose) product required. The glucose-rich 'raffinate' stream may be
recycled but if this is done undesirable oligosaccharides build up in the system.
Immobilised glucoamylase is used in some plants to hydrolyse oligosaccharides in
the raffinate; here the substrate concentration is comparatively low (around 20%
dry solids) so the formation of isomaltose by the enzyme is insignificant.Clearly
the need for a second large fructose enrichment plant in addition to the glucose
isomerase plant is undesirable and attention is being paid to means of producing
55% fructose syrups using only the enzyme. The thermodynamics of the system favour
fructose production at higher temperatures and 55% fructose syrups could be
produced directly if the enzyme reactors were operated at around 95°C. The use of
miscible organic co -solvents may also produce the desired effect. Both these
alternatives present a more than considerable challenge to enzyme technology!
The present world market for HFCS is over 5 million tonnes of which about 60% is
for 55% fructose syrup with most of the remainder for 42% fructose syrup. This
market is still expanding and ensures that HFCS production is the major
application for immobilised-enzyme technology.The high-fructose syrups can be used
to replace sucrose where sucrose is used in solution but they are inadequate to
replace crystalline sucrose. Another ambition of the corn syrup industry is to
produce sucrose from starch. This can be done using a combination of the enzymes
phosphorylase (EC 2.4.1.1), glucose isomerase and sucrose phosphorylase (EC
2.4.1.7), but the thermodynamics do not favour the conversion so means must be
found of removing sucrose from the system as soon as it is formed. This will not
be easy but is achievable if the commercial pull (i.e. money available) is
sufficient:
phosphorylase
starch (Gn) + orthophosphate starch (Gn-1) + α-glucose-1-phosphate [7.1]
glucose isomerase
glucose fructose [7.2]
sucrose phosphorylase
-glucose-1 -phosphate + fructose sucrose + orthophosphate [7.3]
A further possible approach to producing sucrose from glucose is to supply glucose
at high concentrations to microbes whose response to osmotic stress is to
accumulate sucrose intracellularly. Provided they are able to release sucrose
without hydrolysis when the stress is released, such microbes may be the basis of
totally novel processes.
3-Use of immobilised raffinase
The development of a raffinase (α-D-galactosidase) suitable for commercial use is
another triumph of enzyme technology. Plainly, it would be totally unacceptable to
use an enzyme preparation containing invertase to remove this material during
sucrose production. It has been necessary to find an organism capable of producing
an -galactosidase but not an invertase. A mould, Mortierella vinacea var.
raffinoseutilizer, fills the requirements. This is grown in a particulate form and
the particles harvested, dried and used directly as the immobilised-enzyme
preparation. It is stirred with the sugar beet juice in batch stirred tank
reactors. When the removal of raffinose is complete, stirring is stopped and the
juice pumped off the settled bed of enzyme. Enzyme, lost by physical attrition, is
replaced by new enzyme added with the next batch of juice. The galactose released
is destroyed in the alkaline conditions of the first stages of juice purification
and does not cause any further problems while the sucrose is recovered. This
process results in a 3% increase in productivity and a significant reduction in
the costs of the disposal of waste molasses.
Immobilised raffinase may also be used to remove the raffinose and stachyose from
soybean milk. These sugars are responsible for the flatulence that may be caused
when soybean milk is used as a milk substitute in special diets.
4-Use of immobilised Invertase
Invertase was probably the first enzyme to be used on a large scale in an
immobilised form (by Tate & Lyle). In the period 1941 -1946 the acid, previously
used in the manufacture of Golden Syrup, was unavailable, so yeast invertase was
used instead. Yeast cells were autolysed and the autolysate clarified by
adjustment to pH 4.7, followed by filtration through a bed of calcium sulphate and
adsorption into bone char. A layer of the bone char containing invertase was
included in the bed of bone char already used for decolourising the syrup. The
scale used was large, the bed of invertase-char being 2 ft (60 cm) deep in a bed
of char 20 ft (610 cm) deep. The preparation was very stable, the limiting factors
being microbial contamination or loss of decolourising power rather than loss of
enzymic activity. The process was cost-effective but, not surprisingly, the
product did not have the subtlety of flavour of the acid-hydrolysed material and
the immobilised enzyme process was abandoned when the acid became available once
again. Recently, however, it has been relaunched using BrimacTM, where the
invertase -char mix is stabilised by cross-linking and has a half-life of 90 days
in use (pH 5.5, 50°C). The revival is due, in part, to the success of HFCS as a
high-quality low-colour sweetener. It is impossible to produce inverted syrups of
equivalent quality by acid hydrolysis. Enzymic inversion avoids the high-colour,
high salt-ash, relatively low conversion and batch variability problems of acid
hydrolysis. Although free invertase may be used (with residence times of about a
day), the use of immobilised enzymes in a PBR (with residence time of about 15
min) makes the process competitive; the cost of 95% inversion (at 50% (w/w)) being
no more than the final evaporation costs (to 75% (w/w)). A productivity of 16
tonnes of inverted syrup (dry weight) may be achieved using one litre of the
granular enzyme.
5-Production of amino acids
Another early application of an immobilised enzyme was the use of the aminoacylase
from Aspergillus oryzae to resolve racemic mixtures of amino acids.
[7.8]
[7.9] The penicillin-G-amidases may be used 'in reverse' to synthesise penicillin
and cephalosporin antibiotics by non -equilibrium kinetically controlled
reactions. Ampicillin has been produced by the use of penicillin-G-amidase
immobilised by adsorption to DEAE -cellulose in a packed bed column:
[7.10] Many other potential and proven antibiotics have been synthesised in this
manner, using a variety of synthetic β-lactams and activated carboxylic acids.
Preparation of acrylamide
Acrylamide is an important monomer needed for the production of a range of
economically useful polymeric materials. It may be produced by the addition of
water to acrylonitrile.
CH2=CHCN + H2O CH2=CHCONH2 [14.11]
This process may be achieved by the use of a reduced copper catalyst (Cu+);
however, the yield is poor, unwanted polymerisation or conversion to acrylic acid
(CH2=CHCOOH) may occur at the relatively high temperatures involved (80 -140°C)
and the catalyst is difficult to regenerate. These problems may be overcome by the
use of immobilised nitrile hydratase (often erroneously called a nitrilase). The
enzyme from Rhodococcus has been used by the Nitto Chemical Industry Co. Ltd, as
it contains only very low amidase activity which otherwise would produce unwanted
acrylic acid from the acrylamide.
Immobilised nitrile hydratase is simply prepared by entrapping the intact cells in
a cross-linked 10% (w/v) polyacrylamide/dimethylaminoethylmethacrylate gel and
granulating the product. It is used at 10°C and pH 8.0-8.5 in a semibatchwise
process, keeping the substrate acrylonitrile concentration below 3% (w/v). Using
1% (w/v) immobilised-enzyme concentration (about 50,000 U l-1) the process takes
about a day. Product concentrations of up to 20% (w/v) acrylamide have been
achieved, containing negligible substrate and less than 0.02% (w/w) acrylic acid.
Acrylamide production using this method is about 4000 tonnes per year.
The closely related enzymes cyanidase and cyanide hydratase are used to remove
cyanide from industrial waste and in the detoxification of feeds and foodstuffs
containing amygdalin (see equation [7.12]).
HCN + 2H2O HCOO- + NH4+ [7.12]
HCN + H2O HCONH2 [7.13]
Alkaline phosphates
This enzyme is detected in the obstructive jaundice. It is also useful in the
detection of bone disease like ostomalacia, rickets and hyperparathyroidism. This
enzyme is normally found in the serum. This enzyme concentration also increases
during the pregnancy.
Acid phosphatase.
This enzyme is found in highest concentration in the prostrate carcinoma.
In Treatment of cancer
A major potential therapeutic application of enzymes is in the treatment of
cancer. Asparaginase has proved to be particularly promising for the treatment of
acute lymphocytic leukemia. Its action depends upon the fact that tumour cells are
deficient in aspartate-ammonia ligase activity, which restricts their ability to
synthesise the normally non-essential amino acid L-asparagine. Therefore, they are
forced to extract it from body fluids. The action of the asparaginase does not
affect the functioning of normal cells which are able to synthesize enough for
their own requirements, but reduce the free exogenous concentration and so induces
a state of fatal starvation in the susceptible tumour cells. A 60% incidence of
complete remission has been reported in a study of almost 6000 cases of acute
lymphocytic leukemia. The enzyme is administered intravenously. It is only
effective in reducing asparagine levels within the bloodstream, showing a half-
life of about a day (in a dog). This half-life may be increased 20-fold by use of
polyethylene glycol-modified asparaginase.
Enzyme deficiencies
Phenylketonuria is detected by presence of phenylalanine in the urine. Some inborn
error of metabolism is also detected are relatively harmless e.g. albinism ,
alkaptonuria,
Table 8.1 showing List of defective enzyme and their diseases
Alkaptonuria
Phenylketonuria
Maple syrup disease
Galactosomia
uridyltransferasae
Glycogen storage
Fructosuria
Gaucher disease
Tay Sachs
Wilson disease
Acetalasaemia
Xerderma pigmentosa
homogenistate 1 oxidase
phenylalanine 4 monooxygenase
oxo acid decorboxylase
galactose-1 phosphate
glucose 6 phosphate
fructokinase
glucocerbrosidase
β-NAcetykll –D-hexosaminidase
P-type ATPase
catalase
DNA binding protein helicases
Inhibition of HIV protease.The replication of HIV-1 is the cause of AIDS. The HIV-
1 protease catalyses this protein sequence. HIV protease is an aspartyl protease
having a sequence Asp-thr-Gly at its active site. It resemble pepsin, and other
retroviral protease. Many inhibitors have been designed that are analogous like
rennin. Figure below showing structure of HIV protease.
There are number of enzymatic advantage method estimate the metabolite in presence
of many other substances an inhibitor present in serum may completely inhibit
enzyme activity. For the estimation of certain metabolite e.g. glucose, and plasma
glycerides enzyme methods are now used almost exclusively e.g. serum creatine and
non-enzymic method are still being used in clinical chemistry.
Blood glucose
In the investigation of diabetes there are three enzymatic method that are
available; hexokinase couple with glucose 6-phosphate dehydrogenase, glucose
oxidase coupled with peroxidase. The second method is glucose oxidase is more
commonly used.
________________________________________
Table 8.2 Some important therapeutic enzymes
Enzyme EC number Reaction Use
Asparaginase 3.5.1.1 L-Asparagine H2O L-aspartate + NH3 Leukaemia
Collagenase 3.4.24.3 Collagen hydrolysis Skin ulcers
Glutaminase 3.5.1.2 L-Glutamine H2O L-glutamate + NH3 Leukaemia
Hyaluronidasea
3.2.1.35 Hyaluronate hydrolysis Heart attack
Lysozyme 3.2.1.17 Bacterial cell wall hydrolysis Antibiotic
Rhodanaseb
2.8.1.1 S2O32- + CN- SO32- + SCN-
Cyanide poisoning
Ribonuclease 3.1.26.4 RNA hydrolysis Antiviral
β-Lactamase 3.5.2.6 Penicillin penicilloate
Penicillin allergy
Streptokinasec
3.4.22.10 Plasminogen plasmin
Blood clots
Trypsin 3.4.21.4 Protein hydrolysis Inflammation
Uricased
1.7.3.3 Urate + O2 allantoin
Gout
Urokinasee
3.4.21.31 Plasminogen plasmin
Blood clots
a Hyaluronoglucosaminidase, b thiosulphate sulfurtransferase,c streptococcal
cysteine proteinase
d urate oxidase,e plasminogen activator
________________________________________
Disadvantages of Using Enzyme as Therapeutic Agents
As enzymes are specific biological catalysts, they should make the most desirable
therapeutic agents for the treatment of metabolic diseases. Unfortunately a number
of factors severely reduce this potential utility:
a) They are too large to be distributed simply within the body's cells. This is
the major reason why enzymes have not yet been successful applied to the large
number of human genetic diseases. A number of methods are being developed in order
to overcome this by targeting enzymes; as examples, enzymes with covalently
attached external α-galactose residues are targeted at hepatocytes and enzymes
covalently coupled to target-specific monoclonal antibodies are being used to
avoid non-specific side-reactions.
b) Being generally foreign proteins to the body, they are antigenic and can
elicit an immune response which may cause severe and life-threatening allergic
reactions, particularly .on continued use. It has proved possible to circumvent
this problem, in some cases, by disguising the enzyme as an apparently non-
proteinaceous molecule by covalent modification.
Asparaginase, modified by covalent attachment of polyethylene glycol, has been
shown to retain its anti-tumour effect whilst possessing no immunogenicity.
Clearly the presence of toxins, pyrogens and other harmful materials within a
therapeutic enzyme preparation is totally forbidden. Effectively, this encourages
the use of animal enzymes, in spite of their high cost, relative to those of
microbial origin.
Their effective lifetime within the circulation may be only a matter of minutes.
This has proved easier than the immunological problem to combat, by disguise using
covalent modification. Other methods have also been shown to be successful,
particularly those involving entrapment of the enzyme within artificial
liposome’s, synthetic microspheres and red blood cell ghosts. However, although
these methods are efficacious at extending the circulatory lifetime of the
enzymes, they often cause increased immunological response and additionally may
cause blood clots.
In contrast to the industrial use of enzymes, therapeutically useful enzymes are
required in relatively tiny amounts but at a very high degree of purity and
(generally) specificity. The favoured kinetic properties of these enzymes are low
Km and high Vmax in order to be maximally efficient even at very low enzyme and
substrate concentrations. Thus the sources of such enzymes are chosen with care to
avoid any possibility of unwanted contamination by incompatible material and to
enable ready purification. Therapeutic enzyme preparations are generally offered
for sale as lyophilised pure preparations with only biocompatible buffering salts
and mannitol diluent added.
The costs of such enzymes may be quite high but still comparable to those of
competing therapeutic agents or treatments. As an example, urokinase (a serine
protease, see Table 4.4) is prepared from human urine (some genetically engineered
preparations are being developed) and used to dissolve blood clots. The cost of
the enzyme is about Rs. 5000 mg-1, with the cost of treatment in a case of lung
embolism being about Rs. 50000 for the enzyme alone. In spite of this, the market
for the enzyme is worth about Rs 350M year-1.
INDUSTRIAL ENZYME PROCESS AT HIGH TEMPERATURE 8.3
Enzyme operating temperature 0C Major
applications
alpha amylase (bacterial) 90-100 starch hydroysis, brewing baking detergents
Gluco amylase 50-60 Maltodextrin hydrolysis
alpha amylase (fungal) 50-60 Maltose
Pullulanase 50-60 high glucose syrups
Xylose isomerase 45-55 High fructose syrups
Pectinase 20-50 clarification of juices
/wines
Cellulose 45-55 cellulose hydrolysis
Lactase 30-50 lactose hydrolysis ,
food processing
Acid protease 30-50 food processing
fungal protease 40-60 baking ,brewing,food
processing
Alkaline proteases 40-60 Detergents
Lipases 30-70 Detergents, food
processing
Enzyme used in Industries
Thermozymes
Thermozymes are thermostable enzymes that function optimally at 60 0C and 125 0C.
these extremozymes are extremely valuable tools for study of protein stability
Thermozymes are used in the molecular biology experiments for example taq
polymerase and in the detergents (e.g.) proteases and starch processing (e.g.
alpha amylase, glucsoe isomerases) various lipase and proteases oxidoreductase are
used in the diagnostics, waste treatment and pulp and paper manufacture.
Thermozymes are more stable because they are active against denaturing condition
Hyperthermophiles have good potential for use in novel biotechnological processes
including oil coal and waste gas desulphurization, heavy metal leaching and
bioconversion of crude oils. Thermostable enzymes such as DNA polymerase,
amylases, xylanases proteases and lipase are required in basic research and
biotechnology.
Organic solvent tolerant bacteria that exhibit the ability to degrade crude oil,
polyaromatic hydrocarbons, or cholesterol or can utilize sulphure compounds have
been isolated. e.g. Strain Y-40 degrades hydrocarbons and belongs to Candida. It
can grow well in the presence of solvents such as n-octane, isooctane, cyclo-
octane, or kerosene at a concentration of 50 % (v/v) the first strain that
isolated for organic solvent tolerant bacterium e.g. Pseudomonas putida can grow
in more than 50% toluene.
Obligate extremophiles such as thiobacillus thiooxidans and thiobacillus
ferrooxidanse occur in highly acidic environments. T. ferroxidans reduces sulphure
compounds as well as ferrous ion to ferric. This leads to production of acids.
Currently these bacteria are utilized in the Biomining used in minerals leaching
for example. T. ferroxidans used to isolate sulphure from the coal.
Many extremophiles are used for craft industry for leather tanning (B. subtilis
and B. licheniformis) with the help of various alkalophiles. Alkalophiles such as
bacillus strains N-4 are used for cellulose digestion in the waste water treatment
to digest cellulose. xylanases are produced by the alkalophiles Aeromonas strain
212 that can hydrolyze the beta 1.-4 linkage in the xylan polysaccharides in the
crop plant. They show good activity and stability at pH 9. Neutral
metalloproteases from B. amyloliquifaciens can be used in the brewing industry,
when substituting malt with unmlated barley to increase the amount of free amino
acids.
The large-scale use of enzymes in solution
Several enzymes, especially those used in starch processing, high-fructose syrup
manufacture, textile desizing and detergent formulation, are now traded as
commodity products on the world's markets. Although the cost of enzymes for use at
the research scale is often very high, where there is a clear large-scale need for
an enzyme its relative cost reduces dramatically with increased production.
Relatively few enzymes, notably those in detergents, meat tenderizers and garden
composting agents, are sold directly to the public. Most are used by industry to
produce improved or novel products, to bypass long and involved chemical synthetic
pathways or for use in the separation and purification of isomeric mixtures. Many
of the most useful, but least-understood, uses of free enzymes are in the food
industry. Here they are used, together with endogenous enzymes, to produce or
process foodstuffs, which are only rarely substantially refined. Their action,
however apparently straightforward, is complicated due to the effect that small
amounts of by-products or associated reaction products have on such subjective
effects as taste, smell, colour and texture.
The use of enzymes in the non-food (chemicals and pharmaceuticals) sector is
relatively straightforward. Products are generally separated and purified and,
therefore, they are not prone to the subtleties available to food products. Most
such enzymic conversions benefit from the use of immobilised enzymes or biphasic
systems
The use of enzymes in detergents
The use of enzymes in detergent formulations is now common in developed countries,
with over half of all detergents presently available containing enzymes. In spite
of the fact that the detergent industry is the largest single market for enzymes
at 25 - 30% of total sales. details of the enzymes used and the ways in which they
are used, have rarely been published.
Dirt comes in many forms and includes proteins, starches and lipids. In addition,
clothes that have been starched must be freed of the starch. Using detergents in
water at high temperatures and with vigorous mixing, it is possible to remove most
types of dirt but the cost of heating the water is high and lengthy mixing or
beating will shorten the life of clothing and other materials. The use of enzymes
allows lower temperatures to be employed and shorter periods of agitation are
needed, often after a preliminary period of soaking. In general, enzyme detergents
remove protein from clothes soiled with blood, milk, sweat, grass, etc. far more
effectively than non-enzyme detergents. However, using modern bleaching and
brightening agents, the difference between looking clean and being clean may be
difficult to discern. At present only proteases and amylases are commonly used.
Although a wide range of lipases is known, it is only very recently that lipases
suitable for use in detergent preparations have been described.
Detergent enzymes must be cost-effective and safe to use. Early attempts to use
proteases foundered because of producers and users developing hypersensitivity.
This was combatted by developing dust-free granulates (about 0.5 mm in diameter)
in which the enzyme is incorporated into an inner core, containing inorganic salts
(e.g. NaCI) and sugars as preservative, bound with reinforcing, fibres of
carboxymethyl cellulose or similar protective colloid. This core is coated with
inert waxy materials made from paraffin oil or polyethylene glycol plus various
hydrophilic binders, which later disperse in the wash. This combination of
materials both prevents dust formation and protects the enzymes against damage by
other detergent components during storage.
Enzymes are used in surprisingly small amounts in most detergent preparations,
only 0.4 - 0.8% crude enzyme by weight (about 1% by cost). It follows that the
ability to withstand the conditions of use is a more important criterion than
extreme cheapness. Once released from its granulated form the enzyme must
withstand anionic and non-ionic detergents, soaps, oxidants such as sodium
perborate which generate hydrogen peroxide, optical brighteners and various less-
reactive materials (Table 15.4), all at pH values between 8.0 and 10.5. Although
one effect of incorporating enzymes is that lower washing temperatures may be
employed with consequent savings in energy consumption, the enzymes must retain
activity up to 60°C.
________________________________________
Table 15.4 Compositions of an enzyme detergent
Constituent Composition (%)
Sodium tripolyphosphate (water softener, loosens dirt)a
38.0
Sodium alkane sulphonate (surfactant) 25.0
Sodium perborate tetrahydrate (oxidising agent)25.0
Soap (sodium alkane carboxylates) 3.0
Sodium sulphate (filler, water softener) 2.5
Sodium carboxymethyl cellulose (dirt-suspending agent) 1.6
Sodium metasilicate (binder, loosens dirt) 1.0
Bacillus protease (3% active) 0.8
Fluorescent brighteners 0.3
Foam-controlling agents Trace
Perfume Trace
Water to 100%
a A recent trend is to reduce this phosphate content for environmental reasons. It
may be replaced by sodium carbonate plus extra protease.
________________________________________
The enzymes used are all produced using species of Bacillus, mainly by just two
companies. Novo Industri A/S produce and supply three proteases, Alcalase, from B.
licheniformis, Esperase, from an alkalophilic strain of a B. licheniformis and
Savinase, from an alkalophilic strain of B. amyloliquefaciens (often mistakenly
attributed to B. subtilis). GistBrocades produce and supply Maxatase, from B.
licheniformis. Alcalase and Maxatase (both mainly subtilisin) are recommended for
use at 10-65°C and pH 7-10.5. Savinase and Esperase may be used at up to pH 11 and
12, respectively. The -amylase supplied for detergent use is Termamyl, the
enzyme from B. licheniformis which is also used in the production of glucose
syrups. -Amylase is particularly useful in dish-washing and de-starching
detergents.
In addition to the granulated forms intended for use in detergent powders, liquid
preparations in solution in water and slurries of the enzyme in a non-ionic
surfactant are available for formulating in liquid 'spotting' concentrates, used
for removing stubborn stains. Preparations containing both Termamyl and Alcalase
are produced, Termamyl being sufficiently resistant to proteolysis to retain
activity for long enough to fulfil its function.
It should be noted that all the proteolytic enzymes described are fairly non-
specific serine endoproteases, giving preferred cleavage on the carboxyl side of
hydrophobic amino acid residues but capable of hydrolysing most peptide links.
They convert their substrates into small, readily soluble fragments which can be
removed easily from fabrics. Only serine protease; may be used in detergent
formulations: thiol proteases (e.g. papain) would be oxidised by the bleaching
agents, and metalloproteases (e.g. thermolysin) would lose their metal cofactors
due to complexing with the water softening agents or hydroxyl ions.
The enzymes are supplied in forms (as described above) suitable for formulation by
detergent manufacturers. Domestic users are familiar with powdered preparations
but liquid preparations for home use are increasingly available. Household
laundering present’s problems quite different from those of industrial laundering:
the household wash consists of a great variety of fabrics soiled with a range of
materials and the user requires convenience and effectiveness with less
consideration of the cost. Home detergents will probably include both an amylase
and a protease and a lengthy warm-water soaking time will be recommended.
Industrial laundering requires effectiveness at minimum cost so heated water will
be re-used if possible. Large laundries can separate their 'wash' into categories
and thus minimise the usage of water and maximise the effectiveness of the
detergents. Thus white cotton uniforms from an abattoir can be segregated for
washing, only protease being required. A pre-wash soaking for 10-20 min at pH up
to 11 and 30-40°C is followed by a main wash for 10-20 min at pH 11 and 60-65°C.
The water from these stages is discarded to the sewer. A third wash includes
hypochlorite as bleach which would inactivate the enzymes rapidly. The water from
this stage is used again for the pre-wash but, by then, the hypochlorite
concentration is insufficient to harm the enzyme. This is essentially a batch
process: hospital laundries may employ continuous washing machines, which transfer
less-initially-dirty linen from a pre-rinse initial stage, at 32°C and pH 8.5,
into the first wash at 60°C and pH 11, then to a second wash, containing hydrogen
peroxide, at 71°C and pH 11, then to a bleaching stage and rinsing. Apart from the
pre-soak stage, from which water is run to waste, the process operates counter-
currently. Enzymes are used in the pre-wash and in the first wash, the levels of
peroxide at this stage being insufficient to inactivate the enzymes.
There are opportunities to extend the use of enzymes in detergents both
geographically and numerically. They have not found widespread use in developing
countries which are often hot and dusty, making frequent washing of clothes
necessary. The recent availability of a suitable lipase may increase the
quantities of enzymes employed very significantly. There are, perhaps,
opportunities for enzymes such as glucose oxidase, lipoxygenase and glycerol
oxidase as means of generating hydrogen peroxide in situ. Added peroxidases may
aid the bleaching efficacy of this peroxide.
A recent development in detergent enzymes has been the introduction of an
alkaline-stable fungal cellulase preparation for use in washing cotton fabrics.
During use, small fibres are raised from the surface of cotton thread, resulting
in a change in the 'feel' of the fabric and, particularly, in the lowering of the
brightness of colours. Treatment with cellulase removes the small fibres without
apparently damaging the major fibres and restores the fabric to its 'as new'
condition. The cellulase also aids the removal of soil particles from the wash by
hydrolyzing associated cellulose fibres.
15.12 Applications of proteases in the food industry
Certain proteases have been used in food processing for centuries and any record
of the discovery of their activity has been lost in the mists of time. Rennet
(mainly chymosin), obtained from the fourth stomach (abomasum) of unweaned calves
has been used traditionally in the production of cheese. Similarly, papain from
the leaves and unripe fruit of the pawpaw (Carica papaya) has been used to
tenderize meats. These ancient discoveries have led to the development of various
food applications for a wide range of available proteases from many sources,
usually microbial. Proteases may be used at various pH values, and they may be
highly specific in their choice of cleavable peptide links or quite non-specific.
Proteolysis generally increases the solubility of proteins at their isoelectric
points.
15.13 Rennet in cheese making
The action of rennet in cheese making is an example of the hydrolysis of a
specific peptide linkage, between phenylalanine and methionine residues (-Phe105-
Met106-) in the κ-casein protein present in milk . The κ-casein acts by
stabilizing the colloidal nature of the milk, its hydrophobic N-terminal region
associating with the lipophilic regions of the otherwise insoluble - and β-
casein molecules, whilst its negatively charged C-terminal region associates with
the water and prevents the casein micelles from growing too large. Hydrolysis of
the labile peptide linkage between these two domains, resulting in the release of
a hydrophilic glycosylated and phosphorylated oligopeptide (caseino macropeptide)
and the hydrophobic para-κ-casein, removes this protective effect, allowing
coagulation of the milk to form curds, which are then compressed and turned into
cheese (Figure 4.1). The coagulation process depends upon the presence of Ca2+ and
is very temperature dependent (Q10 = 11) and so can be controlled easily. Calf
rennet, consisting of mainly chymosin with a small but variable proportion of
pepsin, is a relatively expensive enzyme and various attempts have been made to
find cheaper alternatives from microbial sources These have ultimately proved to
be successful and microbial rennets are used for about 70% of US cheese and 33% of
cheese production world-wide.
________________________________________
Figure 15. 3 The use of enzymes in processing starch. Typical conditions are
given.
________________________________________
Of the two components of starch, amylopectine presents the great challenge to
hydrolytic enzyme systems. This is due to the residues involved in α-1,6-
glycosidic branch points which constitute about 4 - 6% of the glucose present.
Most hydrolytic enzymes are specific for α-1,4-glucosidic links yet the -1,6-
glucosidic links must also be cleaved for complete hydrolysis of amylopectin to
glucose. Some of the most impressive recent exercises in the development of new
enzymes have concerned debranching enzymes.
It is necessary to hydrolyse starch in a wide variety of processes which may be
condensed into two basic classes:
Processes in which the starch hydrolysate is to be used by microbes or man, and
Processes in which it is necessary to eliminate starch.
In the former processes, such as glucose syrup production, starch is usually the
major component of reaction mixtures, whereas in the latter processes, such as the
processing of sugar cane juice, small amounts of starch which contaminate non-
starchy materials are removed. Enzymes of various types are used in these
processes. Although starches from diverse plants may be utilised, corn is the
world's most abundant source and provides most of the substrate used in the
preparation of starch hydrolysates.
There are three stages in the conversion of starch (Figure 15.3):
gelatinization, involving the dissolution of the nano-gram-sized starch granules
to form a viscous suspension;
liquefaction, involving the partial hydrolysis of the starch, with concomitant
loss in viscosity; and
Saccharification, involving the production of glucose and maltose by further
hydrolysis.
a. Gelatinization is achieved by heating starch with water, and occurs necessarily
and naturally when starchy foods are cooked. Gelatinized starch is readily
liquefied by partial hydrolysis with enzymes or acids and saccharified by further
acidic or enzymic hydrolysis.
The starch and glucose syrup industry uses the expression dextrose equivalent or
DE, similar in definition to the DH units of proteolysis, to describe its
products, where:
(15 .3)
In practice, this is usually determined analytically by use of the closely
related, but not identical, expression:
(15.4)
Thus, DE represents the percentage hydrolysis of the glycosidic linkages present.
Pure glucose has a DE of 100, pure maltose has a DE of about 50 (depending upon
the analytical methods used; see equation (15.4)) and starch has a DE of
effectively zero. During starch hydrolysis, DE indicates the extent to which the
starch has been cleaved. Acid hydrolysis of starch has long been used to produce
'glucose syrups' and even crystalline glucose (dextrose monohydrate). Very
considerable amounts of 42 DE syrups are produced using acid and are used in many
applications in confectionery. Further hydrolysis using acid is not satisfactory
because of undesirably coloured and flavoured breakdown products. Acid hydrolysis
appears to be a totally random process which is not influenced by the presence of
α-1,6-glucosidic linkages.
________________________________________
Table 15.5 Enzymes used in starch hydrolysis
Enzyme EC number Source Action
α-Amylase 3.2.1.1 Bacillus amyloliquefaciens Only α-1,4-oligosaccharide
links are cleaved to give α-dextrins and predominantly maltose (G2), G3, G6 and G7
oligosaccharides
B. licheniformis Only α1,4-oligosaccharide links are cleaved to give
α-dextrins and predominantly maltose, G3, G4 and G5 oligosaccharides
Aspergillus oryzae, A. niger Only α-1,4 oligosaccharide links are
cleaved to give α-dextrins and predominantly maltose and G3 oligosaccharides
Saccharifying α-amylase 3.2.1.1 B. subtilis (amylosacchariticus) Only
α-1,4-oligosaccharide links are cleaved to give α-dextrins with maltose, G3, G4
and up to 50% (w/w) glucose
β-Amylase 3.2.1.2 Malted barley Only α-1,4-links are cleaved, from non-
reducing ends, to give limit dextrins and β-maltose
Glucoamylase 3.2.1.3 A. niger α-1,4 and α1,6-links are cleaved, from
the nonreducing ends, to give α-glucose
Pullulanase 3.2.1.41 B. acidopullulyticus Only α-1,6-links are cleaved
to give straight-chain maltodextrins
________________________________________
The nomenclature of the enzymes used commercially for starch hydrolysis
The nomenclature of the enzymes used commercially for starch hydrolysis is
somewhat confusing and the EC numbers sometimes lump together enzymes with subtly
different activities (Table 15.5). For example, α-amylase may be subclassified as
liquefying or saccharifying amylases but even this classification is inadequate to
encompass all the enzymes that are used in commercial starch hydrolysis. One
reason for the confusion in the nomenclature is the use of the anomeric form of
the released reducing group in the product rather than that of the bond being
hydrolysed; the products of bacterial and fungal -amylases are in the -
configuration and the products of β-amylases are in the β-configuration, although
all these enzymes cleave between α-1,4-linked glucose residues.
The α-amylases (1,4-α-D-glucan glucanohydrolases) are endohydrolases which cleave
1,4-α-D-glycosidic bonds and can bypass but cannot hydrolyze 1,6-α-D-glucosidic
branch points. Commercial enzymes used for the industrial hydrolysis of starch are
produced by Bacillus amyloliquefaciens (supplied by various manufacturers) and by
B. licheniformis (supplied by Novo Industri A/S as Termamyl). They differ
principally in their tolerance of high temperatures, Termamyl retaining more
activity at up to 110°C, in the presence of starch, than the B. amyloliquefaciens
α-amylase. The maximum DE obtainable using bacterial α-amylases is around 40 but
prolonged treatment leads to the formation of maltulose (4-α-D-glucopyranosyl-D-
fructose), which is resistant to hydrolysis by glucoamylase and α-amylases. DE
values of 8-12 are used in most commercial processes where further
saccharification is to occur. The principal requirement for liquefaction to this
extent is to reduce the viscosity of the gelatinised starch to ease subsequent
processing.
Different approaches for starch liquefaction
Various manufacturers use different approaches to starch liquefaction using α-
amylases but the principles are the same. Granular starch is slurried at 30-40%
(w/w) with cold water, at pH 6.0-6.5, containing 20-80 ppm Ca2+ (which stabilizes
and activates the enzyme) and the enzyme is added (via a metering pump). The α-
amylase is usually supplied at high activities so that the enzyme dose is 0.5-0.6
kg tonne-1 (about 1500 U kg-1 dry matter) of starch. When Termamyl is used, the
slurry of starch plus enzyme is pumped continuously through a jet cooker, which is
heated to 105°C using live steam. Gelatinization occurs very rapidly and the
enzymic activity, combined with the significant shear forces, begins the
hydrolysis. The residence time in the jet cooker is very brief. The partly
gelatinized starch is passed into a series of holding tubes maintained at 100-
105°C and held for 5 min to complete the gelatinization process. Hydrolysis to the
required DE is completed in holding tanks at 90-100°C for 1 to 2 h. These tanks
contain baffles to discourage backmixing. Similar processes may be used with B.
amyloliquefaciens α-amylase but the maximum temperature of 95°C must not be
exceeded. This has the drawback that a final 'cooking' stage must be introduced
when the required DE has been attained in order to gelatinize the recalcitrant
starch grains present in some types of starch which would otherwise cause
cloudiness in solutions of the final product.
Saccharification
The liquefied starch is usually saccharified but comparatively small amounts are
spray-dried for sale as 'maltodextrins' to the food industry mainly for use as
bulking agents and in baby food. In this case, residual enzymic activity may be
destroyed by lowering the pH towards the end of the heating period.
Fungal α-amylase also finds use in the baking industry. It often needs to be added
to bread-making flours to promote adequate gas production and starch modification
during fermentation. This has become necessary since the introduction of combine
harvesters. They reduce the time between cutting and threshing of the wheat, which
previously was sufficient to allow a limited sprouting so increasing the amounts
of endogenous enzymes. The fungal enzymes are used rather than those from bacteria
as their action is easier to control due to their relative heat lability,
denaturing rapidly during baking. The liquefied starch at 8 -12 DE is suitable for
saccharification to produce syrups with DE values of from 45 to 98 or more. The
greatest quantities produced are the syrups with DE values of about 97. At present
these are produced using the exoamylase, glucan 1,4-α-glucosidase (1,4-α-D-glucan
glucohydrolase, commonly called glucoamylase but also called amyloglucosidase and
γ-amylase), which releases β-D-glucose from 1,4-α-, 1,6-α- and 1,3-α-linked
glucans. In theory, carefully liquefied starch at 8 -12 DE can be hydrolysed
completely to produce a final glucoamylase reaction mixture with DE of 100 but, in
practice, this can be achieved only at comparatively low substrate concentrations.
The cost of concentrating the product by evaporation decreases that a substrate
concentration of 30% is used. It follows that the maximum DE attainable is 96 - 98
with syrup composition 95 - 97% glucose, 1 - 2% maltose and 0.5 - 2% (w/w)
isomaltose (α-D-glucopyranosyl-(1,6)-D-glucose). This material is used after
concentration, directly for the production of high-fructose syrups or for the
production of crystalline glucose.
Whereas liquefaction is usually a continuous process, saccharification is most
often conducted as a batch process. The glucoamylase most often used is produced
by Aspergillus niger strains. This has a pH optimum of 4.0 - 4.5 and operates most
effectively at 60°C, so liquefied starch must be cooled and its pH adjusted before
addition of the glucoamylase. The cooling must b rapid, to avoid retrogradation
(the formation of intractable insoluble aggregates of amylose; the process that
gives rise to the skin on custard). Any remaining bacterial -amylase will be
inactivated when the pH is lowered; however, this may be replaced later by some
acid-stable -amylase which is normally present in the glucoamylase preparations.
When conditions are correct the glucoamylase is added, usually at the dosage of
0.65 - 0.80 litre enzyme preparation.tonne-1 starch (200 U kg-1). Saccharification
is normally conducted in vast stirred tanks, which may take several hours to fill
(and empty), so time will be wasted if the enzyme is added only when the reactors
are full. The alternatives are to meter the enzyme at a fixed ratio or to add the
whole dose of enzyme at the commencement of the filling stage. The latter should
give the most economical use of the enzyme.
________________________________________
Figure 15. 4. The % glucose formed from 30% (w/w) 12 DE maltodextrin, at 60°C and
pH 4.3, using various enzyme solutions. ———200 U kg-1 Aspergillus niger
glucoamylase; -----------400 U kg-1 A. niger glucoamylase; ••••••••• 200 U kg-1 A.
niger glucoamylase plus 200 U kg-1 Bacillus acidopullulyticus pullulanase. The
relative improvement on the addition of pullulanase is even greater at higher
substrate concentrations.
________________________________________
The saccharification process takes about 72 h to complete but may, of course, be
speeded up by the use of more enzyme. Continuous saccharification is possible and
practicable if at least six tanks are used in series. It is necessary to stop the
reaction, by heating to 85°C for 5 min, when a maximum DE has been attained.
Further incubation will result in a fall in the DE, to about 90 DE eventually,
caused by the formation of isomaltose as accumulated glucose re-polymerises with
the approach of thermodynamic equilibrium (Figure 15.4).
Final step in syrup formation
The saccharified syrup is filtered to remove fat and denatured protein released
from the starch granules and may then be purified by passage through activated
charcoal and ion-exchange resins. It should be remembered that the dry substance
concentration increases by about 11 % during saccharification, because one
molecule of water is taken up for each glycosidic bond hydrolysed (molecule of
glucose produced).
Although glucoamylase catalyses the hydrolysis of 1,6-α-linkages, their breakdown
is slow compared with that of 1,4-α-linkages (e.g. the rates of hydrolyzing the
1,4-α, 1,6-α and 1,3-α-links in tetrasaccharides are in the proportions 300 : 6 :
1). It is clear that the use of a debranching enzyme would speed the overall
saccharification process but, for industrial use such an enzyme must be compatible
with glucoamylase. Two types of debranching enzymes are available: pullulanase,
which acts as an exo hydrolase on starch dextrins; and isoamylase (EC.3.2.1.68),
which is a true endohydrolase. Novo Industri A/S have recently introduced a
suitable pullulanase, produced by a strain of Bacillus acidopullulyticus. The
pullulanase from Klebsiella aerogenes which has been available commercially to
some time is unstable at temperatures over 45°C but the B. acidopullulyticus
enzymes can be used under the same conditions as the Aspergillus glucoamylase
(60°C, pH 4.0-4.5). The practical advantage of using pullulanase together with
glucoamylase is that less glucoamylase need be used This does not in itself give
any cost advantage but because less glucoamylase is used and fewer branched
oligosaccharides accumulate toward the end of the saccharification, the point at
which isomaltose production becomes significant occurs at higher DE (Figure 4.3).
It follows that higher DE values and glucose contents can be achieved when
pullulanase is use (98 - 99 DE and 95 - 97% (w/w) glucose, rather than 97 - 98 DE)
and higher substrate concentrations (30 - 40% dry solids rather than 25 - 30%) may
be treated. The extra cost of using pullulanase is recouped by savings in
evaporation and glucoamylase costs. In addition, when the product is to be used to
manufacture high-fructose syrups, there is a saving in the cost of further
processing.
The development of the B. acidopullulyticus pullulanase is an excellent example of
what can be done if sufficient commercial pull exists for a new enzyme. The
development of a suitable α-D-glucosidase, in order to reduce the reversion, would
be an equally useful step for industrial glucose production. Screening of new
strains of bacteria for a novel enzyme of this type is a major undertaking. It is
not surprising that more details of the screening procedures used are not readily
available.
15.17 Production of syrups containing maltose
Traditionally, syrups containing maltose as a major component have been produced
by treating barley starch with barley β-amylase. β-Amylases (1,4-β-D-glucan
maltohydrolases) are exohydrolases which release maltose from 1,4-α-linked glucans
but neither bypass nor hydrolyse 1,6-α-linkages. High-maltose syrups (40 - 50 DE,
45-60% (w/w) maltose, 2 - 7% (w/w) glucose) tend not to crystallise, even below
0°C and are relatively non-hygroscopic. They are used for the production of hard
candy and frozen deserts. High conversion syrups (60 - 70 DE, 30 - 37% maltose, 35
- 43% glucose, 10% maltotriose, 15% other oligosaccharides, all by weight) resist
crystallisation above 4°C and are sweeter (Table 4.3). They are used for soft
candy and in the baking, brewing and soft drinks industries. It might be expected
that β-amylase would be used to produce maltose-rich syrups from corn starch,
especially as the combined action of β-amylase and pullulanase give almost
quantitative yields of maltose. This is not done on a significant scale nowadays
because presently available β-amylases are relatively expensive, not sufficiently
temperature stable (although some thermostable β-amylases from species of
Clostridium have recently been reported) and are easily inhibited by copper and
other heavy metal ions. Instead fungal β-amylases, characterised by their ability
to hydrolyse maltotriose (G3) rather than maltose (G2) are employed often in
combination with glucoamylase. Presently available enzymes, however, are not
totally compatible; fungal α-amylases requiring a pH of not less than 5.0 and a
reaction temperature not exceeding 55°C.
High-maltose syrups (see Figure 15.3) are produced from liquefied starch of around
11 DE at a concentration of 35% dry solids using fungal -amylase alone.
Saccharification occurs over 48 h, by which time the fungal -amylase has lost
its activity. Now that a good pullulanase is available, it is possible to use this
in combination with fungal -High-conversion syrups are produced using
combinations of fungal α-amylase and glucoamylase. These may be tailored to
customers' specifications by adjusting the activities of the two enzymes used but
inevitably, as glucoamylase is employed, the glucose content of the final product
will be higher than that of high-maltose syrups. The stability of glucoamylase
necessitates stopping the reaction, by heating, when the required composition is
reached. It is now possible to produce starch hydrolysates with any DE between 1
and 100 and with virtually any composition using combinations of bacterial α-
amylases, fungal α-amylases, glucoamylase and pullulanase.
________________________________________
Table 15.6 The relative sweetness of food ingredients
Food ingredient Relative sweetness (by weight, solids)
Sucrose 1.0
Glucose 0.7
Fructose 1.3
Galactose 0.7
Maltose 0.3
Lactose 0.2
Raffinose 0.2
Hydrolysed sucrose 1.1
Hydrolysed lactose 0.7
Glucose syrup 11 DE <0.1
Glucose syrup 42 DE 0.3
Glucose syrup 97 DE 0.7
Maltose syrup 44 DE 0.3
High-conversion syrup 65 DE 0.5
HFCS (42% fructose)a
1.0
HFCS (55% fructose) 1.1
Aspartame 180
a HFCS, high-fructose corn syrup.
15.18 Enzymes in the sucrose industry
The sucrose industry is a comparatively minor user of enzymes but provides few
historically significant and instructive examples of enzyme technology The
hydrolysis ('inversion') of sucrose, completely or partially, to glucose and
fructose provides sweet syrups that are more stable (i.e. less likely crystallise)
than pure sucrose syrups. The most familiar 'Golden Syrup' produced by acid
hydrolysis of one of the less pure streams from the cane sugar refinery but other
types of syrup are produced using yeast (Saccharomyces cerevisiae) invertase.
Although this enzyme is unusual in that it suffers from substrate inhibition at
high sucrose levels ( > 20% (w/w)), this does not prevent its commercial use at
even higher concentrations:
Figure 15. 6 Outline of the relationship between the enzyme activities in the
hydrolysis of cellulose. || represents inhibitory effects. Endo-1,4-β-glucanase is
the rate-controlling activity and may consist of a mixture of enzymes acting on
cellulose of different degrees of crystallinity. It acts synergistically with both
exo-1,4-β-glucosidase and exo-cellobiohydrolase. Exo-1,4-β-glucosidase is a
product-inhibited enzyme. Exo-cellobiohydrolase is product inhibited and
additionally appears to be inactivated on binding to the surface of crystalline
cellulose.
________________________________________
Proper economic analysis reveals that cheap sources of cellulose prove to be
generally more expensive as sources of glucose than apparently more expensive
starch. Relatively pure cellulose is valuable in its own right, as a paper pulp
and chipboard raw material, which currently commands a price of over twice that of
corn starch. With the increasing world shortage of pulp it cannot be seen
realistically as an alternative source of glucose in the foreseeable future.
Knowledge of enzyme systems capable of degrading lignocellulose is advancing
rapidly but it is unlikely that lignocellulose will replace starch as a source of
glucose syrups for food use. It is, however, quite possible that it may be used,
in a process involving the simultaneous use of both enzymes and fermentative
yeasts, to produce ethanol; the utilisation of the glucose by the yeast removing
its inhibitory effect on the enzymes. It should be noted that cellobiose is a non-
fermentable sugar and must be hydrolysed by additional β-glucosidase (EC 3.2.1.21,
also called cellobiase for maximum process efficiency (Figure 15.6).
15.20 The use of lactases in the dairy industry
Lactose is present at concentrations of about 4.7% (w/v) in milk and the whey
(supernatant) left after the coagulation stage of cheese-making. Its presence in
milk makes it unsuitable for the majority of the world's adult population,
particularly in those areas which have traditionally not had a dairy industry.
Real lactose tolerance is confined mainly to peoples whose origins lie in Northern
Europe or the Indian subcontinent and is due to 'lactase persistence'; the young
of all mammals clearly are able to digest milk but in most cases this ability
reduces after weaning. Of the Thai, Chinese and Black American populations, 97%,
90% and 73% respectively, are reported to be lactose intolerant, whereas 84% and
96% of the US White and Swedish populations, respectively, are tolerant.
Additionally, and only very rarely some individuals suffer from inborn metabolic
lactose intolerance or lactase deficiency, both of which may be noticed at birth.
The need for low-lactose milk is particularly important in food-aid programmes as
severe tissue dehydration, diarrhoea and even death may result from feeding
lactose containing milk to lactose-intolerant children and adults suffering from
protein-calorie malnutrition. In all these cases, hydrolysis of the lactose to
glucose and galactose would prevent the (severe) digestive problems.
Another problem presented by lactose is its low solubility resulting in crystal
formation at concentrations above 11 % (w/v) (4°C). This prevents the use of
concentrated whey syrups in many food processes as they have a unpleasant sandy
texture and are readily prone to microbiological spoilage. Adding to this problem,
the disposal of such waste whey is expensive (often punitively so) due to its high
biological oxygen demand. These problems may be overcome by hydrolysis of the
lactose in whey; the product being about four times as sweet (see Table 15.6),
much more soluble and capable of forming concentrated, microbiologically secure,
syrups (70% (w/v)).
Commercially, it may be prepared from the dairy yeast Kluyveromyces fragilis (K.
marxianus var. marxianus), with a pH optimum (pH 6.5-7.0) suitable for the
treatment of milk, or from the fungi Aspergillus oryzae or A. niger, with pH
optima (pH 4.5-6.0 and 3.0-4.0, respectively) more suited to whey hydrolysis.
These enzymes are subject to varying degrees of product inhibition by galactose.
In addition, at high lactose and galactose concentrations, lactase shows
significant transferase ability and produces β-1,6-linked galactosyl
oligosaccharides.
Lactases are now used in the production of ice cream and sweetened flavoured and
condensed milks. When added to milk or liquid whey (2000 U kg-1) and left for
about a day at 5°C about 50% of the lactose is hydrolysed, giving a sweeter
product which will not crystallise if condensed or frozen. This method enables
otherwise-wasted whey to replace some or all of the skim milk powder used in
traditional ice cream recipes. It also improves the 'scoopability' and creaminess
of the product. Smaller amounts of lactase may be added to long-life sterilised
milk to produce a relatively inexpensive lactose-reduced product (e.g. 20 U kg-1,
20°C, 1 month of storage). Generally, however, lactase usage has not reached its
full potential, as present enzymes are relatively expensive and can only be used
at low temperatures.
15.21 Enzymes in the fruit juice, wine, brewing and distilling industries
One of the major problems in the preparation of fruit juices and wine is
cloudiness due primarily to the presence of pectins. These consist primarily of α-
1,4-anhydrogalacturonic acid polymers, with varying degrees of methyl
esterification. They are associated with other plant polymers and, after
homogenisation, with the cell debris. The cloudiness that they cause is difficult
to remove except by enzymic hydrolysis. Such treatment also has the additional
benefits of reducing the solution viscosity, increasing the volume of juice
produced (e.g. the yield of juice from white grapes can be raised by 15%), subtle
but generally beneficial changes in the flavour and, in the case of wine-making,
shorter fermentation times. Insoluble plant material is easily removed by
filtration, or settling and decantation, once the stabilising effect of the
pectins on the colloidal haze has been removed.
Commercial pectolytic enzyme preparations are produced from Aspergillus niger and
consist of a synergistic mixture of enzymes:
polygalacturonase (EC 3.2.1.15), responsible for the random hydrolysis of 1,4- -
D-galactosiduronic linkages;
pectinesterase (EC 3.2.1.11), which releases methanol from the pectyl methyl
esters, a necessary stage before the polygalacturonase can act fully (the increase
in the methanol content of such treated juice is generally less than the natural
concentrations and poses no health risk);
pectin lyase (EC 4.2.2.10), which cleaves the pectin, by an elimination reaction
releasing oligosaccharides with non-reducing terminal 4-deoxymethyl-α-D-galact-4-
enuronosyl residues, without the necessity of pectin methyl esterase action; and
hemicellulase (a mixture of hydrolytic enzymes including: xylan endo-1,3-β-
xylosidase, EC 3.2.1.32; xylan 1,4-β-xylosidase, EC 3.2.1.37; and α-L-
arabinofuranosidase, EC 3.2.1.55), strictly not a pectinase but its adventitious
presence is encouraged in order to reduce hemicellulose levels.
The optimal activity of these enzymes is at a pH between 4 and 5 and generally
below 50°C. They are suitable for direct addition to the fruit pulps at levels
around 20 U l-1 (net activity). Enzymes with improved characteristics of greater
heat stability and lower pH optimum are currently being sought.
In brewing, barley malt supplies the major proportion of the enzyme needed for
saccharification prior to fermentation. Often other starch containing material
(adjuncts) are used to increase the fermentable sugar and reduce the relative
costs of the fermentation. Although malt enzyme may also be used to hydrolyse
these adjuncts, for maximum economic return extra enzymes are added to achieve
their rapid saccharification. It not necessary nor desirable to saccharify the
starch totally, as non-fermentable dextrins are needed to give the drink 'body'
and stabilise its foam 'head'. For this reason the saccharification process is
stopped, by boiling the 'wort', after about 75% of the starch has been converted
into fermentable sugar.
The enzymes used in brewing are needed for saccharification of starch (bacterial
and fungal α-amylases), breakdown of barley β-1,4- and β-1,3- linked glucan (β-
glucanase) and hydrolysis of protein (neutral protease) to increase the (later)
fermentation rate, particularly in the production of high-gravity beer, where
extra protein is added. Cellulases are also occasionally used, particularly where
wheat is used as adjunct but also to help breakdown the barley β-glucans. Due to
the extreme heat stability of the B. amyloliquefaciens α-amylase, where this is
used the wort must be boiled for a much longer period (e.g. 30 min) to inactivate
it prior to fermentation. Papain is used in the later post-fermentation stages of
beer-making to prevent the occurrence of protein- and tannin-containing 'chill-
haze' otherwise formed on cooling the beer. Recently, 'light' beers, of lower
calorific content, have become more popular. These require a higher degree of
saccharification at lower starch concentrations to reduce the alcohol and total
solids contents of the beer. This may be achieved by the use of glucoamylase
and/or fungal -amylase during the fermentation.
A great variety of carbohydrate sources are used world wide to produce distilled
alcoholic drinks. Many of these contain sufficient quantities of fermentable sugar
(e.g. rum from molasses and brandy from grapes), others contain mainly starch and
must be saccharified before use (e.g. whiskey from barley malt, corn or rye). In
the distilling industry, saccharification continues throughout the fermentation
period. In some cases (e.g. Scotch malt whisky manufacture uses barley malt
exclusively) the enzymes are naturally present but in others (e.g. grain spirits
production) the more heat-stable bacterial -amylases may be used in the
saccharification.
15.22 Glucose oxidase and catalase in the food industry
Glucose oxidase is a highly specific enzyme, from the fungi Aspergillus niger and
Penicillium, which catalyses the oxidation of β-glucose to glucono-1,5-lactone
(which spontaneously hydrolyses non-enzymically to gluconic acid) using molecular
oxygen and releasing hydrogen peroxide. It finds uses in the removal of either
glucose or oxygen from foodstuffs in order to improve their storage capability.
Hydrogen peroxide is an effective bacteriocide and may be removed, after use, by
treatment with catalase (derived from the same fungal fermentations as the glucose
oxidase) which converts it to water and molecular oxygen:
catalase
2H2O2 2H2O + O2 [4.4]
For most large-scale applications the two enzymic activities are not separated.
Glucose oxidase and catalase may be used together when net hydrogen peroxide
production is to be avoided.
A major application of the glucose oxidase/catalase system is in the removal of
glucose from egg-white before drying for use in the baking industry. A mixture of
the enzymes is used (165 U kg-1) together with additional hydrogen peroxide (about
0.1 % (w/w)) to ensure that sufficient molecular oxygen is available, by catalase
action, to oxidise the glucose. Other uses are in the removal of oxygen from the
head-space above bottled and canned drinks and reducing non-enzymic browning in
wines and mayonnaises.
Introduction
An enzyme reactor consists of a vessel, or series of vessels, used to perform a
desired conversion by enzymic means. There are several important factors that
determine the choice of reactor for a particular process. In general, the choice
depends on the cost of a predetermined productivity within the product's
specifications. This must be inclusive of the costs associated with substrate(s),
downstream processing, labour, depreciation, overheads and process development, in
addition to the more obvious costs concerned with building and running the enzyme
reactor. Other contributing factors are the form of the enzyme of choice (i.e.
free or immobilised), the kinetics of the reaction and the chemical and physical
properties of an immobilization support including whether it is particulate,
membranous or fibrous, and its density, compressibility, robustness, particle size
and regenerability. Attention must also be paid to the scale of operation, the
possible need for pH and temperature control, the supply and removal of gases and
the stability of the enzyme, substrate and product. These factors will be
discussed in more detail with respect to the different types of reactor.
There are two type of Reactor 1. Batch Reactor; 2. Continuous reactor
Stirred tank batch reactor (STR).
Batch membrane reactor (MR).
Packed bed reactor (PBR).
continuous flow stirred tank reactor (CSTR.
continuous flow membrane reactor (CMR)
fluidised bed reactor (FBR)
16.1 Batch Reactor
Batch reactors generally consist of a tank containing a stirrer (stirred tank
reactor, STR). Note that a batch reactor is one in which all of the product is
removed, as rapidly as is practically possible, after a fixed time. The tank is
normally fitted with fixed baffles that improve the stirring efficiency. Generally
this means that the enzyme and substrate molecules must have identical residence
times within the reactor, although in some circumstances there may be a need for
further additions of enzyme and/or substrate (i.e. fed -batch operation).
a. Disadvantage of using batch reactor
1. The operating costs of batch reactors are higher than for continuous processes
due to the necessity for the reactors to be emptied and refilled both regularly
and often. This procedure is not only expensive in itself but means that there are
considerable periods when such reactors are not productive; it also makes uneven
demands on both labour and services.
2. STRs can be used for processes involving non-immobilised enzymes, if the
consequences of these contaminating the product are not severe.
3. Batch reactors also suffer from pronounced batch-to-batch variations, as the
reaction conditions change with time, and may be difficult to scale-up, due to the
changing power requirements for efficient fixing.
b. Advantage of using Batch Bioreactor
They do, however, have a number of advantageous features. Primary amongst these is
their simplicity both in use and in process development. For this reason they are
preferred for small-scale production of highly priced products, especially where
the same equipment is to be used for a number of different conversions. They offer
a closely controllable environment that is useful for slow reactions, where the
composition may be accurately monitored, and conditions (e.g. temperature, pH,
coenzyme concentrations) varied throughout the reaction. They are also of use when
continuous operation of a process proves to be difficult due to the viscous or
intractable nature of the reaction mix.
________________________________________
Figure 16. 2 This figure shows two related behaviours. (a) The change in substrate
and product concentrations with time, in a batch reactor. The reaction S P is
assumed, with the initial condition [S]0/Km = 10. The concentrations of substrate
(——— and product (-----------) are both normalised with respect to [S]0. The
normalised time (i.e. t° = t Vmax/[S]0) is relative to the time (t° = 1) that
would be required to convert all the substrate if the enzyme acted at Vmax
throughout, the actual time for complete conversion being longer due to the
reduction in the substrate concentration at the reaction progresses. The dashed
line also indicates the variation of the fractional conversion (X) with t°. (b)
The change in substrate and product concentrations with reactor length for a PBR.
The reaction S P is assumed with the initial condition, [S]0/Km = 10. The
concentrations of substrate (———) and product (-----------) are both normalised
with respect to [S]". The normalised reactor length (i.e. I° = lVmax/F, where Vmax
is the maximum velocity for unit reactor length and I is the reactor length) is
relative to the length (i.e. when I° = 1) that contains sufficient enzyme to
convert all the substrate at the given flow rate if the enzyme acted at its
maximum velocity throughout; the actual reactor length necessary for complete
conversion being longer due to the reduction in the substrate concentration as the
reaction progresses. P may be considered as the relative position within a PBR or
the reactor's absolute length.
________________________________________
16.2 Membrane reactors
The main requirement for a membrane reactor (MR) is a semipermeable membrane which
allows the free passage of the product molecules but contains the enzyme
molecules. A cheap example of such a membrane is the dialysis membrane used for
removing low molecular weight species from protein preparations. The usual choice
for a membrane reactor is a hollow-fibre reactor consisting of a preformed module
containing hundreds of thin tubular fibres each having a diameter of about 200
m and a membrane thickness of about 50 m.
Advantage of using Membrane reactor
[1] Membrane reactors may be used in either batch or continuous mode and [2] they
allow the easy separation of the enzyme from the product. [3] They are normally
used with soluble enzymes, avoiding the costs and problems associated with other
methods of immobilization and some of the diffusion limitations of immobilized
enzymes. If the substrate is able to diffuse through the membrane, it may be
introduced to either side of the membrane with respect to the enzyme; otherwise it
must be within the same compartment as the enzyme, a configuration that imposes a
severe restriction on the flow rate through the reactor, if used in continuous
mode.[4] Due to the ease with which membrane reactor systems may be established,
they are often used for production on a small scale (g to kg), especially where a
multi-enzyme pathway or coenzyme regeneration is needed.[5] They allow the easy
replacement of the enzyme in processes involving particularly labile enzymes and
can also be used for biphasic reactions.
The major disadvantage of these reactors concerns the cost of the membranes and
their need to be replaced at regular intervals.
16.3 The kinetics of membrane reactors
The kinetics of membrane reactors are similar to those of the batch STR, in batch
mode, or the CSTR, in continuous mode (see later). Deviations from these models
occur primarily in configurations where the substrate stream is on the side of the
membrane opposite to the enzyme and the reaction is severely limited by its
diffusion through the membrane and the products' diffusion in the reverse
direction. Under these circumstances the reaction may be even more severely
affected by product inhibition or the limitations of reversibility than is
indicated by these models.
16.4 Packed bed reactors (PBR)
The most important characteristic of a PBR is that; they are also called plug flow
reactors (PFR) because material flows through the reactor as a plug. Ideally, all
of the substrate stream flows at the same velocity, parallel to the reactor axis
with no back -mixing. All material present at any given reactor cross -section has
had an identical residence time. The longitudinal position within the PBR is,
therefore, proportional to the time spent within the reactor; all product emerging
with the same residence time and all substrate molecule having an equal
opportunity for reaction. The conversion efficiency of a PBR, with respect to its
length, behaves in a manner similar to that of a well -stirred batch reactor with
respect to its reaction time (Figure 5.2(b)) Each volume element behaves as a
batch reactor as it passes through the PBR. Any required degree of reaction may be
achieved by use of an idea PBR of suitable length.
The flow rate (F) is equivalent to VolS/t for a batch reactor. Therefore equation
(16.5) may be converted to represent an ideal PBR, given the assumption, not often
realised in practice, that there are no diffusion limitations:
(16.6)
In order to produce ideal plug -flow within PBRs, a turbulent flow regime is
preferred to laminar flow, as this causes improved mixing and heat transfer normal
to the flow and reduced axial back-mixing. Achievement of high enough Re may,
however, be difficult due to unacceptably high feed rates. Consequent upon the
plug -flow characteristic of the PBR is that the substrate concentration is
maximised, and the product concentration minimised, relative to the final
conversion at every point within the reactor; the effectiveness factor being high
on entry to the reactor and low close to the exit. This means that PBRs are the
preferred reactors, all other factors being equal, for processes involving product
inhibition, substrate activation and reaction reversibility. At low Re the flow
rate is proportional to the pressure drop across the PBR. This pressure drop is,
in turn, generally found to be proportional to the bed height, the linear flow
rate and dynamic viscosity of the substrate stream and (1 - ε)2/ε3 (where ε is
the porosity of the reactor; i.e. the fraction of the PBR volume taken up by the
liquid phase), but inversely proportional to the cross-sectional area of the
immobilised enzyme pellets. In general PBRs are used with fairly rigid
immobilised-enzyme catalysts (1 -3 mm diameter), because excessive increases in
this flow rate may distort compressible or physically weak particles. Particle
deformation results in reduced catalytic surface area of particles contacting the
substrate-containing solution, poor external mass transfer characteristics and a
restriction to the flow, causing increased pressure drop. A vicious circle of
increased back-pressure, particle deformation and restricted flow may eventually
result in no flow at all through the PBR.
PBRs behave as deep-bed filters with respect to the substrate stream. It is
necessary to use a guard bed if plugging of the reactor by small particles is more
rapid than the biocatalysts' deactivation. They are also easily fouled by
colloidal or precipitating material. The design of PBRs does not allow for control
of pH, by addition of acids or bases, or for easy temperature control where there
is excessive heat output, a problem that may be particularly noticeable in wide
reactors (> 15 cm diameter).
Deviations from ideal plug-flow are due to back-mixing within the reactors, the
resulting product streams having a distribution of residence times. In an extreme
case, back-mixing may result in the kinetic behaviour of the reactor approximating
to that of the CSTR (see below), and the consequent difficulty in achieving a high
degree of conversion. These deviations are caused by channeling, where some
substrate passes through the reactor more rapidly, and hold-up, which involves
stagnant areas with negligible flow rate. Channels may form in the reactor bed due
to excessive pressure drop, irregular packing or uneven application of the
substrate stream, causing flow rate differences across the bed. The use of a
uniformly sized catalyst in a reactor with an upwardly flowing substrate stream
reduces the chance and severity of non-ideal behavior.
16.5 Continuous flow stirred tank reactors (CSTIR)
This reactor consists of a well -stirred tank containing the enzyme, which is
normally immobilised. The substrate stream is continuously pumped into the reactor
at the same time as the product stream is removed. This is the example of
continous reactor. If the reactor is behaving in an ideal manner, there is total
back-mixing and the product stream is identical with the liquid phase within the
reactor and invariant with respect to time. Some molecules of substrate may be
removed rapidly from the reactor, whereas others may remain for substantial
periods. The distribution of residence times for molecules in the substrate stream
is shown in Figure 16.2
Advantages
The CSTR is an easily constructed, versatile and cheap reactor, which allows
simple catalyst charging and replacement.
Its well -mixed nature permits straightforward control over the temperature and
pH of the reaction and the supply or removal of gases.
CSTRs tend to be rather large as the: need to be efficiently mixed. Their volumes
are usually about five to ten time the volume of the contained immobilised enzyme.
This, however, has the advantage that there is very little resistance to the flow
of the substrate stream, which may contain colloidal or insoluble substrates, so
long as the insoluble particles are not able to sweep the immobilised enzyme from
the reactor.
The mechanical nature of the stirring limits the supports for the immobilised
enzymes to materials which do not easily disintegrate to give 'fines' which may
enter the product stream. However, fairly small particle (down to about 10 m
diameter) may be used, if they are sufficiently dense to stay within the reactor.
This minimises problems due to diffusional resistance.
An ideal CSTR has complete back -mixing resulting in a minimisation of the
substrate concentration, and a maximisation of the product concentration, relative
to the final conversion, at every point within the reactor the effectiveness
factor being uniform throughout. Thus, CSTRs are the preferred reactors,
everything else being equal, for processes involving substrate inhibition or
product activation. They are also useful where the substrate stream contains an
enzyme inhibitor, as it is diluted within the reactor. This effect is most
noticeable if the inhibitor concentration is greater than the inhibition constant
and [S]0/Km is low for competitive inhibition or high for uncompetitive
inhibition, when the inhibitor dilution has more effect than the substrate
dilution. Deviations from ideal CSTR behaviour occur when there is a less
effective mixing regime and may generally be overcome by increasing the stirrer
speed, decreasing the solution viscosity or biocatalyst concentration or by more
effective reactor baffling.
Kinetics of CSTR
The rate of reaction within a CSTR can be derived from a simple mass balance to be
the flow rate (F) times the difference in substrate concentration between the
reactor inlet and outlet. Hence:
(16.7)
Therefore:
(16.8)
from equation (5.4):
(16.9)
Therefore:
(16.10)
This equation should be compared with that for the PBR (equation (16.6)). Together
these equations can be used for comparing the productivities of the two reactors
(Figures 16.4 and 16.5).
________________________________________
Figure 16. 3Figure 5.4. The residence time distribution of a CSTR. The relative
number of molecules resident within the reactor for a particular time N, is
plotted against the normalised residence time (i.e. t F/V, where V is the reactor
volume, and F is the flow rate; it is the time relative to that required for one
reactor volume to pass through the reactor). The residence time distribution of
non -reacting media molecules ( ----------- which obeys the relationship , where
[M] is the concentration of media molecules, giving a half-life for remaining in
the reactor of , product (——— ) and substrate (•••••••••) are shown. The reaction
S P is assumed, and substrate molecules that have long residence times are
converted into product, the average residence time of the product being greater
than that for the substrate. The composition of the product stream is identical
with that of the liquid phase within the reactor. This composition may be
calculated from the relative areas under the curves and, in this case, represents
a 90% conversion. Under continuous operating conditions (operating time > 4V/F),
the mean residence time within the reactor is V/F. However, it may be noted from
the graph that only a few molecules have a residence time close to this value
(only 7% between 0.9V/F and 1.1 V/F) whereas 20% of the molecules have residence
times of less than 0.1 V/F or greater than 2.3V/F. It should be noted that 100% of
the molecules in an equivalent ideal PBR might be expected to have residence times
equal to their mean residence time.
________________________________________
Figure 16. 4Figure 5.5. Comparison of the changes in fractional conversion with
flow rate between the PBR (———) and CSTR (-----------) at different values of
[S]0/Km (10,1 and 0.1, higher [S]0/Km giving the higher curves). The flow rate is
normalised with respect to the reactor's volumetric enzyme content ( = FKm/Vmax.
It can be seen that there is little difference between the two reactors at faster
flow rates and lower conversions, especially at high values of [S]0/Km.
________________________________________
Figure 16. 5 Figure 5.6. Comparison of the changes in fractional conversion with
residence time between the PBR (———) and CSTR (-----------) at different values of
[S]0/Km (10, 1 and 0.1; higher [S]0/Km values giving the lower curves). The
residence time is the reciprocal of the normalised flow rate (see Figure 5.5). If
the flow rate is unchanged then the 'normalised residence time' may be thought of
as the reactor volume needed to produce the required degree of conversion.
________________________________________
Equations describing the behaviour of CSTRs and PBRs utilising reversible
reactions or undergoing product or substrate inhibition can be derived in a
similar manner, using equations (1.68), (1.85) and (1.96) rather than (1.8):
a. Substrate -inhibited PBR
(16.11)
Substrate -inhibited CSTR
(16.12)
b. Product -inhibited PBR
(16.13)
Product -inhibited CSTR
(16.14)
Reversible reaction in a PBR
(16.15)
Reversible reaction in a CSTR
(16.16)
X in equations (5.15) and (5.16) is the fractional conversion for a reversible
reaction.
(16.17)
These equations may be used to compare the size of PBR and CSTR necessary to
achieve the same conversion under various conditions (Figure 16.6).
The productivity
Another useful parameter for comparing these reactors is the productivity. This
can be derived for each reactor assuming a first-order inactivation of the enzyme
(equation (1.26)). Combined with equation (5.6) for PBR, or (5.10) for CSTR, the
following relationships are obtained on integration:
PBR (16.18)
CSTR (16.19)
where kd is the first -order inactivation constant (i.e. kd1, in equation (1.25))
and the fractional conversion subscripts refer to time = 0 or t. The change in
productivity (Figure 16.7) and fractional conversion (Figure 16.8) of these
reactors with time can be compared using these equations.
These reactors may be operated for considerably longer periods than that
determined by the inactivation of their contained immobilised enzyme, particularly
if they are capable of high conversion at low substrate concentrations (Figure
16.8). This is independent of any enzyme stabilisation and is simply due to such
reactors initially containing large amounts of redundant enzyme.
________________________________________
Figure 16. 6Figure 5.7. Comparison of the ratio, of the enzyme content in a CSTR
to that in a PBR, necessary to achieve various degrees of conversion for a range
of process conditions. The actual size of the CSTR will be five to ten times
greater than indicated due to the necessity of maintaining stirring within the
vessel. ———Uninhibited reaction; •••••••••••• product inhibited; ---------
substrate inhibited. (curve a) [S]0/Km = 100; (curve b) [S]0/Km = 1; (curve c)
[S]0/Km < 0.01; (curve d) [S]0/Km = 1, product inhibited KP/Km = 0.1 ; (curve e)
[S]0/Km = 1, product inhibited KP/Km = 0.01; (curve f) [S]0/Km = 1, substrate
inhibited [S]0/KS = 10; (curve g) [S]0/Km = 100; substrate inhibited [S]0/KS = 10.
The size of a CSTR becomes prohibitively large at high conversions (e.g. using
curve b, a CSTR contains three times the enzyme in a PBR to achieve a 90%
conversion, but this increases to 18 times for 99% conversion. The difference
between the two types of reactor is increased if the effectiveness factor (η) is
less than one due to diffusional effects.
________________________________________
Figure 16. 7Figure 5.8. The change in productivity of a PBR (---------) and CSTR
(———) with time, assuming an initial fractional conversion (X0) = 0.99 and [S]0/Km
= 100. The units of time are half -lives of the free enzyme ( ) and the
productivity is given in terms of (FXt1/2). Although the overall productivity is
1.6 times greater for a CSTR than a PBR, it should be noted that the CSTR contains
1.9 times more enzyme.
________________________________________
In general, there is little or no back -pressure to increased flow rate through
the CSTR. Such reactors may be started up as batch reactors until the required
degree of conversion is reached, when the process may be made continuous. CSTRs
are not generally used in processes involving high conversions but a chain of
CSTRs may approach the PBR performance. This chain may be a number (greater than
three) of reactors connected in series or a single vessel divided into
compartments, in order to minimise back-mixing CSTRs may be used with soluble
rather than immobilised enzyme if an ultrafiltration membrane is used to separate
the reactor output stream from the reactor contents. This causes a number of
process difficulties, including concentration polarization or inactivation of the
enzyme on the membrane but may be preferable in order to achieve a combined
reaction and separation process or where a suitable immobilised enzyme is not
readily available.
________________________________________
Figure 16. 8Figure 5.9. The change in fractional conversion of PBRs and CSTRs with
time, assuming initial fractional conversion (X0) of 0.99 or 0.80. ————CSTR,
[S]o/Km = 0.01; - - - - - - CSTR, [S]0/Km = 100; •••••••••••• PBR [S]0/Km =
0.01; •-•-•-•-•-•-•-• PBR [S]0/Km = 100. The time is given in terms of the half
-life of the free enzyme ( ). Although the CSTR maintains its fractional
conversion for a longer period than the PBR, particularly at high X0. It should be
noted that a CSTR capable of X0 = 0.99 at a substrate feed concentration of
[S]0/Km = 0.01 contains 22 times more enzyme than an equivalent PBR, but yields
only 2.2 times more product. The initial stability in the fractional conversion
over a considerable period of time, due to the enzyme redundancy, should not be
confused with any effect due to stabilisation of the immobilised enzyme.
5. Fluidised bed reactors
These reactors generally behave in a manner intermediate between CSTRs and PBRs.
They consist of a bed of immobilised enzyme which is fluidised by the rapid
upwards flow of the substrate stream alone or in combination with a gas or
secondary liquid stream, either of which may be inert or contain material relevant
to the reaction. A gas stream is usually preferred as it does not dilute the
product stream. There is a minimum fluidisation velocity needed to achieve bed
expansion, which depends upon the size, shape, porosity and density of the
particles and the density and viscosity of the liquid. This minimum fluidisation
velocity is generally fairly low (about 0.2 -I.0 cm s-1) as most immobilised-
enzyme particles have densities close to that of the bulk liquid. In this case the
relative bed expansion is proportional to the superficial gas velocity and
inversely proportional to the square root of the reactor diameter. Fluidising the
bed requires a large power input but, once fluidised, there is little further
energetic input needed to increase the flow rate of the substrate stream through
the reactor (Figure 16.2). At high flow rates and low reactor diameters almost
ideal plug -flow characteristics may be achieved. However, the kinetic performance
of the FBR normally lies between that of the PBR and the CSTR, as the small fluid
linear velocities allowed by most biocatalytic particles causes a degree of back-
mixing that is often substantial, although never total. The actual design of the
FBR will determine whether it behaves in a manner that is closer to that of a PBR
or CSTR (see Figures 5.5 -5.9). It can, for example, be made to behave in a manner
very similar to that of a PBR, if it is baffled in such a way that substantial
backmixing is avoided. FBRs are chosen when these intermediate characteristics are
required, e.g. where a high conversion is needed but the substrate stream is
colloidal or the reaction produces a substantial pH change or heat output. They
are particularly useful if the reaction involves the utilisation or release of
gaseous material.
The FBR is normally used with fairly small immobilised enzyme particles (20-40 m
diameter) in order to achieve a high catalytic surface area. These particles must
be sufficiently dense, relative to the substrate stream, that they are not swept
out of the reactor. Less-dense particles must be somewhat larger. For efficient
operation the particles should be of nearly uniform size otherwise a non-uniform
biocatalytic concentration gradient will be formed up the reactor. FBRs are
usually tapered outwards at the exit to allow for a wide range of flow rates. Very
high flow rates are avoided as they cause channelling and catalyst loss.
The major disadvantage of development of FBR process is the difficulty in scaling-
up these reactors. PBRs allow scale-up factors of greater than 50000 but, because
of the markedly different fluidisation characteristics of different sized
reactors, FBRs can only be scaled-up by a factor of 10 -100 each time. In
addition, changes in the flow rate of the substrate stream causes complex changes
in the flow pattern within these reactors that may have consequent unexpected
effects upon the conversion rate.
Introduction
Protein engineering is the branch of science in which novel enzymes are being
designed and produce by genetic engineering methods to improve the stability of an
enzyme (stability with respect to chemical oxidation, temperature, and pH).
Therefore protein engineering includes two parts one large scale production of
genes by modification in the gene by gene cloning methods and other modification
in the structure of protein to improve the substrate specificity, the cofactor
requirement (NADPH to NADH) or imparting novel properties to a protein (eg. adding
a Mn binding site into horse heart myoglobin at UBC).In the genetic engineering
methods the availability of a cloned gene is important. Cloned gene is expressed
in the expression vector to obtain the 3-D structure of the enzyme, resolved by X-
ray crystallography. In the absence of detailed 3-D structure, one can do random
mutagenesis and/or directed evolution. There are many directions in which enzyme
technologists are currently applying their art and which are at the forefront of
biotechnological research and development. At present, relatively few enzymes are
available on a large scale (i.e. > kg) and are suitable for industrial
applications. These shortcomings are being addressed in a number of ways:
New enzymes are being sought in the natural environment and by strain selection.
Established industrial enzymes are being used in as wide a variety of ways as can
be conceived.
novel enzymes are being designed and produce by genetic engineering;
New organic catalysts are being designed and synthesized.
More complex enzyme systems are being utilised.
The development of genetically improved enzymes is generally undertaken by
molecular biologists and the design and synthesis of novel enzyme-like catalysts
is done by the organic chemists. Both groups of workers will, however, base their
science on data provided by the enzyme technologist. Space requirements in this
volume do not allow the full treatment of these related areas but will be
discussed briefly here.
17.1 Enzyme engineering
A most exciting development over the last few years is the application of genetic
engineering techniques to enzyme technology. There are a number of properties
which may be improved or altered by genetic engineering for example, the yield and
kinetics of the enzyme, the ease of downstream processing and various safety
aspects. Enzymes from dangerous or unapproved microorganisms and from slow growing
or limited plant or animal tissue may be cloned into safe high-production
microorganisms. In the future, enzymes may be redesigned to fit more appropriately
into industrial processes; for example, making glucose isomerase less susceptible
to inhibition by the Ca2+ present in the starch saccharification processing
stream.
17.2 Enzyme production can be increased by cloning of gene
The amount of enzyme produced by a microorganism may be increased by increasing
the number of gene copies that code for it by inserting a portion of gene for
specific enzyme into the suitable vector. If the vector is expression type then
large amount of protein will be obtained after the translation of vector. The
product can be tested by its specific function. The DNA having gene of interest
for specific enzyme can be isolated by partial digestion of gene or complete
digestion of gene (incomplete or complete fragmentation of gene) and selection of
specific gene can be done with the help of probe. This principle has been used to
increase the activity of penicillin-G-amidase in Escherichia coli. The cellular
DNA from a producing strain is selectively cleaved by the restriction endonuclease
Hind III. This hydrolyses the DNA at relatively rare sites containing the
5'-AAGCTT-3' base sequence to give identical 'staggered' ends.
Figure 17. 1 figure showing staggered cut of DNA double strand by the restriction
endonuclease. Note that single stranded DNA is rarely cut by the Restriction
enzyme.
R.E.
Intact DNA cleaved DNA
Figure 17. 2 showing structure of vector and their site containing antibiotic
resistance gene as the marker of the gene for selection of recombinant gene.
The total DNA is cleaved into about 10000 fragments, only one of which contains
the required genetic information. These fragments are individual cloned into a
cosmid vector and thereby returned to E. coli. These colonies containing the
active gene are identified by their inhibition of a 6-amino-penicillanic acid-
sensitive organism. Such colonies are isolated and the penicillin-G-amidase gene
transferred on to pBR322 plasmids and recloned back into E. coli. The engineered
cells, aided by the plasmid amplification at around 50 copies per cell, produce
penicillin-G-amidase constitutively and in considerably higher quantities than
does the fully induced parental strain. Such increased yields are economically
relevant not just for the increased volumetric productivity but also because of
reduced downstream processing costs, the resulting crude enzyme being that much
purer. Another extremely promising area of genetic engineering is protein
engineering. New enzyme structures may be designed and produced in order to
improve on existing enzymes or create new activities. An outline of the process of
protein engineering is shown in Figure 17.1. Such factitious enzymes are produced
by site-directed mutagenesis (Figure 17.2). Unfortunately from a practical point
of view, much of the research effort in protein engineering has gone into studies
concerning the structure and activity of enzymes chosen for their theoretical
importance or ease of preparation rather than industrial relevance. This emphasis
is likely to change in the future.
Figure 17. 3 showing structure and location of plasmid DNA inside the E.coli
vector.
Figure 17. 7 The protein engineering cycle. The process starts with the isolation
and characterization of the required enzyme. This information is analyzed together
with the database of known and putative structural effects of amino acid
substitutions to produce a possible improved structure. This factitious enzyme is
constructed by site-directed mutagenesis, isolated and characterised. The results,
successful or unsuccessful, are added to the database, and the process repeated
until the required result is obtained.
________________________________________
Protein engineering, therefore, is presently rather a hit or miss process which
may be used with only little realistic likelihood of immediate success. Apparently
quite small sequence changes may give rise to large conformational alterations and
even affect the rate-determining step in the enzymic catalysis. However it is
reasonable to suppose that, given a sufficiently detailed database plus suitable
software, the relative probability of success will increase over the coming years
and the products of protein engineering will make a major impact on enzyme
technology.
17.2 Application of Enzyme Engineering
17.2.1 Subtilisin
Much protein engineering has been directed at subtilisin (from Bacillus
amyloliquefaciens), the principal enzyme in the detergent enzyme preparation,
Alcalase. This has been aimed at the improvement of its activity in detergents by
stabilising it at even higher temperatures, pH and oxidant strength. Most of the
attempted improvements have concerned alterations to:
The P1 cleft, which holds the amino acid on the carbonyl side of the targeted
peptide bond; 2. The oxyanion hole (principally Asn155), which stabilises the
tetrahedral intermediate; 3. the neighborhood of the catalytic histidyl residue
(His64), which has a general base role; and 4.the methionine residue (Met222)
which causes subtilisin's lability to oxidation.
It has been found that the effect of a substitution in the P1 cleft on the
relative specific activity between substrates may be fairly accurately predicted
even though predictions of the absolute effects of such changes are less
successful. Many substitutions, particularly for the glycine residue at the bottom
of the P1 cleft (Gly166), have been found to increase the specificity of the
enzyme for particular peptide links whilst reducing it for others. These effects
are achieved mainly by corresponding changes in the Km rather than the Vmax.
Increases in relative specificity may be useful for some applications. They should
not be thought of as the usual result of engineering enzymes, however, as native
subtilisin is unusual in being fairly non-specific in its actions, possessing a
large hydrophobic binding site which may be made more specific relatively easily
(e.g. by reducing its size). The inactivation of subtilisin in bleaching solutions
coincides with the conversion of Met222 to its sulfoxide, the consequential
increase in volume occluding the oxyanion hole. Substitution of this methionine by
serine or alanine produces mutants that are relatively stable, although possessing
somewhat reduced activity.
________________________________________
Figure 17. 8
Introduction
A biosensor is an analytical device which converts a biological response into an
electrical signal (Figure 19.1). The term 'biosensor' is often used to cover
sensor devices used in order to determine the concentration of substances.
Clark and Lyons first demonstrated the modern concept of biosensors, in which an
enzyme was immobilized into an electrode to form a biosensor. When the biological
component of biosensor is a component of the immune system then it is referred to
as Immunosensors. The emphasis of this Chapter concerns enzymes as the
biologically responsive material, but it should be recognised that other
biological systems may be utilised by biosensors, for example, whole cell
metabolism, ligand binding and the antibody-antigen reaction.
19.1 The use of enzymes in analysis
Specificity: Biosensor has got the remarkable ability to distinguish between the
analyte of interest and other similar substances. With biosensor, an analyte can
be detected with great accuracy .
Response time: Analytic tracers or catalytic product can be detected directly and
instantaneously with the help of biosensors. Thus they are very much suitable for
on-line monitoring.
Simplicity: The sensing molecule and the transducer are integrated on to a single
probe. Thus handling of biosensors is very easy.
Continuous monitoring ability: Biosensors can be regenerated and reused. Thus they
are suitable for continuous monitoringJ purposes which can never be done with
conventional analysis methods.
Reproducibility: Biosensors are very reliable; reproducibility of the values is
also a great advantage.
Portability: Portability of such sensors adds to the advantages which can never be
the case with a spectrophotometer.
Cost: The cost of the biosensor has too some extend limited its application.
Figure 19. 1 Schematic diagram showing the main components of a biosensor. The
biocatalyst (a) converts the substrate to product. This reaction is determined by
the transducer (b) which converts it to an electrical signal. The output from the
transducer is amplified (c), processed (d) and displayed (e).
________________________________________
A biosensor is a device that detects, transmits and records information regarding
a physiological or biochemical change. Technically, it is a probe that integrates
a biological component with an electronic transducer thereby converting a
biochemical signal into a quantifiable electrical response. The sensor works by
converting the signal produced by the biological sensing element on response to a
specific analyte to a measurable electrical signal with the help of the
transducer. The amplifier increases the intensity of the signal so that it can be
readily measured. The digital display then displays the reading in a suitable
unit. All these components are generally integrated onto a single probe to make
the handling easier.
Biosensor is device that on matching with appropriate biological sample gives
signal to electrical components. Biological component is bound or immobilized on
the electronic component called as transducer.
Figure 19. 2
The electrical signal from the transducer is often low and superimposed upon a
relatively high and noisy (i.e. containing a high frequency signal component of an
apparently random nature, due to electrical interference or generated within the
electronic components of the transducer) baseline. The signal processing normally
involves subtracting a 'reference' baseline signal, derived from a similar
transducer without any biocatalytic membrane, from the sample signal, amplifying
the resultant signal difference and electronically filtering (smoothing) out the
unwanted signal noise. The relatively slow nature of the biosensor response
considerably eases the problem of electrical noise filtration. The analogue signal
produced at this stage may be output directly but is usually converted to a
digital signal and passed to a microprocessor stage where the data is processed,
converted to concentration units and output to a display device or data store.
19.4 Classification of Biosensor
There are several type of Biosensor depends on the physical characteristic like
heat , electrical signal . light, electron ,charge, and mass. Biosensors may be
classified according to several criteria, such as transducers, bioactive
components, or immobilization techniques used.
The heat output (or absorbed) by the reaction (calorimetric biosensors),
changes in the distribution of charges causing an electrical potential to be
produced (potentiometric biosensors),
movement of electrons produced in a redox reaction (amperometric biosensors),
light output during the reaction or a light absorbance difference between the
reactants and products (optical biosensors), or
Effects due to the mass of the reactants or products (piezo-electric biosensors).
There are three so-called 'generations' of biosensors
First generation biosensors where the normal product of the reaction diffuses to
the transducer and causes the electrical response.
Second generation biosensors which involve specific 'mediators' between the
reaction and the transducer in order to generate improved response.
Third generation biosensors where the reaction itself causes the response and no
product or mediator diffusion is directly involved.
A typical biosensor has got two main parts
Biological component which can be enzyme, antibody, nucleic acid, microorganism,
tissue, cell, etc.
Electronic device, i.e., transducer which can be electrochemical, optical,
piezoelectric, thermal, etc.
The biological component is generally immobilized near or onto the transducer
surface in order to facilitate reuse, to minimize interference and to maximize
response. In each case it is the ability of the biological component to react or
respond specifically to an analyte (or a group of analytes) that makes the
biomolecule suitable for use as the sensing element of a biosensor. For example,
an antibody will only bind to the specific antigen under suitable conditions. The
biological signal that is produced is converted by means of a suitable transducer
into a quantifiable electrical signal.Biosensors are suitable for detecting a wide
variety of analytes including pollutants, explosives, viruses, biochemical &
pharmaceutical products, vitamins, amino acids, heavy metals, ions, gases etc . In
fact, every single analyte, be it simple or complex can be detected provided a
biomolecule that response specifically to it is identified.
1. Transducers
This is the component of biosensor which converts the biological signal to a
quantifiable electrical signal.
Electrochemical: In this configuration, sensing molecules are either coated onto
or covalently bonded to a probe surface. A membrane holds the sensing molecule in
place, excluding interfering species from the analyte solution. The sensing
molecule reacts specifically with compounds to be detected, sparking an electrical
signal proportional to the concentration of the analyte. The most common detection
method for electrochemical biosensors involves measurement of current, voltage,
capacitance, conductance and impedance.
Among such sensors, amperometric (e.g. Oxygen or hydrogen peroxide) and
potentiometric (e.g. pH and carbon dioxide) transducers have found the widest
applications.
Optical: In optical biosensors, the optical fibers allow detection of analytes on
the basis of absorption, fluorescence or light scattering. Since they are non-
electrical, optical biosensors have the advantages of lending themselves to in
vivo applications and allowing multiple analytes to be detected by using different
monitoring wave-lengths. The versatility of fiber optics probes is due to their
capacity to transmit signals that reports on changes in wavelength, wave
propagation, time, intensity, distribution of the spectrum or polarity of light.
Piezoelectric: In this mode, sensing molecules are attached to a piezoelectric
surface-a mass to frequency transducer-in which interactions between the analyte
and the sensing molecules set up mechanical vibrations that can be translated into
an electrical signal proportional to the analyte. Example of such sensor is quartz
crystals.
Thermal: In this mode, the biocomponent is immobilized in proximity to the heat
sensing transducer, generally a thermister. Most of the enzymatic or microbial
reactions are accompanied by considerable heat evolution making this sensor
applicable to a very wide range of detection. However the use of sophisticated and
expensive instrumentation is the major drawback of this technique.
2. Bioactive components
This is the biological part of the biosensor which specifically reacts with the
analyte of interest sparking a signal that is detectable by the attached
transducer.
Enzymes: Purified enzymes have been commonly used in the construction of
biosensors due to their high specific activities as well as high analytical
specificity. They are mostly used in catalytic type biosensors. Purified enzymes,
however, are expensive and unstable, thus limiting their application sin the field
of biosensors. As most of the enzymes being employed are intracellular, isolation
and purification becomes tough.
Antibodies: The binding between an antigen and its corresponding antibody is very
specific. This property of antibody is exploited while designing biosensors based
on antibodies. The binding reaction between the antibody and antigen can be
monitored as a time dependent change of fluorescence signal which is proportional
to the reaction ratio of antibody to analyte.
Cells: Either whole microorganisms or tissues can be used as the biocomponent.
Whole cells can be used either in a viable or non-viable form. Viable microbes
metabolize various organic compounds either anaerobically or aerobically resulting
in various end products like ammonia, carbon dioxide, acids etc that can be
monitored using a variety of transducers. Viable cells are mainly used when the
overall substrate assimilation capacity of microorganism is taken as an index of
respiratory metabolic activity, as in the case of estimation of BOD, vitamins,
sugars, organic acids, etc. Another mechanism used for the viable microbial
biosensor involves the inhibition of microbial respiration by the analyte of
interest, like environmental pollutants. The major limitation to the use of whole
cells is the diffusion of substrate and products through the cell wall resulting
in a slow response as compared to enzyme-based sensors.
Nucleic acids: The ability of a single stranded nucleic acid to hybridize with
another fragment of DNA by complementary base pairing is the principle behind the
nucleic acid sensors. Technological innovation is introduced in the manner in
which the nucleic acid oligomer is attached to the surface of the detector and the
manner in which the hybridized nucleic acid is detected and transduced into a
measurable signal. Ammonia derivetised oligonucleotides can be detected by
attaching to glass surfaces such as fiber-optics cables, glass beads or
microscopic slides through covalent bonding with a chemical linker.
Lipids: An active biological receptor can be immobilized and stabilized in a
polymeric film for determining an analyte of interest in a sample.
3. Immobilization techniques for the bio-component:
The biological material should bring the physico-chemical changes in close
proximity of a transducer. Immobilization not only helps in forming the required
close proximity between the biomaterial and the transducer, but also helps in
stabilizing it for reuse.The selection of a technique and/or support material
would depend on the nature of the biomaterial and the substrate and configuration
of the transducer used.
Covalent binding, a commonly used technique for the immobilization of enzymes and
antibodies, has not been useful for the immobilization of cells. On the other
hand, cross-linking using bifunctional reagents like glutaraldehyde has been
successfully used for the immobilization of cells in various supports. Thus cross-
linking technique will be useful in obtaining immobilized non-viable cell
preparations containing active intracellular enzymes. Entrapment and adsorption
techniques are more useful when viable cells are used. The synthetic polymers used
for microbial biosensor applications include polyacrylamide, polyurethane-based
hydrogels, photo cross-linkable resins and polyvinyl alcohol. Natural polymers
used for the entrapment of the cells include alginate, carrageenam, low-melting
agarose, chitosan, etc. But entrapment technique adds another diffusional
barrier.Passive trapping of cells into the pores or adhesion onto the surfaces of
cellulose or other synthetic membranes has the major advantage of direct contact
between the liquid phase and the cell, thus reducing or eliminating the problem of
mass transfer
Figure 19. 4
An alternative method for determining the rate of this reaction is to measure the
production of hydrogen peroxide directly by applying a potential of +0.68 V to the
platinum electrode, relative to the Ag/AgCl electrode, and causing the reactions:
Pt anode H2O2 O2 + 2H+ + 2e- [19.6]
Ag cathode 2AgCl + 2e- 2Ag0 + 2Cl-[19.7]
The major problem with these biosensors is their dependence on the dissolved
oxygen concentration. This may be overcome by the use of 'mediators' which
transfer the electrons directly to the electrode bypassing the reduction of the
oxygen co-substrate. In order to be generally applicable these mediators must
possess a number of useful properties.
They must react rapidly with the reduced form of the enzyme.
They must be sufficiently soluble, in both the oxidised and reduced forms, to be
able to rapidly diffuse between the active site of the enzyme and the electrode
surface. This solubility should, however, not be so great as to cause significant
loss of the mediator from the biosensor's microenvironment to the bulk of the
solution. However soluble, the mediator should generally be non-toxic.
The overpotential for the regeneration of the oxidised mediator, at the electrode,
should be low and independent of pH.
The reduced form of the mediator should not readily react with oxygen.
The ferrocenes represent a commonly used family of mediators (Figure 19.5 a).
Their reactions may be represented as follows,
Figure 19. 9 Schematic diagram of the section across the width of an ENFET. The
actual dimensions of the active area is about 500 m long by 50 m wide by 300 m
thick. The main body of the biosensor is a p-type silicon chip with two n-type
silicon areas; the negative source and the positive drain. The chip is insulated
by a thin layer (0.1 m thick) of silica (SiO2) which forms the gate of the FET.
Above this gate is an equally thin layer of H+-sensitive material (e.g. tantalum
oxide), a protective ion selective membrane, the biocatalyst and the analyte
solution, which is separated from sensitive parts of the FET by an inert
encapsulating polyimide photopolymer. When a potential is applied between the
electrodes, a current flows through the FET dependent upon the positive potential
detected at the ion-selective gate and its consequent attraction of electrons into
the depletion layer. This current (I) is compared with that from a similar, but
non-catalytic ISFET immersed in the same solution. (Note that the electric
current is, by convention, in the opposite direction to the flow of electrons).
Many enzyme catalysed reactions are exothermic, generating heat (Table 19.3) which
may be used as a basis for measuring the rate of reaction and, hence, the analyte
concentration. This represents the most generally applicable type of biosensor.
The temperature changes are usually determined by means of thermistors at the
entrance and exit of small packed bed columns containing immobilised enzymes
within a constant temperature environment (Figure 19.10). Under such closely
controlled conditions, up to 80% of the heat generated in the reaction may be
registered as a temperature change in the sample stream. This may be simply
calculated from the enthalpy change and the amount reacted. If a 1 mM reactant is
completely converted to product in a reaction generating 100 kJ mole-1 then each
ml of solution generates 0.1 J of heat. At 80% efficiency, this will cause a
change in temperature of the solution amounting to approximately 0.02°C. This is
about the temperature change commonly encountered and necessitates a temperature
resolution of 0.0001°C for the biosensor to be generally useful.
________________________________________
Table 19.3. Heat output (molar enthalpies) of enzyme catalysed reactions.
Reactant Enzyme Heat output
-ΔH (kJ mole-1)
Cholesterol Cholesterol oxidase 53
Esters Chymotrypsin 4 - 16
Glucose Glucose oxidase 80
Hydrogen peroxide Catalase 100
Penicillin G Penicillinase 67
Peptides Trypsin 10 - 30
Starch Amylase 8
Sucrose Invertase 20
Urea Urease 61
Uric acid Uricase 49
________________________________________
Figure 19. 10. Schematic diagram of a calorimetric biosensor. The sample stream
(a) passes through the outer insulated box (b) to the heat exchanger (c) within an
aluminium block (d). From there, it flows past the reference thermistor (e) and
into the packed bed bioreactor (f, 1ml volume), containing the biocatalyst, where
the reaction occurs. The change in temperature is determined by the thermistor (g)
and the solution passed to waste (h). External electronics (l) determines the
difference in the resistance, and hence temperature, between the thermistors.
________________________________________
The thermistors, used to detect the temperature change, function by changing their
electrical resistance with the temperature, obeying the relationship
(19.26)
therefore:
(19.27)
Where R1 and R2 are the resistances of the thermistors at absolute temperatures T1
and T2 respectively and B is a characteristic temperature constant for the
thermistor. When the temperature change is very small, as in the present case,
B(1/T1) - (1/T2) is very much smaller than one and this relationship may be
substantially simplified using the approximation when x<<1 that exÅ1 + x (x here
being B(1/T1) - (1/T2),
(19.28)
As T1 Δ T2, they both may be replaced in the denominator by T1.
(19.29)
The relative decrease in the electrical resistance (ΔR/R) of the thermistor is
proportional to the increase in temperature (ΔT). A typical proportionality
constant (-B/T12) is -4%°C-1. The resistance change is converted to a proportional
voltage change, using a balanced Wheatstone bridge incorporating precision wire-
wound resistors, before amplification. The expectation that there will be a linear
correlation between the response and the enzyme activity has been found to be
borne out in practice. A major problem with this biosensor is the difficulty
encountered in closely matching the characteristic temperature constants of the
measurement and reference thermistors. An equal movement of only 1°C in the
background temperature of both thermistors commonly causes an apparent change in
the relative resistances of the thermistors equivalent to 0.01°C and equal to the
full-scale change due to the reaction. It is clearly of great importance that such
environmental temperature changes are avoided, which accounts for inclusion of the
well-insulated aluminium block in the biosensor design .
The sensitivity (10-4 M) and range (10-4 - 10-2 M) of thermistor biosensors are
both quite low for the majority of applications although greater sensitivity is
possible using the more exothermic reactions (e.g. catalase). The low sensitivity
of the system can be increased substantially by increasing the heat output by the
reaction. In the simplest case this can be achieved by linking together several
reactions in a reaction pathway, all of which contribute to the heat output. Thus
the sensitivity of the glucose analysis using glucose oxidase can be more than
doubled by the co-immobilisation of catalase within the column reactor in order to
disproportionate the hydrogen peroxide produced. An extreme case of this
amplification is shown in the following recycle scheme for the detection of ADP.
Figure 19. 11
ADP is the added analyte and excess glucose, phosphoenol pyruvate, NADH and oxygen
are present to ensure maximum reaction. Four enzymes (hexokinase, pyruvate kinase,
lactate dehydrogenase and lactate oxidase) are co-immobilised within the packed
bed reactor. In spite of the positive enthalpy of the pyruvate kinase reaction,
the overall process results in a 1000 fold increase in sensitivity, primarily due
to the recycling between pyruvate and lactate. Reaction limitation due to low
oxygen solubility may be overcome by replacing it with benzoquinone, which is
reduced to hydroquinone by flavo-enzymes. Such reaction systems do, however, have
the serious disadvantage in that they increase the probability of the occurrence
of interference in the determination of the analyte of interest. Reactions
involving the generation of hydrogen ions can be made more sensitive by the
inclusion of a base having a high heat of protonation. For example, the heat
output by the penicillinase reaction may be almost doubled by the use of Tris
(tris-(hydroxymethyl)aminomethane) as the buffer.In conclusion, the main
advantages of the thermistor biosensor are its general applicability and the
possibility for its use on turbid or strongly coloured solutions. The most
important disadvantage is the difficulty in ensuring that the temperature of the
sample stream remains constant (± 0.01°C).
19.5.5 Immunosensors
Chapter-19
Abstract:-
The Gibbs free energy, G, is made up the two terms enthalpy (H) and entropy (S),
related by the equation:
Although both these interactions have small free energies per residue, they are
important because there are so many of them. The same is true for those
interactions which stabilize the unfolded state. The most important of which is
conformational entropy. Thus, the overall free energy of a folded protein is given
by the small difference between two large numbers. This is a major reason for the
difficulty of quantitative computational calculation of protein stability. In a
recent analysis of the factors contributing to the stability of RNase T1, the
stabilizing and destabilizing interactions were estimated at 271 and 286 kcal/mol,
respectively (Pace et al., 1996). Hydrogen bonding and hydrophobic interactions
were estimated to contribute 260 kcal/mol to the stabilizing interactions, while
the bulk of the destabilizing factors were attributed to loss of conformational
entropy on folding, and unfavourable burial of peptide and polar groups. See
table.
At room temperature, the enthalpy of transfer from organic solution into aqueous
solution is negligible; the interaction enthalpies are the same in both cases.
The entropy however is negative. Water tends to form ordered cages around the non-
polar molecule and this leads to a decrease in entropy. At high temperatures (~
110°C) these cages are no longer any stronger than bulk water, and the entropy
contribution tends to zero. The enthalpy of transfer, however, is now positive
(unfavourable). Because the temperature dependence of entropy and enthalpy are not
the same, there is some temperature at which the hydrophobic effect is strongest,
and the effect decreases at temperatures above and below this temperature. The
decrease in the strength of the hydrophobic effect with decreasing temperatures is
probably the major cause of cold-denaturation in proteins.
The contribution of the hydrophobic effect to globular protein stability has been
estimated empirically both by measuring the thermodynamics of transfer of model
compounds (e.g. blocked amino acids, cyclic peptides...) from organic solvents to
water, and by site directed mutagenesis studies on proteins. The number arrived at
is usually given as a function of the change in the solvent accessible non-polar
surface area upon going from the unfolded to the folded state.
The model compound studies predict that the hydrophobic effect of exposing one
buried methylene group to bulk water is 0.8 kcal/mol (in Pace, 1995). The site
directed mutagenesis studies yielded a larger number with greater statistical
variation: the average hydrophobic effect estimated by SDM for a buried methylene
group is about 1.3 kcal/mol. However, when the SDM results for methylene were
plotted against the size of the cavity created by the residue substitution, and
extrapolated to zero, the result at zero cavity size is 0.8 kcal/mol - in
agreement with the value found for the transfer of model compounds from octanol to
water (Pace et al., 1996 and references therein). In the SDM studies, cavities
created by residue substitution have an additional destabilizing effect: the loss
of favourable VDWs interactions (as compared to the wild-type). Thus, the
"hydrophobic effect" measured by SDM includes both an entropic component due to
solvent ordering and a (primarily) enthalpic component due to loss of VDWs
contacts within the protein.
Such an SDM study of T4 lysozyme replaced the 80% buried Ile3 residue by Val
(Eriksson et al, 1992): the loss of this methyl group gave rise to a decrease in
stability of 0.6 kcal/mol (corrected to 100% burial). This is smaller than
expected (c.f. 0.8 kcal/mol for methylene) and suggests that the mutation
introduced some smaller stabilizing influence, perhaps such as the alleviation of
strain within the protein.
Correlation between the number of side chain methylene and methyl groups, in a
radius of 6 Å of the group deleted from wild-type, and the changes in the free
energy of unfolding for mutations of hydrophobic residues in barnase. (Taken from
Serrano et al, 1992. with permission)
The average free energy decrease for removal of a completely buried methylene
group was found to be 1.5±0.6 kcal/mol. This is additive, such that Ile or Leu to
Ala can destabilize a protein by up to 5 kcal/mol. (Remember that many mesophilic
proteins are stable by <10 kcal/mol, so two deletions such as this would be enough
to destabilize a protein completely).
Hydrogen Bonds
A hydrogen bond occurs when two electronegative atoms, such as nitrogen and
oxygen, interact with the same hydrogen. The hydrogen is normally covalently
attached to one atom, the donor, but interacts electrostatically with the other,
the acceptor. This interaction is due to the dipole between the electronegative
atoms and the proton.
There is a geometric component involved in hydrogen bonds, and for single donor
acceptor systems, such as N-H---O, the strongest hydrogen bonds are collinear
(Creighton, 1993 and references therein). Electrostatic calculations suggest that
deviation of 20° from linearity leads to a decrease in binding energy of
approximately 10% (Pimentel & McClellan, 1960).
In double acceptor systems, bifurcated hydrogen bonds with non-linear angles are
preferred. The occurrence of hydrogen bonds in protein structure has been
extensively reviewed by Baker & Hubbard (1984), albeit before the pdb database was
as large as it is today. They found that 90% of N-H---O bonds in proteins lie
between 140 and 180°, and that they are centred around 158°C. For C=O---H, the
range is more broadly distributed between 90° and 160° and centred around 129°.
The strength of a hydrogen bond is between 2 and 10 kcal/mol, and one might think
that this is the amount of energy one hydrogen bond contributes towards
stabilization of a folded protein. However, in the unfolded state, all potential
hydrogen bonding partners in the extended polypeptide chain are satisfied by
hydrogen bonds to water. When the protein folds, these protein-to-water H-bonds
are broken, and only some are replaced by (often sub-optimal) intra-protein H-
bonds. McDonald & Thornton (1994) showed that while only 1.3% of backbone amino
groups and 1.8% of carbonyl groups in proteins fail to H-bond (without any
obviously compensating interactions), 80% of main chain carbonyls fail to form a
second hydrogen bond. Thus, if one considers enthalpy terms alone, it would appear
that hydrogen bonding is destabilizing to folded protein structure.
However, one must also consider entropy. When a protein folds, and those hydrogen
bonds that the protein made to bulk water are broken, the entropy of the solvent
increases. The balance between the entropy and enthalpy terms are close, and in
the recent past it was considered that H-bonds made no contribution overall to
protein stability. But, it is now generally accepted that H-bonds make a positive
contribution to protein stabilisation (reviewed in Pace et al., 1996).
Estimation of the contribution of hydrogen bonding to protein stability has been
made by a combination of experiments on model compounds and site-directed
mutational (SDM) studies. The difficulty with the SDM studies is that when a
smaller residue replaces a larger one, a cavity is created. For example, mutating
Asn to Ala creates a cavity of 37.4 Å3 (Harpaz et al , 1994). This cavity may then
be filled by water, replacing the hydrogen bonding of the asparagine NH group.
Even in more conservative mutations such as Thr to Val (which is isosteric) or Ser
to Ala, one must take into account the contribution of side chain entropy and the
hydrophobic effect to the ( G) values. Dissection of the latter contributions
from those due only to hydrogen bonds is not trivial. An estimation has been made
of a positive contribution of 1.5±1.0 kcal/mol (Pace et al., 1996, Fersht, 1987)
from the formation of a buried intramolecular uncharged hydrogen bond. However, in
order to form, the unfavourable interaction energy from burial of a polar group
must be overcome. Thus, the net energy gain for formation of a buried H-bond is
approximately 0.6 kcal/mol.
Despite the small contribution made to protein stability by hydrogen bonds, we
must remember that if we break or delete an intramolecular hydrogen bond in a
protein without the possibility of forming a compensating H-bond to solvent, that
protein will be destabilized. In globular proteins, much of the H-bonding
potential of the backbone amide and carbonyl groups is satisfied by the formation
of regular structure such as alpha helix and beta sheet (links to PPS); regular
structure comprises 80 - 90% of globular protein structure.
There is evidence that hydrogen bonds contribute to stability in hyper-
thermostable proteins. A comparison of glyceraldehyde-3-phosphate dehydrogenase
(GADH) from four organisms with a range of thermostabilities and more than 50%
sequence identity found that the strongest correlation to thermostability was with
the number of buried charged residues H-bonded to buried neutral residues (Tanner
et al, 1996). The rationalization given for this preference of charged-to-neutral
over neutral-to-neutral or charged-to-charged residue H-bonding was as follows:
The enthalpy of H-bond formation is in the order, charged-to-charged > charged-to-
neutral > neutral-to-neutral, but the entropic cost of desolvation is in the
inverse order. The greatest overall free energy benefit is proposed to be for the
charged-to-neutral H-bonds.
Salt Bridges
Salt bridges or ion-pairs are a special form of particularly strong hydrogen bonds
made up of the interaction between two charged residues.
The contribution of salt bridges to protein stability is a somewhat contentious
issue in the literature. On the one hand is the observation that thermophilic and
hyper-thermophilic analogues of mesophilic proteins tend to have increased numbers
of salt-bridges (Tanner et al., 1996; Perutz & Raidt, 1975; Perutz, 1978; Dekker
et al., 1991). On the other hand are mutational studies showing that the
contribution of salt bridges to stability is small. Perhaps at higher temperatures
salt bridges make more of a contribution to stability.
Horovitz et al . (1990) measured the stability of a surface salt bridge triad
between Asp8, Asp12 and Arg110 on the surface of barnase by construction of a
thermodynamic cycle of all possible combinations of 1, 2, or 3 alanine mutants.
The free energy contribution to the stability of the protein is only 1.25 kcal/mol
for the Asp12/Arg110 pair and 0.98 kcal/mol for the Asp8/Arg110 pair. Removal of
Arg 110 has no effect on stability!
Other studies have had similar results (Akke & Forsen, 1990). One reason that
these contributions are not as large as might be expected from the strength of
such an ion pair is that, in order form a salt bridge, strong hydrogen bonds with
water have to be broken. In fact, it is possible that most of the energy of
stabilization comes from the increase in solvent entropy upon formation of the ion
pair.
In contrast to surface salt bridges, removal of one partner from a buried salt
bridge leads to destabilization of 3-4 kcal/mol. However, it has been found that
replacing a buried salt-bridge triad by well packed hydrophobic residues (found by
random mutagenesis at the three charged residue positions) leads to an increase in
stability of 4.5 kcal/mol in the arc repressor (Waldburger et al., 1995). Thus,
hydrophobic interactions contribute more to stability than a salt bridge triad.
This is illustrated below and is presumably due to the cost of desolvating the
charged groups on going from the unfolded to the folded state. The mutant is R31M,
E36Y, R40L.
Interestingly, it was also shown that the wild-type arc repressor folds between 10
and 1250 more slowly than the mutant (Waldburger et al., 1996). This is proposed
to be due to the high energy barrier to burying charged residues. The transition
state would have a particularly high energy if one charged residue had to be
buried before the other. Even if the salt bridge had formed prior to the
transition state, the geometry of the salt bridge might well be sub-optimal until
that part of the protein attained its native conformation. Hydrophobic
interactions have less of a steric requirement.
Aromatic-Aromatic Interactions
About 60% of the aromatic side chains (Phe, Tyr, and Trp), found in proteins are
involved in aromatic pairings. Studies with model compounds suggest that the
optimal geometry is perpendicular, such that the partially positively charged
hydrogens on the edge of one ring can interact favourably with the pi electrons
and partially negatively charged carbons of the other. From these observations, it
might be expected that such interactions make a contribution to protein stability.
This has been tested on the solvent exposed Tyr13 / Tyr17 pair on the surface of
barnase (Serrano et al., 1991). Tyr13 and Tyr17 were mutated to both Ala and Phe.
Mutation of the Tyr13 or Tyr17 to Phe leads to a decrease in stability of 0.30 or
0.41 kcal/mol, and 0.61 kcal/mol in the double mutant. As both hydroxyl groups are
exposed to solvent (as they would be in the unfolded state), it is unclear as to
the source of this small destabilization. However, mutation to the double alanine
mutant leads to a decrease in stability of 4.6 kcal/mol. Most of this
destabilization can be explained in terms of the loss of interactions between the
tyrosine residues and the rest of the protein; however, analysis of the data using
thermodynamic cycles (Carter, 1984; Horovitz & Fersht, 1990) indicates that the
interaction energy between the two aromatic groups contributes only 1.3 kcal/mol
to the protein stability. This is only very slightly higher than the stabilization
expected from the hydrophobic contribution from burying surface area between them.
In this case, therefore, there is little apparent extra stabilization due to the
aromatic pair.
Metal Binding
Another method by which the folded state of proteins can be stabilized is metal
binding, in which metal ions are coordinated, usually by lone pair donation from
oxygen or nitrogen atoms.
Experiments have shown that metal binding can contribute 6 - 9 kcal/mol (Braxton,
1996 and references therein) to stability. However, this is a little misleading as
the comparisons made are between the apo- and the holo- enzyme; in the apo-enzyme
there is often a destabilising cluster of negative charge from coordinating acidic
side chains. Perhaps a fairer estimation of the contribution of metal binding to
protein stability comes from an experiment in which a metal chelating site was
introduced into an alpha helix of iso-cytochrome c and gave rise to a 1 kcal/mol
increase in stability in the presence of saturating Cu(II) (Kellis et al., 1991).
Another interesting study was that of Kuroki et al. (1989). They observed that the
sequence and tertiary structure of alpha-lactalbumin (Ca2+ binding) and c-type
lysozymes (non-Ca2+ binding) are homologous.
They recruited the binding site from alpha-lactalbumin into human c-type lysozyme
(Q86D/A92D). The mutant protein binds one mole of calcium ions and has optimal
activity at about 10°C higher than the wild-type. Interestingly, the apo-enzyme is
about 5 °C less stable than wild-type.
Disulphide Bonds
Disulphide bonds are formed by the oxidation of two cysteine residues to form a
covalent sulphur-sulphur bond which can be intra- (examples are shown in Jane
Richardson's Protein Tourist kinamage) or inter- (exemplified by insulin at this
PPS link) molecular bridges.
One might imagine that as the enthalpy of a covalent disulphide bond is very high,
it contributes a great deal to stability. However, this bond is present in both
the folded and the unfolded state, thus its enthalpic contribution to the free
energy difference is negligible. All of the stabilizing effect of a disulphide
bond is proposed to come from the decrease in conformational entropy of the
unfolded state, as described in Conformational Entropy of Unfolding, above.
Calculations suggest that a disulphide bond should give rise to 2.5 - 3.5 kcal/mol
of stabilization, depending on the primary sequence separation between the
crosslinks (Braxton, 1996). Experiments in which naturally occurring disulphides
are either mutated to alanine, or chemically reduced and blocked, lead to
decreased stability ranging from 2 - 8 kcal/mol (Betz, 1993 and references
therein). Unfortunately, because these experiments also leave cavities, or buried
polar groups, or otherwise have more consequences than just removal of the
disulphide bridge, it is hard to estimate the stabilization due to crosslinks
alone.
Introduction of novel disulphides into proteins has also had mixed results. Five
disulphides have been introduced into T4 lysozyme (which has no disulphides in the
wild-type). Two are destabilizing, and three are stabilizing relative to their
reduced form, but all five are destabilized relative to wild-type (Betz, 1993)!
However, there have been successful stabilizations by introduction of disulphides:
The stability of RNase Hn is increased by 2.8 kcal/mol upon introduction of a
disulphide. Engineering disulphides into the ribonuclease barnase gave rise to
increased stability of 1.2 and 4.1 kcal/mol (Clarke et al., 1995). Interestingly,
the former disulphide encompasses a loop of 34 residues, while the latter
encompasses 17.
If the stabilization is purely due to conformational entropy, the magnitude of
stabilization would be the opposite way round; further, the degree of
stabilization observed for the 17 residue loop (4.1 kcal/mol) is higher than would
be predicted by the theory (Betz, 1993 ). Thus, it is clear that we are still far
from understanding the role of disulphides in protein structure.
It is worth noting that small proteins are often naturally rich in disulphide
bonds, perhaps, when the geometry is optimal, they compensate for the small number
of non-covalent interactions.
Disulphide linkages are rare in hyper-thermostable proteins, presumably because
they are chemically labile at high temperatures .
Disulphides can also contribute a great deal to Kinetic Stability .
V Chemical Degradation
It should be mentioned that however stable a protein can be made by stabilizing
the folded state, the ultimate limit of protein stability must come from covalent
degradation. At high temperatures (80 - 120 °C) Asn and Gln are susceptible to
deamidation, Asp-Xaa peptide bonds are susceptible to hydrolysis, disulphides
bonds rupture, and Xaa-Pro peptide bonds undergo cis-trans isomerisation (where
Xaa is any amino acid).
Interestingly, the upper limit for protein chemical thermostability may be higher
than one would calculate from studies involving model mesophilic enzymes. Apart
from the trivial response of just avoiding these residues (disulphides are absent
and Asn/Gln content is reduced in hyper-thermophiles), it is observed that the
deamidation rate of Gln and Asn residues is reduced, presumably by steric
constraint, in fully folded hyper-thermophilic structures (Vielle & Zeikus, 1996
and references therein).
VI Conclusions
This dissertation has discussed some of the many forces that make small and
conflicting contributions to protein stability. It is the sum of these various
stabilising and destabilising interactions that gives rise to the final stability
of a protein. The total destabilising and the total stabilising energies are both
large, and their difference is small. This is one of the reasons that current
computational methods struggle to predict protein stability from structure.
Furthermore, our understanding of these many forces is incomplete; as often as not
mutations have the opposite effect to that which had been predicted. In addition,
the activation energy for folding is an important determinant of both kinetic
stability and whether a protein will fold to a global minimum. However, it also
clear that great strides have been made, and the search for the solution to The
Folding Problem, one of the great remaining questions in biology, is and continues
to be, an exciting one.
Chapter -20
Study of drug stratgies
INTRODUCTION
DNA is the carrier of all genetic information in most organisms and thus a
biological molecule of paramount importance. DNA replication and transcription are
the basic steps in the processes of cell division and gene expression. DNA
replication and transcription are regulated by several small DNA binding proteins
such as transcription factors and polymerases. A number of molecules have been
artificially created that mimic the interactions between the DNA and these
regulatory proteins. These molecules have served as useful drugs that can be used
to inibit, activate or modulate the processes of DNA replication and
transcription by binding to the DNA instead of the regulatory proteins. Though the
actions of activation and modulation are possible, mostly DNA is targeted in an
inhibitory mode, to destroy cells for antitumor and antibiotic action.
We are already aware of the Watson and Crick model of DNA double helix in which
there are two sugar phosphate backbone strands running spirally around each other
in an antiparallel fashion and between them base pairs stacked one above the
other. DNA binding drugs interact with DNA either non-covalently or covalently.
NON COVALENT INTERACTIONS
Non covalent interactions are generally reversible. Drugs that undergo non
covalent interactions with the DNA can be classified into two main classes:
• Minor Groove binders
• Intercalators
Minor groove binding drugs are usually shaped such that they easily fit into
the groove. The binding mainly is promoted by van der Waals interactions. These
drugs can also form hydrogen bonds with N-3 of adenine and O-2 of thymine.
Generally minor groove binding has negligible influence on the conformation of
DNA. Most minor groove binding drugs bind to A/T rich sequences.
Example: Berenil.
Recently, a few synthetic polyamides like lexitropsins and imidazole-pyrrole
polyamides specific forG-C and C-G regions in the grooves have been designed.
These polyamides are linked systems that recognize DNA base pairs through specific
orientation of imidazole (Im) and pyrrole (Py) rings.
Example: The eight ring hairpin polyamide ImPyPyPy-g-ImPyPyPy-b-Dp (Dp
dimethylamino propylamide) has been found to inhibit the expression of 5S RNA in
fibroblast cells (skin cancer cells) by blocking the transcription factor IIIA-
binding site.
INTERCALATORS
COVALENT INTERACTIONS
It platinates N-7 of guanine on the major groove site of DNA double helix. This
leads to the cross-linking of two adjacent guanines on the same DNA strand
hindering the mobility of DNA polymerases.
COUNTER IONS
DNA carries a large negative charge because of the phosphate backbone.
Therefore, small positively charged counter ions such as Na+, or Ca++ and Mg++
ions may be present around the DNA. The counter ions can effectively screen the
negative backbone surface thereby allowing non electrolytes as well as positively
charged drug ligands to interact more strongly with the target base pairs.
SOLVENT
In the process of drug DNA binding, a displacement of solvent from the binding
site on both the DNA and drug takes place. There also occurs a partial
compensation of charges as the DNA and drug are oppositely charged which causes
some partially solvated counterions to be released into the bulk solvent and
become fully solvated.
Hydrophobic effect is the major driving force of hydrophobic ligand receptor
interaction. It is seen in the case of intercalating drugs as the hydrophobic,
aromatic sidechains interact favorably with the aromatic environment of the base
pair stacking.
STRUCTURAL MODIFICATIONS
So that the DNA and the drug molecule can accommodate each other, some structural
deformation/adaptation occurs in both.
Cancer cells exhibit rapid cell division. They lose the property of contact
inhibition and do not undergo appoptosis. Chemotherapy makes use of DNA binding
drugs to kill cancerous cells. The chemotherepeutic drugs bind to the DNA of the
cancer cells and halt the cell division. When the cancer cells fail to divide they
die, ultimately causing the entire tumor to shrink. Some of the important DNA
binding drugs used in chemotherapy are cisplatin, amifosatine and mitomycin C.
Hair loss
Nausea
Low RBC count
Decreased immunity
Faliure of certain organs
Even death.
For designing better drug delivery strategies, we should focus upon the
differences between cancer cells and normal cells at olecular level. Conventional
methods target rapidly dividing cells. The disadvantge of this approach is that,
it cannot distinguish cancer cells from the stem cells, which leads to a number
serious side effects.
The properties of cancer cells that are unique to them should be exploited for
drug targetting. A few moleculare features of cancer cells that may serve as
molecular targets in chemotherapy are listed below-
Cancer cells have been found to be much less adhesive to other cells and non
cellular substrates. It is this lack of adhesiveness that permits cancer cells to
metastasize. This happens because of the expression of new cell surface proteins
reffered to as tumor associated antigens in cancer cells that can induce
modiications at the cell surface, thereby leading to the loss of adhesiveness.
Cancer cells require large amounts of glucose for energy production and
growth. When cells become cancerous, they require more energy and the level of
proteins needed for glucose transport and metabolism increases.
These differences could be employed for transpoting the DNA binding drugs to the
cancer cells without affecting the healthy cells of the body.
A DNA binding drug binds with the DNA based on simple rules of chemistry.
The interactions that stablise most drug-DNA complexes are simple hydogen bonds,
hydrophobic effects and electrostatic interations.
The whole concept rounds upto the fact that the product (drug DNA complex)
must be more stable than the starting elemnt - unbound drug.
CONCLUSION
Thus, we see that DNA binding drugs of all categories have displayed a
promising potential in the treatment various deadly viral diseases and cancers.
For this reason they have become targets of clinical research across the globe.
DNA binding drugs such as cis-Platin have revolutionised chemotherapy so that now
it is possible to completely root out cancers. However, there several hurdles
still to be cleared before these drugs can be considered as a safe cure for
cancer. The scientific community understands this and therefore full fledged
research work is being conducted in several big research institutes and
laborataries to design better and safer drugs.
SUMMARY
• Certain molecules are able to mimic the naturally occuring DNA binding
proteins such as transcription factors and DNA polymerases.
• These molecules are used as drugs that can be bound physically to the DNA
for interrupting key cellular activities such as DNA replication and gene
expression.
• DNA drug interactions can be covalent or non covalent.
• DNA binding drugs can be grouped into 3 categories – minor groove binders,
intercalators and covalent binders.
• Important forces contributing to drug DNA interactions are- hydrophobic
force, hydration/dehydration energies, van der waals interactions and hydrogen
bonds, ion effects, etc
• Sveral DNA binding drugs have played an invaluable role in cancer
chemotherapy, such as cis-Platin, daunomycin, and so on.
• Side effects of chemotherapy can be minimised by designing strategies for
efficient drug targetting and destabilising the drug-DNA complexes in healthy
cells.
Assignment
Structural Biology
Introduction to DNA
2. Replication: DNA is responsible for its own regeneration, i.e., DNA self
replicates.
DNA is present in the body in the form of a double helix, where each strand is
composed of a combination of four nucleotides, adenine (A), thymine (T), guanine
(G) and cytosine (C). Within a strand these nucleotides are connected via
phosphodiester linkages. The two strands are held together primarily via Watson
Crick hydrogen bonds where A forms two hydrogen bonds with T and C forms three
hydrogen bonds with G (Figure2).
Transcription and replication are vital to cell survival and proliferation as well
as for smooth functioning of all body processes. DNA starts transcribing or
replicating only when it receives a signal, which is often in the form of a
regulatory protein binding to a particular region of the DNA. Thus, if the binding
specificity and strength of this regulatory protein can be mimicked by a small
molecule, then DNA function can be artificially modulated, inhibited or activated
by binding this molecule instead of the protein. Thus, this synthetic/natural
small molecule can act as a drug when activation or inhibition of DNA function is
required to cure or control a disease (Table 1).
DNA and Drug Binding
DNA activation would produce more quantities of the required protein, or could
induce DNA replication; depending on which site the drug is targeted. DNA
inhibition would restrict protein synthesis, or replication, and could induce cell
death. Though both these actions are possible, mostly DNA is targeted in an
inhibitory mode, to destroy cells for antitumor and antibiotic action.
Drugs bind to DNA both covalently as well as non-covalently.
Upon administration, a chloride ligand undergoes slow displacement with water (an
aqua ligand) molecules, in a process termed aquation. The aqua ligand in the
resulting [PtCl(H2O)(NH3)2]+ is easily displaced, allowing cisplatin to coordinate
a basic site in DNA. Subsequently, the platinum cross-links two bases via
displacement of the other chloride ligand.[1] Cisplatin crosslinks DNA in several
different ways, interfering with cell division by mitosis. The damaged DNA elicits
DNA repair mechanisms, which in turn activate apoptosis when repair proves
impossible.
Non-covalently bound drugs :
1. Minor groove binders- Minor groove binding drugs are usually crescent
shaped, which complements the shape of the groove and facilitates binding by
promoting van der Waals interactions. Additionally, these drugs can form hydrogen
bonds to bases, typically to N3 of adenine and O2 of thymine. Most minor groove
binding drugs bind to A/T rich sequences.
Table 1. Drug, action and mode of binding for some DNA binding drugs.
1. Neidle, S., Thurston, D.E. (2005) Chemical approaches to the discovery and
development of cancer therapies Nat Rev Cancer, 5, 285-96.
2. Geierstanger, B.H., Wemmer, D.E. (1995) Complexes of the minor groove of DNA.
Annu. Rev. Biophys. Biomol. Struct., 24, 463-493.
3. Chaires, J. B. (1998) Drug--DNA interactions. Curr. Opin. Struc. Biol., 8, 314-
320.
4. Neidle, S. (2001) DNA minor-groove recognition by small molecules. Nat. Prod.
Rep., 18, 291-309.
5. Hurley, L. H. (2002) DNA and its associated processes as targets for cancer
therapy. Nature Reviews Cancer, 2, 188-200.
6. Wemmer, D. E., Dervan, P. B. (1997) Targeting the minor groove of DNA. Curr.
Opin. Struc. Biol., 7, 355-61.
7. Jones, S, van Heyningen, P, Berman, H. M., Thornton, J. M. (1999) Protein-DNA
interactions: A structural analysis. J. Mol. Biol., 287, 877-896.
8. Jen-Jacobson, L. (1997) Protein-DNA recognition complexes: conservation of
structure and binding energy in the transition state. Biopolymers, 44,153-180.
9. Janin, J. (1999) Wet and dry interfaces: the role of solvent in protein-protein
and protein-DNA recognition. Structure Fold Des., 7, R277-279.
10. Turner, P. R., Denny, W. A. (2000) The genome as a drug target: sequence
specific minor groove binding ligands Curr. Drug Targ., 1, 1-14.
11. Goodsell, D. S. (2001) Sequence recognition of DNA by lexitropsins. Curr. Med.
Chem., 8, 509-516.
12. Reddy, B. S., Sondhi, S. M., Lown, J. W. (1999) Synthetic DNA minor groove-
binding drugs. Pharmacol. Ther., 84, 1-111.
13. Dervan, P. B., Edelson, B. S. (2003) Recognition of the DNA minor groove by
pyrrole-imidazole polyamides. Curr. Opin. Struct. Biol., 13, 284-299.
14. Jayaram, B., Beveridge, D.L. (1996) Modeling DNA in aqueous solutions:
theoretical and computer simulation studies on the ion atmosphere of DNA. Annu.
Rev. Biophys. Biomol. Struct., 25, 367-394.
15. Auffinger, P., Westhof, E. (1998) Simulations of the molecular dynamics of
nucleic acids. Curr. Opin. Struct. Biol., 8, 227–236.
STRUCTURAL BIOLOGY ASSIGNMENT
DNA-DRUG INTERACTION
MADE BY:
DNA is present in the body in the form of a double helix, where each strand is
composed of a combination of four nucleotides, adenine (A), thymine (T), guanine
(G) and cytosine (C). Within a strand these nucleotides are connected via
phosphodiester linkages. The two strands are held together primarily via Watson
Crick hydrogen bonds where A forms two hydrogen bonds with T and C forms three
hydrogen bonds with G (Figure2).
Fig.2 Watson Crick Base pairing, A-T and G-C base pairing
DNA-Drug Interaction :
Transcription and replication are vital to cell survival and proliferation as well
as for smooth functioning of all body processes. DNA starts transcribing or
replicating only when it receives a signal, which is often in the form of a
regulatory protein binding to a particular region of the DNA. Thus, if the binding
specificity and strength of this regulatory protein can be mimicked by a small
molecule, then DNA function can be artificially modulated, inhibited or activated
by binding this molecule instead of the protein. Thus, this synthetic/natural
small molecule can act as a drug when activation or inhibition of DNA function is
required to cure or control a disease (Table 1).
DNA activation would produce more quantities of the required protein, or could
induce DNA replication; depending on which site the drug is targeted. DNA
inhibition would restrict protein synthesis, or replication, and could induce cell
death. Though both these actions are possible, mostly DNA is targeted in an
inhibitory mode, to destroy cells for antitumor and antibiotic action.
Non-covalently bound drugs mostly fall under the following two classes:
2. Intercalators-
These contain planar heterocyclic groups which stack between adjacent DNA base
pairs. The complex, among other factors, is thought to be stabilized by π-π
stacking interactions between the drug and DNA bases. Intercalators introduce
strong structural perturbations in DNA.
The structure of the antibiotic triostin A shows the presence of two quinoxaline
(groups to the right; double aromatic rings) units linked through a cyclic peptide
structure (center left) which is stabilized at its center by a cystein pair
(disulfhydril covalent bond).
The space filled side view indicates how the two quinoxaline rings are positioned
by the linker peptide in co-planar fashion suitable for intercalating with DNA
base pairs. As a rule, the more intercalating sidechains are linked within a
single ligand structure, the stronger the expected binding affinity.
Triostatin A belongs to a family of antibiotics which are characterized by cross-
linked octapeptide rings bearing two quinoxaline chromophores. Since the spacing
between the chromophores is 3.5A, the intercalation process sandwiches two base
pairs between the two quinoxalines. This phenomenon is called bis-intercalation
and has first been described for echinomycin by showing that bis-intercalating
drugs cause twice the DNA helix extension and unwinding seen as compared to single
intercalating molecule like ethidium. The latter is a chromophore which is
activated by UV light and is used by molecule biologists to label nucleic acids in
gel electrophoresis or ion gradient centrifugation.
The following characteristics of non covalent bond formation are associated with
the binding sites indicated above:
Hairpin minor grove binding molecules have been identified and synthesized that
bind to GC reach nucleotide sequences. Hairpin polyamides are linked systems that
exploit a set of simple recognition rules for DNA base pairs through specific
orientation of imidazole (Im) and pyrrole (Py) rings. The hairpin polyamides
originated from the discovery of the three-ring Im-Py-Py molecule that bound to
minor groove DNA as an antiparallel side by side dimer.
Fig. Structure of hairpin ligand (right) on DNA minor groove (left)
The compound was found to recognize GC base pairs. Solid phase synthesis of
polyamides of variable length has produced efficient ligands, e.g. the eight ring
hairpin polyamide ImPyPyPy-g-ImPyPyPy-b-Dp (Dp dimethylamino propylamide) shown in
the figure above. This small synthetic molecule has an binding constant in the
order of 0.03nM.
The optimal goal of polyamide ligand design has been reached with finding
structures able to recognize DNA sequences of specific genes. The structure shown
above inhibits the expression of 5S RNA in fibroblast cells (skin cancer cells) by
interfering with the transcription factor IIIA-binding site.
A new strategy of rational drug design exploits the combination of polyamides with
bis-intercalating structures. WP631 is a dimeric analog of the clinically proven
anthracycline antibiotic daunorobuicin.
Fig. Structure of WP631
This new synthetic compound shows an affinity of 10pM and also showed to be
resistant against multidrug resistance mechanisms often encountered in antitumor
therapy. Multidrug resistance is a phenomenon where small aromatic compounds are
efficiently expelled from the cell by cell membrane transport proteins commonly
referred to as ABC transporters (or ATP Binding Cassette proteins).
Structural and conformational changes in the DNA and drug on binding in solution
are associated with enthalpic and entropic contributions to the binding free
energy, which can be theoretically estimated from ensembles of structures
generated via simulations. The only drawback of this approach is the long time
taken for the simulations.
The other terms, namely, electrostatics, van der Waals, hydrophobic component,
rotational and translational entropy can be estimated from single structures.
The web tool, PreDDICTA, estimates the components of DNA-drug binding free energy
which can be calculated from a single structure, and correlates it with
experimental binding free energy and ∆Tm, thus providing a swift method for
evaluation of potential lead candidates for researchers pursuing structure based
drug design for DNA.
Chapter-21
Technique to study protein
Introduction:
Proteins are fundamental components of all living cells. They exhibit an enormous
amount of chemical and structural diversity, enabling them to carry out an
extraordinarily diverse range of biological functions. Scientists know that the
critical feature of a protein is its ability to adopt the right shape for carrying
out a particular function. But sometimes a protein twists into the wrong shape or
has a missing part, preventing it from doing its job. Many diseases, such as
Alzheimer's and "mad cow", are now known to result from proteins that have adopted
an incorrect structure.
X-ray Crystallography
. The basic building block of a crystal is called a unit cell. Each unit cell
contains exactly one unique set of the crystal's components, the smallest possible
set that is fully representative of the crystal. Crystals of a complex molecule,
like a protein, produce a complex pattern of X-ray diffraction, or scattering of
X-rays. When the crystal is placed in an X-ray beam, all of the unit cells present
the same face to the beam; therefore, many molecules are in the same orientation
with respect to the incoming X-rays. The X-ray beam enters the crystal and a
number of smaller beams emerge: each one in a different direction, each one with a
different intensity. If an X-ray detector, such as a piece of film, is placed on
the opposite side of the crystal from the X-ray source, each diffracted ray,
called a reflection, will produce a spot on the film. However, because only a few
reflections can be detected with any one orientation of the crystal, an important
component of any X-ray diffraction instrument is a device for accurately setting
and changing the orientation of the crystal. The set of diffracted, emerging beams
contains information about the underlying crystal structure.
Nuclear Magnetic Resonance(NMR)Spectroscopy
1-D spectra contain the information about all the chemical shifts of all the H in
the protein. The frequency resolution is often not enough to distinguish
individual chemical shifts. 2-D NMR solves these problems by containing
information about the relative position of H in molecular structures. 2-D NMR
spectra contain information about interaction between H that is covalently linked
through one or two other atoms (COSY or correlation spectroscopy). Alternatively,
pairs of H that can be close in space, even if they are from residues that are not
close in sequence (NOE spectra, or Nuclear Overhauser Effect). A complete
structure can thus be calculated by sequentially assigning cross peak correlations
in 2-D spectra. Currently, the size limit for proteins amenable to NMR solution
structure analysis is about 200 amino acids. An important feature of the
identification of cross peaks is that regular patterns can be recognized that stem
from secondary structure elements such as alpha helices and parallel or anti-
parallel beta sheets because they contain typical hydrogen bonding networks.
NMR also requires the knowledge of the amino acid sequence, but the protein does
not have to be in an ordered crystal, yet high concentrations of solubilized
protein must be available (NMR structures are therefore also called solution
structures). In biopolymers, the primary structure (sequence) logically breaks up
the molecule into groups of coupled spins normally one or two groups per residue.
This is true not only for proteins, but also for nucleic acids and
polysaccharides.
The distances measured in this way for both the 6-s-cis- and 6-s-trans-retinoic
acid model compounds agreed well with crystallographically known distances. In
bacteriorhodopsin the exchange trajectory between C-8 and C-18 was in good
agreement with the internuclear distance for a 6-s-trans configuration [4.2
angstroms (A)] and inconsistent with that for a 6-s-cis configuration (3.1 A). The
results illustrate that rotational resonance can be used for structural studies in
membrane proteins and in other situations where diffraction and solution NMR
techniques yield limited information.
Structure of bacteriorhodopsin:
General:
Current strategies for determining the structures of membrane proteins in lipid
environments by NMR spectroscopy rely on the anisotropy of nuclear spin
interactions, which are experimentally accessible through experiments performed on
weakly and completely aligned samples. Importantly, the anisotropy of nuclear spin
interactions results in a mapping of structure to the resonance frequencies and
splittings observed in NMR spectra. Distinctive wheel-like patterns are observed
in two-dimensional 1H-15N heteronuclear dipolar/15N chemical shift PISEMA
(polarization inversion spin-exchange at the magic angle) spectra of helical
membrane proteins in highly aligned lipid bilayer samples. One-dimensional dipolar
waves are an extension of two-dimensional PISA (polarity index slant angle) wheels
that map protein structures in NMR spectra of both weakly and completely aligned
samples. Dipolar waves describe the periodic wave-like variations of the
magnitudes of the heteronuclear dipolar couplings as a function of residue number
in the absence of chemical shift effects. Since weakly aligned samples of proteins
display these same effects, primarily as residual dipolar couplings, in solution
NMR spectra, this represents a convergence of solid-state and solution NMR
approaches to structure determination
References:
2. Wikipedia.
3. Biochemistry by Lehninger,
Chapter no.4:
“The three dimensional structure of Proteins”, page no.116.
Chapter-22
Enzymology of DNA folding and unfolding
WHAT IS DNA???
DNA STRUCTURE
DNA is a long polymer made from repeating units called nucleotides.[1][2] The DNA
chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit
is 3.3 Ångstroms (0.33 nanometres) long.[3] Although each individual repeating
unit is very small, DNA polymers can be enormous molecules containing millions of
nucleotides. For instance, the largest human chromosome, chromosome number 1, is
220 million base pairs long.[4]
In living organisms, DNA does not usually exist as a single molecule, but instead
as a tightly-associated pair of molecules.[5][6] These two long strands entwine
like vines, in the shape of a double helix. The nucleotide repeats contain both
the segment of the backbone of the molecule, which holds the chain together, and a
base, which interacts with the other DNA strand in the helix. In general, a base
linked to a sugar is called a nucleoside and a base linked to a sugar and one or
more phosphate groups is called a nucleotide. If multiple nucleotides are linked
together, as in DNA, this polymer is referred to as a polynucleotide.[7]
The backbone of the DNA strand is made from alternating phosphate and sugar
residues.[8] The sugar in DNA is 2-deoxyribose, which is a pentose (five carbon)
sugar. The sugars are joined together by phosphate groups that form phosphodiester
bonds between the third and fifth carbon atoms of adjacent sugar rings. These
asymmetric bonds mean a strand of DNA has a direction. In a double helix the
direction of the nucleotides in one strand is opposite to their direction in the
other strand. This arrangement of DNA strands is called antiparallel. The
asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′
(three prime) ends. One of the major differences between DNA and RNA is the sugar,
with 2-deoxyribose being replaced by the alternative pentose sugar ribose in
RNA.[6]
The DNA double helix is stabilized by hydrogen bonds between the bases attached to
the two strands. The four bases found in DNA are adenine (abbreviated A), cytosine
(C), guanine (G) and thymine (T). These four bases are shown below and are
attached to the sugar/phosphate to form the complete nucleotide, as shown for
adenosine monophosphate.
These bases are classified into two types; adenine and guanine are fused five- and
six-membered heterocyclic compounds called purines, while cytosine and thymine are
six-membered rings called pyrimidines.[6] A fifth pyrimidine base, called uracil
(U), usually takes the place of thymine in RNA and differs from thymine by lacking
a methyl group on its ring. Uracil is not usually found in DNA, occurring only as
a breakdown product of cytosine, but a very rare exception to this rule is a
bacterial virus called PBS1 that contains uracil in its DNA.[9] In contrast,
following synthesis of certain RNA molecules, a significant number of the uracils
are converted to thymines by the enzymatic addition of the missing methyl group.
This occurs mostly on structural and enzymatic RNAs like transfer RNAs and
ribosomal RNA.[
0]
Animation of the structure of a section of DNA. The bases lie horizontally between
the two spiraling strands. Large version[11]
The double helix is a right-handed spiral. As the DNA strands wind around each
other, they leave gaps between each set of phosphate backbones, revealing the
sides of the bases inside (see animation). There are two of these grooves twisting
around the surface of the double helix: one groove, the major groove, is 22 Å wide
and the other, the minor groove, is 12 Å wide.[12] The narrowness of the minor
groove means that the edges of the bases are more accessible in the major groove.
As a result, proteins like transcription factors that can bind to specific
sequences in double-stranded DNA usually make contacts to the sides of the bases
exposed in the major groove.[13]
Replication
Cell division is essential for an organism to grow, but when a cell divides it
must replicate the DNA in its genome so that the two daughter cells have the same
genetic information as their parent. The double-stranded structure of DNA provides
a simple mechanism for DNA replication. Here, the two strands are separated and
then each strand's complementary DNA sequence is recreated by an enzyme called DNA
polymerase. This enzyme makes the complementary strand by finding the correct base
through complementary base pairing, and bonding it onto the original strand. As
DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different
mechanisms are used to copy the antiparallel strands of the double helix.[71] In
this way, the base on the old strand dictates which base appears on the new
strand, and the cell ends up with a perfect copy of its DNA
DNA DENATURATION :
The two DNA strands, which form the double helix, are in opposite orientations
(one runs in 5'-3'direction, the complementary in 3'-5'direction) and are
connected by hydrogen bonds (see DNA structure). The rupture of these hydrogen
bonds causes the DNA to separate or to "denature". Inside the cell, a partial
separation of the DNA strands is necessary for replication and transcription and
is caused by several proteins that use ATP. But in vitro the rupture of the
hydrogen bonds can be caused by heat, alcaline conditions or chemical compounds
Distilled water can also cause some degree of denaturation. It inhibits the
neutralisation of the phosphate groups by salts like magnesium or sodium. The
negative charge of the phopsphate group causes a repulsion and therefore a
physical separation of the DNA strands.
Chemical compounds like urea or formamide denature the DNA by directly reacting
with the bases, thereby preventing normal base-pairing. The Tm is reduced
proportionally to the concentration of denaturating chemical agents. If we
decrease the concentration of either urea or formamide, DNA will renature again.
Urea is used in denaturing gels to sequence DNA.
DNA RENATURATION :
The temperature at which DNA is half unfolded is called the melting temperature.
Tm is a measure of the stability of DS-DNA under a given set of conditions.
Stability, and therefore Tm, is affected by....
Base Composition - higher the GC content, the higher the Tm.
Ionic Strength - as the ionic strength increases, so does Tm. Double helical DNA
is stabilised by cations.
Divalent cations (eg Mg2+) are more effective than monovalent cations (<NA+ or
K+).
Organic Solvents - formamide for instance lowers the Tm by weakening the
hydrophobic interactions.
ADVANTAGES OF DENATURATION…
The performance and convenience of a PCR melting profile (PCR MP) technique based
on using low denaturation temperatures during ligation mediated PCR (LM PCR) of
bacterial DNA is shown. We found that PCR MP technique is a rapid method that
offers good discriminatory power, excellent reproducibility and may be applied for
epidemiological studies. Results from strain genotyping illustrate that PCR MP is
useful for the study of intraspecific genetic relatedness of strains and is as
effective in discriminating closely related strains as the PFGE method, which is
currently considered to be the gold standard for epidemiological studies. The
usefulness of the PCR MP for molecular typing was shown for clinical strains of
Escherichia coli, Enterococcus faecium VRE and Stapylococcus aureus.
3.GENOMIC SEQUENCING
Unique DNA sequences can be determined directly from mouse genomic DNA. A
denaturing gel separates by size mixtures of unlabeled DNA fragments from complete
restriction and partial chemical cleavages of the entire genome. These lanes of
DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a
short 32P-labeled single-stranded probe produces the image of a DNA sequence
"ladder" extending from the 3' or 5' end of one restriction site in the genome.
Numerous different sequences can be obtained from a single membrane by reprobing.
Each band in these sequences represents 3 fg of DNA complementary to the probe.
Sequence data from mouse immunoglobulin heavy chain genes from several cell types
are presented. The genomic sequencing procedures are applicable to the analysis of
genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein
interactions at single nucleotide resolution
4.SUPERCOIL SEQUENCING:A FAST AND SIMPLE METHOD FOR SEQUENCING PLASMID DNA
A method, using LiAc to yield competent cells, is described that increased the
efficiency of genetic transformation of intact cells of Saccharomyces cerevisiae
to more than 1 X 10(5) transformants per microgram of vector DNA and to 1.5%
transformants per viable cell. The use of single stranded, or heat denaturated
double stranded, nucleic acids as carrier resulted in about a 100 fold higher
frequency of transformation with plasmids containing the 2 microns origin of
replication. Single stranded DNA seems to be responsible for the effect since M13
single stranded DNA, as well as RNA, was effective. Boiled carrier DNA did not
yield any increased transformation efficiency using spheroplast formation to
induce DNA uptake, indicating a difference in the mechanism of transformation with
the two methods.
The dideoxy sequencing method in which denatured plasmid DNA is used as a template
was improved. The method is simple and rapid: the recombinant plasmid DNA is
extracted and purified by rapid alkaline lysis followed by ribonuclease treatment.
The plasmid DNA is then immediately denatured with alkali and subjected to a
sequencing reaction utilizing synthetic oligonucleotide primers. It takes only
several hours from the start of the plasmid extraction to the end of the
sequencing reaction. We examined each step of the procedure, and several points
were found to be crucial for making the method reproducible and powerful: (i) the
plasmid DNA should be free from RNA and open circular (or linear) DNA; (ii) a
heptadecamer rather than a pentadecamer is recommended as a primer; and (iii) the
sequencing reaction should be done at 37 degrees C or higher rather than at room
temperature. The method enabled us to determine the sequence of more than a
thousand nucleotides from a single template DNA.
The rate of renaturation of T2 DNA has been studied as a fuction of ethidium bound
per nucleotide of denatured DNA. The Binding constants and number of binding sites
for ethidium have been determined by spectral titration for denatured DNA at 55,
65, and 75°C and for native DNA at 65°C in 0.4M Na+. The rate of renaturation of
T2 DNA was found to be independentof ethidium binding up to 0.03 moles per mole of
nucleotide. Above 0.03 moles, the rate drops off precipitously approaching zero at
0.08 and 0.06 moles bound ethidium per nucleotide at 65°C respectively. A study
was also made of the use of bound ethidium fluorescence as a probe for monitoring
DNA renaturation reactions.
Solvents which accelerate DNA renaturation rates have been investigated. Addition
of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at
45°C and then leads to a loss of second-order behavior. The greatest accelerations
are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most
effective method of accelerating DNA renaturation with concentrated DNA. Addition
of dextran sulfate beyond 10-12% in 2.4M Et4NCl fails to increase the acceleration
beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35-
40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to
be more effective, although acceleration may be achieved in solvents containing
formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of
the normal concentration and temperature dependence of DNA renaturation and is
also independent of dextran sulfate concentration if sufficient dextran sulfate is
used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
Introduction
Only very few enzymes present hazards, because of their catalytic activity, to
those handling them in normal circumstances but there are several areas of
potential hazard arising from their chemical nature and source. These are
allergenicity, activity-related toxicity, residual microbiological activity, and
chemical toxicity.
All enzymes, being proteins, are potential allergens and have especially potent
effects if inhaled as a dust. Once an individual has developed an immune response
as a result of inhalation or skin contact with the enzyme, re-exposure produces
increasingly severe responses becoming dangerous or even fatal. Because of this,
dry enzyme preparations have been replaced to a large extent by liquid
preparations, sometimes deliberately made viscous to lower the likelihood of
aerosol formation during handling. Where dry preparations must be used, as in the
formulation of many enzyme detergents, allergenic responses by factory workers are
a very significant problem particularly when fine-dusting powders are employed.
Workers in such environments are usually screened for allergies and respiratory
problems. The problem has been largely overcome by encapsulating and granulating
dry enzyme preparations, a procedure that has been applied most successfully to
the proteases and other enzymes used in detergents. Enzyme producers and users
recognise that allergenicity will always be a potential problem and provide safety
information concerning the handling of enzyme preparations. They stress that dust
in the air should be avoided so weighing and manipulation of dry powders should be
carried out in closed systems. Any spilt enzyme powder should be removed
immediately, after first moistening it with water. Any waste enzyme powder should
be dissolved in water before disposal into the sewage system. Enzyme on the skin
or inhaled should be washed with plenty of water. Liquid preparations are
inherently safer but it is important that any spilt enzyme is not allowed to dry
as dust formation can then occur. The formation of aerosols (e.g. by poor
operating procedures in centrifugation) must be avoided as these are at least as
harmful as powders.
Activity-related toxicity is much rarer but it must be remembered that proteases
are potentially dangerous, particularly in concentrated forms and especially if
inhaled. No enzyme has been found to be toxic, mutagenic or carcinogenic by itself
as might be expected from its proteinaceous structure. However, enzyme
preparations cannot be regarded as completely safe as such dangerous materials may
be present as contaminants, derived from the enzyme source or produced during its
processing or storage.
The organisms used in the production of enzymes may themselves be sources of
hazardous materials and have been the chief focus of attention by the regulatory
authorities. In the USA, enzymes must be Generally Regarded As Safe (GRAS) by the
FDA (Food and Drug Administration) in order to be used as a food ingredient. Such
enzymes include α-amylase,β-amylase, bromelain, catalase, cellulase, ficin, -
galactosidase, glucoamylase, glucose isomerase, glucose oxidase, invertase,
lactase, lipase, papain, pectinase, pepsin, rennet and trypsin.
In the UK, the Food Additives and Contaminants Committee (FACC) of the Ministry
of Agriculture, Fisheries and Food classified enzymes into five classes on the
basis of their safety for presence in the foods and use in their manufacture.
Group A. Substances that the available evidence suggests are acceptable for use
in food.
Group B. Substances that on the available evidence may be regarded as
provisionally acceptable for use in food but about which further information must
be made available within a specified time for review.
Group C. Substances for which the available evidence suggests toxicity and which
ought not to be permitted for use in food until adequate evidence of their safety
has been provided to establish their acceptability.
Group D. Substances for which the available information indicates definite or
probable toxicity and which ought not to be permitted for use in food.
Group E. Substances for which inadequate or no toxicological data are available
and for which it is not possible to express an opinion as to their acceptability
for use in food.
This classification takes into account the potential chemical toxicity from
microbial secondary metabolites such as mycotoxins and aflotoxins. The growing
body of knowledge on the long-term effects of exposure to these toxins is one of
the major reasons for the tightening of legislative controls.
The enzymes that fall into group A are exclusively plant and animal enzymes such
as papain, catalase, lipase, rennet and various other proteases. Group B contains
a very wide range of enzymes from microbial sources, many of which have been used
in food or food processing for many hundreds of years. The Association of
Microbial Food Enzyme Producers (AMFEP) has suggested subdivisions of the FACC's
group B into:
Class ain8 microorganisms that have traditionally been used in food or in food
processing, including Bacillus subtilis, Aspergillus niger, Aspergillus oryzae,
Rhizopus oryzae, Saccharomyces cerevisiae, Kluyveromyces fragilis, Kluyveromyces
lactis and Mucor javanicus.
Class bin8 microorganisms that are accepted as harmless contaminants present in
food, including Bacillus stearothermophilus, Bacillus licheniformis, Bacillus
coagulans, and Klebsiella in8aerogenes.
Class cin8 microorganisms that are not included in Classes b and c, including
Mucor miehei, Streptomyces albus, Trichoderma reesei, Actinoplanes missouriensis,
and Penicillium emersonii.
It was proposed that Class a should not be subjected to testing and that Classes b
and c should be subjected to the following tests:
acute oral toxicity in mice and rats,
subacute oral toxicity for 4 weeks in rats,
oral toxicity for 3 months in rats, and
in vitro mutagenicity.
In addition Class c should be tested for microorganism pathogenicity and, under
exceptional circumstances, in vivo mutagenicity, teratogenicity, and
carcinogenicity.
The cost of the various tests needed to satisfy the legal requirements are very
significant and must be considered during the determination of process costs.
Plainly the introduction of an enzyme from a totally new source will be a very
expensive matter. It may prove more satisfactory to clone such an enzyme into one
of AMFEP's Class a organisms but this will first require new legislation to
regulate the use of cloned microbes in foodstuffs. Some of the safety problems
associated with the use of free enzymes may be overcome by using immobilised
enzymes . This is an extremely safe technique, so long as the materials used are
acceptable and neither they, nor the immobilised enzymes, leak into the product
stream.
Course Objective:
The course aims to provide an understanding of the principles and application of
proteins, secondary metabolites and enzyme biochemistry in therapeutic
applications and clinical diagnosis. The theoretical understanding of biochemical
systems would certainly help to interpret the results of laboratory experiments.
Course Contents:
Module I
Enzymes: Introduction and scope, Nomenclature, Mechanism of Catalysis.
Module II
Specificity of enzyme action, monomeric and oligomeric enzymes, Enzyme inhibition.
Module III
Enzyme Kinetics: Single substrate steady state kinetics; Michaelis Menten
equation, Linear plots, King-Altman’s method; Inhibitors and activators;
Multisubstrate systems; ping-pong mechanism, Alberty equation, Sigmoidal kinetics
and Allosteric enzymes
Module IV
Extraction & purification of enzymes.
Module V
Immobilization of Enzymes; Advantages, Carriers, adsorption, covalent coupling,
cross-linking and entrapment methods, Micro-environmental effects.
Module VI
Biotechnological applications of enzymes: Large scale production and purification
of enzymes, enzyme utilization in industry, enzymes and recombinant DNA technology
Examination Scheme:
References
• Enzymes Biochemistry, Biotechnology, Clinical Chemistry, Trevor Palner
Dr. S. M. Bhatt smbhatt@amity.edu , smbhatt_bhu@rediffmail.com phone 9313993840
Amity University Uttar Pradesh
•
• Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady State
Enzyme Systems, I.H. Segel, Wiley-Interscience
• Industrial Enzymes & their applications, H. Uhlig, John Wiley and Sons Inc.
Course Objective:
The laboratory will help the students to isolate enzymes from different sources,
enzyme assays and studying their kinetic parameters which have immense importance
in industrial processes.
Course Contents:
Module I
Isolation of enzymes from plant and microbial sources.
Module II
Enzyme assay; activity and specific activity – determination of amylase, nitrate
reductase, cellulase, protease
Module III
Purification of Enzyme by ammonium sulphate fractionation
Module IV
Enzyme Kinetics: Effect of varying substrate concentration on enzyme activity,
determination of Michaelis-Menten constant (Km) and Maximum Velocity (Vmax.) using
Lineweaver-Burk plot.
Module V
Effect of Temperature and pH on enzyme activity
Module VI
Enzyme immobilization
Examination Scheme:
Major Experiments: 40
Minor Experiments: 20
Spotting: 10
Viva: 20
Records: 10
Total: 100
Definition
Introduction
Historical aspects in enzyme discovery
Classification of Enzymes.
application of enzymes
Chapter- 1
Enzymes an introduction
Definition
Kinetics: Field of study that deals with determining the rates of biological,
chemical, and physical processes (e.g., how quickly reactants are converted into
products) under various conditions.
Metalloprotein: Protein that incorporates one or more metals into its molecular
structure by binding individual metal ions [e.g., iron (Fe2+ or Fe3+), zinc
(Zn2+), or magnesium (Mg2+)] or nonprotein organic compounds containing metals.
Metalloprotein are important components of electron transport chains.
Steady State: Growth state in which the concentration of bacterial cells is in
equilibrium with the concentration of nutrients or substrates (i.e., the
concentrations remain constant over time).
1860 Bertholate disrupted yeast cell and isolated extract that catalyzed
conversion of sucrose to glucose and fructose.
1894 Fisher proposed lock and key hypothesis to explain the mechanism of
1920 Sumner crystallized Urease first time that hydrolyze the urea into CO2 and
NH3.
1958 Koshland proposed induced fit model to account for enzyme catalytic power
and specificity.
1986 RNase was found to work as catalyst by Cech. They were called as
Classes of enzyme: there are six classes of enzyme according to reaction type they
performed
D-hexose-6-phosphotransferase (hexokinase)
D hexose + ATP------------------------------------ D hexose-6-
phosphate + ADP
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligase
Electron transfer
Group transfer
Hydrolysis
Formation of C-C,C-S,C-O,C-N.
Cytochrome oxidase
Carbonic anhydrase
Alcohol dehydrogenase
Hexokinase
Glucose -6-phosphate
Pyruvate kinase.
Arginase
Ribonucleotide reductase
Pyruvate kinase.
Urease
Dinitrogenase
Glutathione peroxidase
Fe+2 or Fe+3
Cu+2
Zn+2
Mg+2
Mn+2
K+
Ni+2
Mo
Se
Chapter-2
Types of Enzymes
A. Simple enzymes
They are composed solely of protein, single or multiple subunits. If they consist
of single polypeptide unit they are termed as monomeric enzyme ( sometime like in
chymotrypsinogen they are of three polypeptide and are inctive zymogen form and
after cleavage from pie to delta and finally to alpha trypsinogen they become
active and consist of two polypepide and still they are termed as monomeic enzyme
since they are read in continous sequences). Monomeric enzymes are of few 200-300
amino acid and molecular weight ranges from 15,000 kd to 35,000 kd (kilodalton)
like trypsin , elastases, that are termed as serine proteases because of an active
serine residue. Serine residue become active due to relay mechanism of electron
transfer (adjacent amino acid can transfer electron in series of pathway and make
the serine active sufficient to active at electron deficient or carbocation center
of substrate making breaking of bond possible. Thus a slight decrease in entropy
make free energy negative that is essential for stabilization of intermediate
transition state). Other enzyme consisting of two or more polypeptide are termed
as oligomeric enzyme. Like alcohol dehydrogenase (contains two polypeptide and
Zn+2 and act by electrostatic meechansim) and lactate dehydrogenase that requires
cofactor NAD+ or NADP+ for its activity and occurs in multiple unit like H4, H3M,
H2M2, HM3, and M4. Thus they contain four subunit and substrate can bind to each
of four subunit and they are termed as isozyme. Actually Ogstien considered three
sites on enzyme one or two binding site along with one catalytic subunit. Lactate
is formed from pyruvate in aneorbic condition and thus pyruvate accumulation are
avoided. Lactate arev then transported to other organs.
B. Complex enzymes Complex enzymes
They involve protein plus small organic molecule(s) or metal. Entire complex
called “holoenzyme”. Protein part called “apoenzyme”. Non-protein part called
“coenzyme” or “prosthetic Group”. They form the integral part of the enzyme and
remain adjacent to the catalytic center to provide coordination for interacting
with substrate functional group. Therefore multiple substrates can interact with
enzyme and react with them. The detailed mechanism will be discussed in next topic
under the head of enzyme specificities. These rules give each enzyme a unique
number.
Enzymes are also classified on the basis of their composition. Enzymes composed
completely of protein are known as simple enzymes in contrast to complex enzymes,
which are composed of protein plus a relatively small organic molecule. Complex
enzymes are also known as holoenzymes. In this terminology the protein component
is known as the apoenzyme, while the non-protein component is known as the
coenzyme or prosthetic group where prosthetic group describes a complex in which
the small organic molecule is bound to the apoenzyme by covalent bonds; when the
binding between the apoenzyme and non-protein components is non-covalent, the
small organic molecule is called a coenzyme. Many prosthetic groups and coenzymes
are water-soluble derivatives of vitamins. It should be noted that the main
clinical symptoms of dietary vitamin insufficiency generally arise from the
malfunction of enzymes, which lack sufficient cofactors derived from vitamins to
maintain homeostasis.
The non-protein component of an enzyme may be as simple as a metal
ion or as complex as a small non-protein organic molecule. Enzymes that require a
metal in their composition are known as metalloenzymes if they bind and retain
their metal atom(s) under all conditions that is with very high affinity. Those
have a lower affinity for metal ion, but still require the metal ion for activity,
are known as metal-activated enzymes.
Role of Coenzymes
A. Catalysts
Catalysts are substances that increase product formation by lowering the energy
barrier (activation energy) for the product to form and increase the favorable
orientation of colliding reactant molecules for product formation to be
successful.
There are two types of catalysts:
1. Heterogeneous Catalysts
2. Homogeneous Catalysts
Heterogeneous catalysts are those that provide a surface for the reaction to
proceed upon. The catalyst and the reactant molecules are not in the same phase.
This is sometimes referred to as surface catalysts. Certain transition state
metals like Palladium, Platinum, Nickel, and Iron serve as industrial catalysts
that catalyze a wide variety of reactions such as Hydrogenation.
Homogeneous catalysts are catalysts that exist in the same phase as the reactant
molecules usually in a solution. Acids and Bases in solution serve as catalysts in
a wide variety of Organic reactions. Most industrial catalysts are responsible for
more than one catalysis among reactants and are considered relatively non-specific
in what they catalyze. Enzymes are very different. All current research suggests
that enzymes are extremely specific in what a given enzyme catalyzes. Indeed, most
enzyme molecules catalyze only one specific reaction but it does so in a
phenomenally efficient manner. One enzyme molecule might be responsible for
converting thousands of reactant molecules called substrate molecules into
product.
B. Biocatalyst or Enzymes
ES
Free energy G
E
Enzyme lowers the activation energy.
Reaction coordinate
R= reactant
P = product
∆G = ∆H – T ∆S this is the thermodynamical term used to explain the stability
of reactions. A negative free energy stabilizes the system and makes the reaction
possible. ∆H denotes the enthalpy and ∆S denotes the entropy. In unstabilized or
uncatalysed system ∆S is positive and formation of transition complex renders
them lowering of entropy leading to make overall free energy negative. A more
ordered system also has lower entropy for example free amino acid has more entropy
than the amino acid linked with the peptide bond.
In cells and organisms most reactions are catalyzed by enzymes, which are
regenerated during the course of a reaction. These biological catalysts are
physiologically important because they speed up the rates of reactions many folds
(up to 10 6 to 10 15 times than normal one) that would otherwise be too slow to
support life. Enzymes increase reaction rates--- sometimes by as much as one
millionfold, but more typically by about one thousand fold. Catalysts speed up the
forward and reverse reactions proportionately so that, although the magnitude of
the rate constants of the forward and reverse reactions is are increased, the
ratio of the rate constants remains the same in the presence or absence of enzyme.
Since the equilibrium constant is equal to a ratio of rate constants, it is
apparent that enzymes and other catalysts have no effect on the equilibrium
constant of the reactions they catalyze. Enzymes increase reaction rates by
decreasing the amount of energy required to form a complex of reactants that is
competent to produce reaction products. This complex is known as the activated
state or transition state complex for the reaction. Enzymes and other catalysts
accelerate reactions by lowering the energy of the transition state. The free
energy required to form an activated complex is much lower in the catalyzed
reaction. The amount of energy required to achieve the transition state is
lowered; consequently, at any instant a greater proportion of the molecules in the
population can achieve the transition state. The result is that the reaction rate
is increased.
Unit of activity
Micromole substrate consumed or product formed per minute is referred as IU
international unit. SI unit is ‘katal’ that is defined as Micromole substrate
consumed or product formed per second.
Chapter 3
Enzyme Specificity
Although enzymes are highly specific for the kind of reaction they catalyze, the
same is not always true of substrates they attack. For example, while succinic
dehydrogenase (SDH) always catalyzes an oxidation-reduction reaction and its
substrate is invariably succinic acid, alcohol dehydrogenase (ADH) always
catalyzes oxidation-reduction reactions but attacks a number of different
alcohols, ranging from methanol to butanol. Generally, enzymes having broad
substrate specificity are most active against one particular substrate. In the
case of ADH, ethanol is the preferred substrate.
Enzymes also are generally specific for a particular steric configuration (optical
isomer) of a substrate. Enzymes that attack D sugars will not attack the
corresponding L isomer. Enzymes that act on L amino acids will not employ the
corresponding D optical isomer as a substrate. The enzymes known as racemases
provide a striking exception to these generalities; in fact, the role of racemases
is to convert D isomers to L isomers and vice versa. Thus racemases attack both D
and L forms of their substrate.
As enzymes have a more or less broad range of substrate specificity, it follows
that a given substrate may be acted on by a number of different enzymes, each of
which uses the same substrate(s) and produces the same product(s). The individual
members of a set of enzymes sharing such characteristics are known as isozymes.
These are the products of genes that vary only slightly; often, various isozymes
of a group are expressed in different tissues of the body. The best studied set of
isozymes is the lactate dehydrogenase (LDH) system. LDH is a tetrameric enzyme
composed of all possible arrangements of two different protein subunits; the
subunits are known as H (for heart) and M (for skeletal muscle). These subunits
combine in various combinations leading to 5 distinct isozymes. The all H isozymes
is characteristic of that from heart tissue, and the all M isozymes is typically
found in skeletal muscle and liver. These isozymes all catalyze the same chemical
reaction, but they exhibit differing degrees of efficiency. The detection of
specific LDH isozymes in the blood is highly diagnostic of tissue damage such as
occurs during cardiac infarct.
Thus enzyme may be group specific if they act over on several closely related
substrate for example alcohol dehydrogenase on which several alcohol are
substrate, or act over by specific substrate like glucokinase that transfer
phosphate from ATP to glucose. They exhibit absolute specificity. They may be of
product specific or substrate specific or stereospecific act on specific stereo
molecules like alanine recemase acts on only L–alanine to convert them into D-
alanine.
Specificity is actually decided by amino acid residue present in the active site
of enzyme that is capable of binding to the substrate molecule. The amino acids
that are not involved in binding to the substrate do not have any contribution
towards the specificity. Therefore both the subunit of enzyme like binding and
catalytic site is the active center of the enzymes. They are only small part of
the total enzyme and they must be accessible to the substrate. For example
chymotrypisn are inactive because their zymogen form don’t have accessible
catalytic center. Therefore further cleavage occurs to make them active exposing
the catalytic center. For proper catalytic activity their side chains must be of
suitable size, shape, and character and must not block the substrate from binding.
For example of several seine proteases like chymostrypsinogen, trypsin and
elastases having almost similar structure but differ in specificity due to
variations in the side chain amino acids. In Elastases substrate are blocked from
binding due to presence of two bulky side chain valine and threonine while
chymostrypsin and trypsin have no bulky group but instead contains glycine amino
acid that facilitates the substrate to approach easily. Replacement of glycine by
alanine make the enzyme more active. Active site most often contains both polar as
well as non-polar amino acid thus facilitates the interaction with both
hydrophilic and hydrophobic amino acid. This is the reason why sometime in
presence of non-polar solvent like DMSO dimethylsulphoxide some enzyme are more
reactive. Other examples include chymotrypsin, alcohol dehydrogenase, etc., ie. a
variety of enzymes from different classes have been shown to function in non-
aqueous media. Specificity May Be Very Strict Or Relatively Broad
Broad specificity is shown by many degradative enzymes e.g. alkaline phosphatase,
which removes phosphates from a wide range of molecules, or carboxypeptidase which
snips the C-terminal amino-acid off many polypeptide chains.
Intermediate specificity is most common e.g. alcohol (ethanol) dehydrogenase of E.
coli will act on C2, C3, and C4 alcohols; pyruvate dehydrogenase will also use the
C4 homolog of pyruvate etc.Some enzymes are absolutely specific. Aspartase
catalyses the interconversion of aspartate and fumarate:
L-Aspartate ↔ Fumarate + NH3
Fig . showing asymmetric binding site in the enzymes. The model of enzyme
structure was proposed by fisher as three point one catalytic site and others are
binding site. Sometime enzymes have both catalytic as well as binding site as same
site. Such enzymes follows michaelis behaviour while others having complex and
separate site behave in more complex way as allosteric site.
It will only use aspartate (not similar amino acids such as glutamate) and only
the L-isomer. Nor will it add NH3 to maleate, the cis isomer of fumarate.
Three theory were proposed to explain the specificity of enzyme but all of them
are correct and none of them are alone operative in the enzyme specificity.
1- Lock and key hypothesis
2- Induced fit hypothesis.
3- Transition state stabilization
Chapter 4
Enzyme-Substrate Interactions
The favored model of enzyme substrate interaction is known as the induced fit
model. This model proposes that the initial interaction between enzyme and
substrate is relatively weak, but that these weak interactions rapidly induce
conformational changes in the enzyme that strengthen binding and bring catalytic
sites close to substrate bonds to be altered. After binding takes place, one or
more mechanisms of catalysis generate transition- state complexes and reaction
products. The possible mechanisms of catalysis are five in number:
1. Catalysis by approximation
2. General acid, general base catalysis
3. Catalysis by electrostatic effects
4. Covalent catalyis (nucleophilic or electrophilic)
5. Catalysis by strain or distortion
d. Covalent Catalysis:
• In catalysis that takes place by covalent mechanisms, the substrate is
oriented to active sites on the enzymes in such a way that a covalent intermediate
forms between the enzyme or coenzyme and the substrate. One of the best-known
examples of this mechanism is that involving proteolysis by serine proteases,
which include both digestive enzymes (trypsin, chymotrypsin, and elastase) and
several enzymes of the blood clotting cascade. These proteases contain an active
site serine whose R group hydroxyl forms a covalent bond with a carbonyl carbon of
a peptide bond, thereby causing hydrolysis of the peptide bond. Biologically
important nucleophiles are negatively charged or contain unshared electrons
• Biologically important electrophiles generally are either positively
charged, or contain unfilled valence electron shells, or contain an
electronegative atom
Covalent Intermediates
Here the strategy is to lower the transition state energy "hump" by taking an
alternative reaction pathway therefore sometime it is also called as alternative
pathway catalysis. Sometime nucleophilic catalyst form intermediate more rapidly
than normal catalysis.
In covalent catalysis, a covalent bond is transiently formed between the substrate
and the enzyme (or coenzyme). This reaction usually involves a nucleophilic group
on the enzyme and an electrophilic group on the substrate
Uncatalysed: BX + Y BY + X
Catalysed: BX + Enz Enz-B + X
Enz-B + Y Enz + BY
Where, B is usually some chemical group such as a phosphate group, acyl group or
glycosyl group. Phosphoenzymes usually attach the phosphate to serine or
histidine. Serine type - phosphoglucomutase, alkaline phosphatase. Histidine type
- glucose 6 phosphatase, phosphotransferase system. Acyl enzymes usually attach
the acyl group at an active serine or cysteine residue. Most proteases (eg
trypsin, elastase, subtilisin are serine enzymes. Cysteine enzymes include papain
(a protease), glyceraldehyde phosphate dehydrogenase and most enzymes using acyl
CoA derivatives.
The proteases are globular, water soluble proteins that function as enzymes. They
catalyze the hydrolyses of peptide bonds in proteins. Being enzymes, proteases can
be characterized by their substrate affinity and the catalytic rate of the
reaction. Using proteases to study the effects of single amino acid substitutions
(mutations) on catalytic rate and substrate affinity demonstrated that these two
properties are linked and that this linkage can be explained by analyzing the
conformation of the catalytic or active site of the enzyme. This analysis showed
that four major functional groups are found in the catalytic site of proteases and
based on this functional groups, 4 families of proteases have been defined:
a. Serine proteases
b. Cystein proteases
c. Aspartate proteases
d. Metallo proteases
This classification uses the functional group within the enzyme, and does not
relate to the substrate specificity of the proteases themselves. The name of the
protease family refers to an amino acid (e.g. aspartate) or a metal as co-enzyme
at the active site of the enzyme.
• The serine proteases are a class of enzymes that degrade proteins in which a
serine in the active site plays an important role in catalysis.
• The family includes among many others, Chymotrypsin and trypsin, which we’ve
talked about, and Elastase.
• All three enzymes are similar in structure, and they all have three
important conserved residues–a histidine, an aspartate, and a serine.
SUMMARY
The maximum binding energy between an enzyme and a substrate will occur when there
is
maximal complementarity between the structure of the binding site and the
structure of the
substrate.
• The structure of the substrate changes during the reaction, becoming first
the transition state and then products.
• The structure of the enzyme can only be complementary to one form of the
substrate.
• If the structure of the active site is complementary to the transition
state, then binding increases as the reaction proceeds, which lowers the
activation energy.
• Having the active site bind the transition most strongly also means that
products are bound weakly, which favors dissociation of the products from the
enzyme once the reaction is complete.
• When the active site is complementary to the transition state the full
substrate binding energy is only realized as the reaction reaches the transition
state, which lowers the activation energy of the reaction by the magnitude of the
binding energy.
• It is possible that the substrate and enzyme interact unfavorably and this
unfavorable interaction is relived in the transition state.
• We might think that the substrate is under stress meaning that it is
subjected to forces but not distorted by them.
• It is more likely that the enzyme is strained, as for example in induced
fit.
Catalytic Power
Enzymes lower the energy of the transition state by stabilizing the original
reaction intermediate or by providing an alternative reaction pathway. Rate
increases by enzymes range from 108 to 1020 relative to the uncatalysed,
spontaneous reaction (e.g. 109 for alcohol dehydrogenase; 1016 for alkaline
phosphatase). Factors involved in enzyme rate increases: a) Proximity - up to 106
fold; b)Orientation - up to 100 fold c) Covalent enzyme-substrate intermediates -
around 1010 fold d) General acid-base catalysis - around 1010 fold ;e) Metal ion
catalysis - around 1010 fold; f) Distortion of the substrate - up to 108 fold (but
largely hypothetical)
a) Proximity
The enzyme binds the substrate so that the susceptible bond is very close to the
catalytic group in the active site or in close proximity in the active site. It
increases their concentration and and reduces entropy loss for subsequent
formation of a transition state. This has been called as proximation effect or
approximation effect. Therefore it appears that enzyme bound transition state is
the single most in determining whether the reaction should proceed. Calculations
indicate that the local concentration of substrate in the active site may be as
much as 50M whereas its concentration in the cytoplasm may be less than 1mM. Since
chemical reaction rates are proportional to the concentrations of the reactants a
rate enhancement of up to 106 may be generated by local concentration effects.
This effect is counteracted to some extent by the fact that the concentration of
enzyme active sites is low (the active site is a small portion of a very large
molecule; the total protein concentration in cytoplasm is 1 to 10mM at most).
b) Orientation
Proximity alone is insufficient. The reacting groups must be properly oriented.
Orbital steering hypothesis - binding of the substrate(s) to the enzyme aligns the
reactive groups so that the relevant molecular orbitals overlap. This increases
the probability of forming the transition state. For a typical bimolecular
reaction in free solution about 1/100 collisions between molecules of sufficient
energy actually leads to a reaction. Thus the maximum effect of orientation would
be 100-fold.
Consider the attack on an aryl ester by a carboxylic acid.
Now let's put both reacting groups on the same molecule - i.e. we will link R1 and
R2 together. As the five examples show, the relative rate gets greater as the
reacting groups are brought closer together. In addition, holding them in the
correct orientation also helps. (Ar = methoxyphenyl group.)
Enzymes are biological catalysts. With the exception of ribozymes, enzymes are
mainly proteins in nature, and may also possess lipid or sugar moieties. Their
main task is to decrease the activation energy (Eact) of a chemical reaction. The
whole biotechnology field depends on the activities of enzymes, either acting
alone or in concert.
Exploitation of enzymes is not a recent development. They have been used
throughout the ages in leather tanning, in cheese-making, in the preparation of
malted barley for beer brewing & the leavening of bread. These processes use
enzymes in the form of whole cells. Conceptually, it is easy to decide whether one
should use whole cells or isolated enzymes in a biotechnological process to
produce or transform compounds. Some processes require multi-step transformations,
eg. the synthesis of antibiotics, interferons, monoclonal antibodies, or ethanol
production from glucose. These transformations involve a number of enzymes acting
sequentially, along with the requirement for co-factor regeneration in several
steps. They are clearly candidates for using whole cells.
There may be some drawbacks to using whole cells in catalysis. These include
1. Competing side reactions from other enzymes.
2. Sterility problems often arise when one deals with whole cells.
3. Some conditions may lead to cell lysis, and this can result in loss of
biocatalysts or severely decrease reaction rate depending on the nature and type
of enzyme reaction.
4. Formation of by-products.
5. On the other hand, with one-step or two-step stereospecific transformations,
enzymes can be superior because their use will eliminate some of the potential
problems with using whole cells. The advantages of using enzymes include:
6. High catalytic rate possible.
7. Functions in moderate conditions.
8. Non-polluting catalysis.
9. Less by-products formed.
10. Less problem with sterility.
11. Optimizing 1 or 2 enzyme catalyzed reactions is easier than optimizing the
whole pathway in a whole cell.
12. Enzymes catalyze a wide range of reactions, some with high
stereospecificity, such as oxidation, reduction, dehydrogenation, dehalogenation,
hydration, dehydration, etc. Therefore, the scope of enzyme technology is very
broad.
13. Despite all these striking characteristics, enzyme have not been used widely
as compared to chemical catalysis. This is because the use of enzymes also suffers
from some serious drawbacks:
14. Most isolated enzymes are not stable enough for use under industrial
conditions. This may include poor stability with respect to temperature, pH, the
presence of metal ions, etc. This is not surprising considering that most enzymes
have evolved to function in a biological milieu where the conditions may differ
from those used in industry.
15. In cells, all enzymes are subject to turnover, ie. old ones are replaced by
new ones. This is difficult to do with isolated enzymes in vitro.
16. Most enzymes are water-soluble, and therefore, may be difficult to separate
from reactants or products.
17. Many useful enzymes are intracellular, and hence are difficult to isolate.
Abzymes
Catalytic antibodies are also known as abzymes, are capable of catalyzing specific
chemical reactions. They are able to perform this task because they have been
elicited against antigen known as transition state analogues, these are molecules
that closely resemble in shape and charge the reaction transition state (the
highest energy spices in reaction pathway known as activated complex). Enzyme
observed to bind transition complex but not the substrate, and the product. Enzyme
by forming the active site similar to the transition state, enzyme stabilizes or
lowers down the energy of this species. The effect is to accelerate the reaction
because the activation barrier is more easily overcome. This complementarity in
shape and charge to the transition state is readily demonstrated by the
effectiveness of transition state analogue is a phosphonate containing molecule
that mimics the transition state of the hydrolysis of the corresponding acyl
derivative. When an ester is hydrolysed the central carbonyl group changes from
planer sp2 structure to tetrahedral sp3. the phosphonate containing molecule
analogue is able to reproduce the shape of the transition state as well as the
partially negative charged oxygen. In addition, it is chemically stable, where as
the actual transition state exists only fleetingly. In this example, an enzyme
that catalysed the hydrolysis of this ester would also bind tightly to phosphonate
analogue. The general strategies behind the production of catalytic antibody is to
(i) design and synthesize a molecule whose shape is closely resemble to that of
transition state of the reaction one wishes to catalyze, (2) tether this molecule
to larger molecule, (3) elicit an immune response to this conjugate, (4) screen
the resultant monoclonal antibodies for catalytic activity of the type desired.
Antibodies that are elicited against transition state analogue and therefore have
the ability to bind them will be chemically and sterically complementary to the
transition state and will therefore be potentially capable of catalyzing the
reaction.
Table 7. 1
Exercises
LONG TYPE
1. Describe the six classes of enzyme with examples?
2. Define Biocatalyst ? Describe how biocatalyst lower down the activation
energy?
3. Define Enzyme ? Classify the Enzyme on the basis of enzyme commission?
4. Define holoenzyme ? write the role of apoenzyme, cofactor, and
metalloenzymes on enzyme activity.
5. Define enzyme specific activity? Write the different method of enzyme
substrate interaction in brief?
Short type
1. write short notes on following
a. Enzyme activity
b. Enzyme specificity
c. Enzyme commission.
d. Holoenzyme.
e. Cofactor
f. Metalloenzymes.
g. Coenzyme.
Module II
Specificity of enzyme action, monomeric and oligomeric enzymes, Enzyme inhibition.
Chapter-5
ENZYME KINETICS & INHIBITION
TERMS
Enzymes are protein catalysts of biological origin that, like all catalysts, speed
up the rate of a chemical reaction without being used up in the process. They
achieve their effect by temporarily binding to the substrate.
Competitive inhibition, when the substrate and inhibitor compete for binding to
the same active site.
Noncompetitive inhibition, when the inhibitor binds somewhere else on the enzyme
molecule reducing its efficiency.
Enzyme kinetics The study of the rate at which an enzyme works is called enzyme
kinetics.
Alloenzymes. If a gene exists in a heterozygous state, two different polypeptide
chains will be generated. They may be separated by gel electrophoresis under
favourable conditions. They may also differ in their rate of substrate turnover.
The gene product a, for example, may be inactive while that of A is fully active.
But all states in between are also possible. Furthermore, it was shown in numerous
examples that A may be favourable under certain environmental conditions while a,
is favourable under other conditions (more in the section about evolution).
Polypeptides (enzymes) that are encoded by different alleles are called
alloenzymes.
Isoenzymes. By duplication of the genetic material a gene may be present within a
haploid genome for two or more times. It is not important whether the gene loci
are on one chromosome or distributed over several chromosomes. The gene products
(enzymes) of the different gene loci (pseudoalleles) are called isoenzymes.
Competitive inhibitors are molecules that bind to the same site as the substrate -
preventing the substrate from binding as they do so - but are not changed by the
enzyme.
Noncompetitive inhibitors are molecules that bind to some other site on the enzyme
reducing its catalytic power.
INTRODUCTION
A B----------------------------1
-[A] = k[B]-----------------------2
[B] = k[A]--------------------3
In the second equation (of the 3 above) the negative sign signifies a decrease in
concentration of A as the reaction progresses, brackets define concentration in
molarity and the k is known as a rate constant. Rate constants are simply
proportionality constants that provide a quantitative connection between chemical
concentrations and reaction rates. Each chemical reaction has characteristic
values for its rate constants; these in turn directly relate to the equilibrium
constant for that reaction. Thus, reaction can be rewritten as an equilibrium
expression in order to show the relationship between reaction rates, rate
constants and the equilibrium constant for this simple case. The rate constant for
the forward reaction is defined as k+1 and the reverse as k-1.
At equilibrium the rate (v) of the forward reaction (A B) is by
definition is equal to that of the reverse or back reaction (B A), a
relationship which is algebraically symbolized as:
V forward = v reverse---------------4
V forward = k+1[A]---------------5
V reverse = k-1[B]----------------6
In the above equations, k+1 and k-1 represent rate constants for the forward and
reverse reactions, respectively. The negative subscript refers only to a reverse
reaction, not to an actual negative value for the constant. To put the
relationships of the two equations into words, we state that the rate of the
forward reaction [v forward] is equal to the product of the forward rate constant
k+1 and the molar concentration of A. The rate of the reverse reaction is equal to
the product of the reverse rate constant k-1 and the molar concentration of B.
At equilibrium, the rate of the forward reaction is equal to the rate of the
reverse reaction leading to the equilibrium constant of the reaction and is
expressed by:
This equation demonstrates that the equilibrium constant for a chemical reaction
is not only equal to the equilibrium ratio of product and reactant concentrations,
but is also equal to the ratio of the characteristic rate constants of the
reaction.
FIGURE 10. 1
FIGURE 10. 2
For this reaction the forward reaction rate would be written as:
V forward = k1 [ADP][H2PO4]---------------9
L. Michaelis and M. Menten in 1913 postulated that enzyme first combine reversibly
with the substrate to form an enzyme substrate complex in a relatively fast
reversible step and then product is released along with free enzyme.
Initial velocity
Michaelis-Menton constant
E + S ES ES* EP E +
P-------------------10
and
K1
E+S ES ………. 11
k-1
The ES complex then breaks down in a slower second step to
yield the free enzyme and the reaction product P: k2
ES -------- E+P ……………..(12)
Since the second step is slower and therefore it limits the rate of overall
reaction. It means that, overall rate of enzyme-catalyzed reaction must be
proportional to the concentration of species that reacts in the second step, which
is ES.
At any time the enzyme-catalyzed reaction, the enzyme exists in the combined form
E or uncombined form ES. At low [S], most of the enzyme will be in uncombined form
E. here the rate will be proportional to the [s] because the equilibrium of
equation will shift for the formation of more ES as S is increased. The maximum
initial rate is observed when the entire enzyme E0 is present as ES complex and
the concentration of E is very small. Under these state the enzyme is “saturated”
with its substrate, so that further increase in [S] have no effect on rate. This
is the condition when [S] is sufficiently high that essentially all the free
enzyme is converted into the ES form. After the ES complex breaks down to yield
product P the enzyme is free to catalyze another reaction.
a. Pre-steady state:--
The duration in which ES formation takes place is called as pre-steady
state. It is too difficult to observe because of very short time.
b. Steady state:--
Here ES complex is constant over a period of time.
Derivation:
To Simplify the equation add the term k1[E] [S] to both side, we finally get
K1[Et][S]
[ES] = ------------------
--------------------------------(20)
k1[S] + k-1+ k2
or
[Et][S]
[ES] = ------------------
--------------------------------(21)
[S] +( k-1+ k2)/ k1
The term ( k-1+ k2)/ k1 is called as Michaelis—Menten equation, the rate equation
of one substrate, enzyme catalyzed reaction and is denoted by the Km. this defines
the rate of initial velocity and maximum velocity. Putting value of ES in equation
21 from equation 13 gives new final equation that is
What will happen if the initial velocity is exactly one-half of maximum velocity?
So if V0 = Vmax/2, then
--------------------24
This represent that Km is equivalent to the substrate concentration at which Vo is
one half Vmax. Note that Km has unit of molarity. This shows that the Michaelis-
Menten constant equals the substrate concentration at half-maximal reaction
velocity. Consequently, the dimension of kM is Mol. The smaller the value of kM ,
the higher is the enzyme's affinity for its substrate. See figure 10.3. Km is
(roughly) an inverse measure of the affinity or strength of binding between the
enzyme and its substrate. The lower the Km, the greater the affinity (so the lower
the concentration of substrate needed to achieve a given rate).
Note :for the Michaelis-Menten reaction, k2 is the rate limiting ; thus
k2<<k-1
So Km reduces to
Km=k-1/k1, and it is defined as dissociation constant,
Ks for the ES complex.
Figure 10. 4 Graphical method to find the value of Km by plotting the graph
between the 1/Vo verses 1/[S]
10.4 Catalytic efficiency and Turnover number.
Catalytic efficiency is denoted by the ratio of Kcat/ Km. K cat is the turn over
number of enzyme . See from the table below the enzyme having very high value of
Kcat have high capacity to convert substrate into the product The turnover number
is a measure of catalytic activity. The kcat is a direct measure of the catalytic
production of product under saturating substrate conditions.l kcat, the turnover
number, is the maximum number of substrate molecules converted to product per
enzyme molecule per unit of time. According to M-M model, k cat = Vmax /Et.
Values of k cat range from less than 1/sec to many millions per sec. in multistep
enzymatic reaction, one step may be rate limiting that rate limiting step is
equivalent to Kcat. Equation 22 can be written as by placing the value of Vmax =
Kcat x Et
-------------------26
figure 10. 5 showing turn over number of different enzyme. Note that high the TON
of an enzyme, best is the enzyme for maximum conversion of substrate into the
product.
FIGURE 10. 6
The constant Kcat has unit S-1, reciprocal of time. Note that two enzymes
catalyzing different reaction may have the same Kcat value (turnover number) yet
the rate may be different. It also denotes about the reaction between the enzyme
and substrate since at low K cat, Km value will also be unsatisfactory. From
equation 26, Vo depends on both Et and S, therefore K cat /Km is a second order
rate constant. Therefore Kcat /Km is the best way to compare the catalytic
efficiency of the enzyme. Many enzymes have K cat /Km value in the range 108 to
109 .
FIGURE 10. 7
The kinetics of simple reactions like that above was first characterized by
biochemists Michaelis and Menten. The concepts underlying their analysis of enzyme
kinetics continue to provide the cornerstone for understanding metabolism today,
and for the development and clinical use of drugs aimed at selectively altering
rate constants and interfering with the progress of disease states.
ENZYME KINETICS
It is also useful to write down two other definitions and assumptions before we
continue:
1. The first thing we need to realize is that the total concentration of enzyme in
all of its forms
should be equal to the original free enzyme concentration:
2. The second point is that the rate of the reaction should be equal to formation
of products, so
the initial velocity, vo, and maximum possible velocity, or Vmax, obtained when
all the enzyme
is substrate-bound, can be written as
Now, before making the steady-state approximation, we can look at the kinetic
scheme above
and deduce that the rate of change in the concentration of the enzyme-substrate
complex should
be equal to the rate of formation of the complex minus the rate of decay of the
complex. The rate
of formation is dependent upon the rate constant k+2 and the enzyme and substrate
complexes.
The rate of decay involves two possible pathways. One is to form products, and the
other is to
reform the reactants. Therefore the rate of decay of the enzyme-substrate complex
will be the
sum of two rate constants, k+2 and k-1. Therefore we can write
and from the steady-state approximation, this has to equal zero. Before making
this
approximation, that equation is insoluble. Now, however, you can solve it fairly
simply (despite
what I did in class). First, if the steady-state approximation holds, then you can
rearrange the
equation to look like this:
Now group all of the rate constants together
We can define this collection of rate constants as something called the Michaelis
Constant, or
Km. Note that this is not an equilibrium constant.
Now we have an even simpler expression:
We are almost done. However, we want an expression in terms of constants and
measurable quantities such as the substrate concentration, [S], and the initial
velocity, vo. To get the equation into that form, we need two things from above.
The first is our statement that the total enzyme concentration is equal to the
concentration of enzyme in all of its forms, which in turn is the same as the
starting concentration of enzyme, i.e.,E total = Eo = [E] + [ES] or conveniently
[E] = [Eo] – [ES] more, . Then we can substitute that into our previously
simplified equation to obtain
Solve for ES
Chapter-6
Factor affecting the rate of catalysis.
1- Substrate concentration.
2- Temperature
3- pH
4- Inhibitors
3. The presence of inhibitors. The study of the rate at which an enzyme works
is called enzyme kinetics. Many toxic substances owe their toxic properties to
their ability to act as inhibitors (slow down the rate of reactions by different
mechanism) to important enzymes responsible for catalyzing important biochemical
processes. Once the enzyme is inhibited the process cannot take place, and a
toxicological symptom occurs that often leads to paralysis, coma or even death of
the organism. For example, cyanide poisoning is due to the cyanide ion
competitively inhibiting the active site of the cytochromases enzymes responsible
for catalyzing the Oxidation and Reduction processes of the Electron Transport
System which is responsible for cellular respiration.
Competitive Inhibition occurs when a molecule that is close enough to the shape of
the true substrate will fit into the active site. Once locked into position, the
blocker molecule prevents the true substrate molecule from getting into position.
This effectively blocks the active site. The molecule competes for the active site
with the true substrate molecule which is concentration dependent. If the
concentration of substrate becomes more than the inhibitor they may replace the
inhibitor later on. This is the reason why ethyl alcohol is given to person that
has consumed the toxic alcohol (methyl alcohol) so that methyl alcohol can be
competitively replaced by ethyl alcohol.
Other inhibitors latch themselves not to the active site itself but to some
portion of the enzyme molecule close to the active site which results in the
changing of the shape of the active site. This is referred to as non-competitive
inhibition or mixed inhibition. Many heavy metals like Lead, Mercury, and Chromium
will function as non-competitive inhibitors. Toxicology is the study of how
toxicological substances can interfere with life sustaining enzymes via
inhibition.
The pesticide and herbicide industries make use of competitive and Non-Competitive
Inhibitors. Biological warfare owes its success to enzyme inhibition but so does
the life giving chemotherapeutic treatment of cancerous tumor growths with agents
that inhibit important cancel cell enzymes. All in all the use of inhibitors can
be used for the benefit of mankind or its destruction.
FIGURE 10. 8
FIGURE 10. 9
10.4.2 Effect of temperature and pressure
Every enzyme has a temperature range of optimum activity. Outside that temperature
range the enzyme is rendered inactive and is said to be totally inhibited. This
occurs because as the temperature changes this supplies enough energy to break
some of the intramolecular attractions between polar groups (Hydrogen bonding,
dipole-dipole attractions) as well as the Hydrophobic forces between non-polar
groups within the protein structure. When these forces are disturbed and changed,
this causes a change in the secondary and tertiary levels of protein structure,
and the active site is altered in its conformation beyond its ability to
accommodate the substrate molecules it was intended to catalyze. Most enzymes (and
there are hundreds within the human organism) within the human cells will shut
down at a body temperature below a certain value which varies according to each
individual. This can happen if body temperature gets too low (hypothermia) or too
high (hyperthermia).
Temperature is an important factor in the regulation of enzyme activity. At some
temperature activity becomes zero and at some temperature enzyme efficiency of
conversion of substrate into product becomes high. Of all most important factor is
the active site, because active site contains amino acid residues inside the
pocket, and the ability of these residue to interact with the substrate functional
group and capacity to breaking and making bonds is certainly going to be effected
by the .
Rates of all reactions, including those catalyzed by enzymes, rise with increase
in temperature in accordance with the Arrhenius equation.
K = A e –ΔG*/RT --------------27
OR
log K = log A –EA /2.3 RT
where k is the kinetic rate constant for the reaction, A is the Arrhenius
constant, also known as the frequency factor, ΔG* =EA is the standard free energy
of activation (kJ M-1) which depends on entropic and enthalpy factors, R is the
gas law constant and T is the absolute temperature. Typical standard free energies
of activation (15 - 70 kJ M-1) give rise to increases in rate by factors between
1.2 and 2.5 for every 10°C rise in temperature. This factor for the increase in
the rate of reaction for every 10°C rise in temperature is commonly denoted by the
term Q10 (i.e. in this case, Q10 is within the range 1.2 - 2.5). All the rate
constants contributing to the catalytic mechanism will vary independently, causing
changes in both Km and Vmax. It follows that, in an exothermic reaction, the
reverse reaction (having higher activation energy) increases more rapidly with
temperature than the forward reaction. This, not only alters the equilibrium
constant, but also reduces the optimum temperature for maximum conversion as the
reaction progresses. The reverse holds for endothermic reactions such as that of
glucose isomerase where the ratio of fructose to glucose, at equilibrium,
increases from 1.00 at 55°C to 1.17 at 80°C.
In general, it would be preferable to use enzymes at high temperatures in order to
make use of this increased rate of reaction plus the protection it affords against
microbial contamination. Enzymes, however, are proteins and undergo essentially
irreversible denaturation (i.e.. conformational alteration entailing a loss of
biological activity) at temperatures above those to which they are ordinarily
exposed in their natural environment. These denaturing reactions have standard
free energies of activation of about 200 - 300 kJ mole-1 (Q10 in the range 6 - 36)
which means that, above a critical temperature, there is a rapid rate of loss of
activity (Figure 8.5). The actual loss of activity is the product of this rate and
the duration of incubation (Figure 8.6). It may be due to covalent changes such as
the deamination of asparagine residues or non-covalent changes such as the
rearrangement of the protein chain. Inactivation by heat denaturation has a
profound effect on the enzymes productivity (Figure 8.7).
________________________________________
FIGURE 10. 10
FIGURE 10. 11
A schematic diagram showing the effect of the temperature on the activity of an
enzyme catalyzed reaction. —— short incubation period; ----- long incubation
period. Note that the temperature at which there appears to be maximum activity
varies with the incubation time.
________________________________________
________________________________________
FIGURE 10. 12
A schematic diagram showing the effect of the temperature on the productivity of
an enzyme catalyzed reaction. —— 55°C; —— 60°C; —— 65°C. The optimum productivity
is seen to vary with the process time, which may be determined by other additional
factors (e.g. overhead costs). It is often difficult to get precise control of the
temperature of an enzyme catalyzed process and, under these circumstances, it may
be seen that it is prudent to err on the low temperature side.
where T is the absolute temperature (K), R is the gas law constant (8.314 J M-1 K-
1), Δ H is the heat of ionisation and the numeric constant (2.303) is the natural
logarithm of 10, as pKa's are based on logarithms with base 10. This variation is
sufficient to shift the pI of enzymes by up to one unit towards lower pH on
increasing the temperature by 50°C.
These charge variations, plus any consequent structural alterations, may be
reflected in changes in the binding of the substrate, the catalytic efficiency and
the amount of active enzyme. Both Vmax and Km will be affected due to the
resultant modifications to the kinetic rate constants k+1, k-1 and kcat (k+2 in
the Michaelis-Menten mechanism), and the variation in the concentration of active
enzyme. The effect of pH on the Vmax of an enzyme catalysed reaction may be
explained using the, generally true, assumption that only one charged form of the
enzyme is optimally catalytic and therefore the maximum concentration of the
enzyme-substrate intermediate cannot be greater than the concentration of this
species. In simple terms, assume EH- is the only active form of the enzyme,
The variation of activity with pH, within a range of 2-3 units each side of the
pI, is normally a reversible process. Extremes of pH will, however, cause a time-
and temperature-dependent, essentially irreversible, denaturation. In alkaline
solution (pH > 8), there may be partial destruction of cystine residues due to
base catalysed b-elimination reactions whereas, in acid solutions (pH < 4),
hydrolysis of the labile peptide bonds, sometimes found next to aspartic acid
residues, may occur. The importance of the knowledge concerning the variation of
activity with pH cannot be over-emphasized. However, a number of other factors may
mean that the optimum pH in the Vmax-pH diagram may not be the pH of choice in a
technological process involving enzymes. These include the variation of solubility
of substrate(s) and product(s), changes in the position of equilibrium for a
reaction, suppression of the ionization of a product to facilitate its partition
and recovery into an organic solvent, and the reduction in susceptibility to
oxidation or microbial contamination. The major such factor is the effect of pH on
enzyme stability. This relationship is further complicated by the variation in the
effect of the pH with both the duration of the process and the temperature or
temperature-time profile. The important parameter derived from these influences is
the productivity of the enzyme (i.e. how much substrate it is capable of
converting to product). The variation of productivity with pH may be similar to
that of the Vmax-pH relationship but changes in the substrate stream composition
and contact time may also make some contribution. Generally, the variation must be
determined under the industrial process conditions. It is possible to alter the
pH-activity profiles of enzymes. The ionisation of the carboxylic acids involves
the separation of the released groups of opposite charge. This process is
encouraged within solutions of higher polarity and reduced by less polar
solutions. Thus, reducing the dielectric constant of an aqueous solution by the
addition of a co-solvent of low polarity (e.g. dioxan, ethanol), or by
immobilisation, increases the pKa of carboxylic acid groups. This method is
sometimes useful but not generally applicable to enzyme catalysed reactions as it
may cause a drastic change on an enzyme's productivity due to denaturation (. The
pKa of basic groups are not similarly affected as there is no separation of
charges when basic groups ionise. However, protonated basic groups which are
stabilised by neighbouring negatively charged groups will be stabilised (i.e. have
lowered pKa) by solutions of lower polarity. Changes in the ionic strength (I) of
the solution may also have some effect. The ionic strength is defined as half of
the total sum of the concentration (ci) of every ionic species (i) in the solution
times the square of its charge (zi); i.e. I=0.5Σ(CiZi2) .For example, the
ionic strength of a 0.1 M solution of CaCl2 , is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3
M. At higher solution ionic strength, charge separation is encouraged with a
concomitant lowering of the carboxylic acid pKas. These changes, extensive as they
may be, have little effect on the overall charge on the enzyme molecule at neutral
pH and are, therefore, only likely to exert a small influence on the enzyme's
isoelectric point. Chemical derivatisation methods are available for converting
surface charges from positive to negative and vice-versa. It is found that a
single change in charge has little effect on the pH-activity profile, unless it is
at the active site. However if all lysines are converted to carboxylates (e.g. by
reaction with succinic anhydride) or if all the carboxylates are converted to
amines (e.g. by coupling to ethylene diamine by means of a carbodiimide the
profile can be shifted about a pH unit towards higher or lower pH, respectively.
The cause of these shifts is primarily the stabilisation or destabilisation of the
charges at the active site during the reaction, and the effects are most
noticeable at low ionic strength.
The ionic strength of the solution is an important parameter affecting enzyme
activity. This is especially noticeable where catalysis depends on the movement of
charged molecules relative to each other. Thus both the binding of charged
substrates to enzymes and the movement of charged groups within the catalytic
'active' site will be influenced by the ionic composition of the medium. If the
charges are opposite then there is a decrease in the reaction rate with increasing
ionic strength whereas if the charges are identical, an increase in the reaction
rate will occur (e.g. the rate controlling step in the catalytic mechanism of
chymotrypsin involves the approach of two positively charged groups, 57histidine+
and 145arginine+ causing a significant increase in kcat on increasing the ionic
strength of the solution). Even if a more complex relationship between the rate
constants and the ionic strength holds, it is clearly important to control the
ionic strength of solutions in parallel with the control of pH.
FIGURE 10. 14 showing molecule activation at high and low temperature
Enzyme Substrate Product Rate without
Enzyme
µmoles/L
per min Rate with
Enzyme
µmoles/L
per min Acceleration
due to Enzyme
Hexokinase Glucose Glucose
6-Phosphate <.0000001 1300 > 13 billion
Phosphorylase <.000000005 1600 > 320 billion
Alcohol
Dehydrogenase Ethanol Acetaldehyde <.000006 2700 > 450 million
Creatine
Kinase Creatine Creatine
Phosphate <.003 40 > 13, 000
o From: Daniel Koshland, Jr. Molecular geometry in enzyme action. Journal of
Cellular & Comparative Physiology 47: 217-234, 1956.
Chapter-7
Enzyme inhibition
A number of substances may cause a reduction in the rate of an enzyme catalysed
reaction. Some of these (e.g. urea) are non-specific protein denaturants. Others,
which generally act in a fairly specific manner, are known as inhibitors. Loss of
activity may be either reversible, where activity may be restored by the removal
of the inhibitor, or irreversible, where the loss of activity is time dependent
and cannot be recovered during the timescale of interest. If the inhibited enzyme
is totally inactive, irreversible inhibition behaves as a time-dependent loss of
enzyme concentration (i.e.. lower Vmax), in other cases, involving incomplete
inactivation.There may be time-dependent changes in both Km and Vmax. Heavy metal
ions (e.g. mercury and lead) should generally be prevented from coming into
contact with enzymes as they usually cause such irreversible inhibition by binding
strongly to the amino acid backbone.
More important for most enzyme-catalysed processes is the effect of reversible
inhibitors. These are generally discussed in terms of a simple extension to the
Michaelis-Menten reaction scheme.
--------------------42
where I represents the reversible inhibitor and the inhibitory (dissociation)
constants Ki and Ki' are given by
--------------------43
and,
--------------------------44
For the present purposes, it is assumed that neither EI nor ESI may react to form
product. Equilibrium between EI and ESI is allowed, but makes no net contribution
to the rate equation as it must be equivalent to the equilibrium established
through:
------45
Binding of inhibitors may change with the pH of the solution, as discussed earlier
for substrate binding, and result in the independent variation of both Ki and Ki'
with pH.
In order to simplify the analysis substantially, it is necessary that the rate of
product formation (k+2) is slow relative to the establishment of the equilibria
between the species.
Therefore:
-----------46
also
----------------------------47
where:
-----------48
therefore
---------------49
Substituting from equations (43), ( 44) and (46), followed by simplification,
gives:
--------------50
therefore
--------------51
If the total enzyme concentration is much less than the total inhibitor
concentration (i.e. [E]0<< [I]0), then:
--------------------52
This is the equation used generally for mixed inhibition involving both EI and ESI
complexes (Figure 10.19a). A number of simplified cases exist that are reversible.
1. Competitive inhibition.
2. Noncompetitive inhibition
3. Uncompetitive inhibition.
Figure 11. 2 figure showing competitive inhibition 1/Vo (1/ M/min) verses 1/[S]
(1/ mM). note that on increasing inhibitor concentration 1/Vmax remain unchanged
while Km value changes.
Figure 11. 4
figure 11.6 A schematic diagram showing the effect of reversible inhibitors on the
rate of enzyme-catalysed reactions. —— no inhibition, (a) —— mixed inhibition
([I] = Ki = 0.5 Ki'); lower Vmaxapp (= 0.67 Vmax), higher Kmapp (= 2 Km). (b) ——
competitive inhibition ([I] = Ki); Vmaxapp unchanged (= Vmax), higher Kmapp (= 2
Km). (c) —— uncompetitive inhibition ([I] = Ki'); lower Vmaxapp (= 0.5 Vmax) and
Kmapp (= 0.5 Km). (d) —— noncompetitive inhibition ([I] = Ki = Ki'); lower
Vmaxapp (= 0.5 Vmax), unchanged Kmapp (= Km).
________________________________________
A special case of uncompetitive inhibition is substrate inhibition which occurs at
high substrate concentrations in about 20% of all known enzymes (e.g. invertase is
inhibited by sucrose). It is primarily caused by more than one substrate molecule
binding to an active site meant for just one, often by different parts of the
substrate molecules binding to different sites within the substrate binding site.
If the resultant complex is inactive this type of inhibition causes a reduction in
the rate of reaction, at high substrate concentrations. It may be modeled by the
following scheme
---------------65
where
---------------------66
The assumption is made that ESS may not react to form product. It follows from
equation (52) that:
-------------------------67
Even quite high values for KS lead to a leveling off of the rate of reaction at
high substrate concentrations, and lower KS values cause substantial inhibition
(Figure 10.20).
________________________________________
Figure 11. 9
Figure 11. 7 The direct linear plot. A plot of the initial rate of reaction
against the initial substrate concentration also showing the way estimates can be
directly made of the Km and Vmax. Every pair of data points may be utilised to
give a separate estimate of these parameters (i.e. n(n-1)/2 estimates from n data
points with differing [S]0). These estimates are determined from the intersections
of lines passing through the (x,y) points (-[S]0,0) and (0,v); each intersection
forming a separate estimate of Km and Vmax. The intersections are separately
ranked in order of increasing value of both Km and Vmax and the median values
taken as the best estimates for these parameters. The error in these estimates can
be simply determined from sub-ranges of these estimates, the width of the sub-
range dependent on the accuracy required for the error and the number of data
points in the analysis. In this example there are 7 data points and, therefore, 21
estimates for both Km and Vmax. The ranked list of the estimates for Km (mM) is
0.98,1.65, 1.68, 1.70, 1.85, 1.87, 1.89, 1.91, 1.94, 1.96, 1.98, 1.99, 2.03, 2.06,
1.12, 2.16, 2.21, 2.25, 2.38, 2.40, 2.81, with a median value of 1.98 mM. The Km
must lie between the 4th (1.70 mM) and 18th (2.25 mM) estimate at a confidence
level of 97% (Cornish-Bowden et al., 1978). The list of the estimates for Vmax (
M.min-1) is ranked separately as 3.45, 3.59, 3.80, 3.85, 3.87, 3.89, 3.91, 3.94,
3.96, 3.96, 3.98, 4.01, 4.03, 4.05, 4.13, 4.14, 4.18, 4.26, 4.29, 4.35, with a
median value of 3.98 M.min-1. The Vmax must lie between the 4th (3.85 M.min-1)
and 18th (4.18 M.min-1) estimate at a confidence level of 97%. It can be seen
that outlying estimates have little or no influence on the results. This is a
major advantage over the least-squared statistical procedures where rogue data
points cause heavily biased effects.
________________________________________
Three ways in which the hyperbolic relationship between the initial rate of
reaction and the initial substrate concentration
--------------74
Figure 11. 9 (b) Eadie-Hofstee plot of v against v/[S]0 giving intercepts at Vmax
and Vmax/Km
(75)
Figure 11. 11 FIGURE 10. 15 . A schematic plot showing the amount of product
formed (productivity) against the time of reaction, in a closed system. The
specificity constant may be determined by a weighted least-squared fit of the data
to the relationship given by equation (73).
Table -2
Module III
Enzyme Kinetics: Single substrate steady state kinetics; Michaelis Menten
equation, Linear plots, King-Altman’s method; Inhibitors and activators;
Multisubstrate systems; ping-pong mechanism, Alberty equation, Sigmoidal kinetics
and Allosteric enzymes
Chapter-8
Multisubstrate enzymes
Many Enzymes react with two or more substrates simultaneously (includes cofactors
: ATP, NADPH, NADP, FADH, FAD etc) Michaelis Menten kinetics is observed when only
one substrate is varied with the other(s) held constant (usually the cofactors)
Common observed Mechanisms:
Sequential – All substrates are bound by enzyme before the any products are formed
and released
Ordered : Substrates bind and products released in specific order
Random : no order
Ping Pong – When one or more product(s) are released before all substrates are
bound by enzyme (acyl/phosphoryl enzyme intermediate)
sequential means all substrates on before any products off, while ping pong has
products off before all substrates on - can be ordered or random - e.g.:
________________________________________
First order because rate depends only on the formation of the carbocation, which
in turn depends only on [R3CCl]
• Second order: r = k[A][B] for A + B P; or can have r = k[A]2 ;
o Example - SN2 from organic chemistry: A + B C + D as 2nd order reaction, as
in the hydroxylation of primary alkylchlorides:
Now 2nd order because both RH2CCl and OH- (reverse of figure above) are involved
in slow step.
• Higher order reactions occur, but uncommon.
• Zero order: r = k: Only occurs with catalysts, important in enzyme
catalysis. 0 order also only occurs above a minimum [A].
one-substrate enzymes:
For simple enzyme, S P get rectangular hyperbola type plot for vi vs [S] (text
Figure 6-11), similar to Mb binding curve.
•
•
• Let's look at a mathematical model and attempt to generate curve. This was
first done by Michaelis and Menten for an equilibrium model. Better is the steady
state model of Haldane and Briggs (more general), which we will derive.
• For S P assume
•
• And for initial reaction conditions [P] = 0 & therefore k4 = 0, so have
•
• Now vi = d[P]/dt = k3[ES] (Note that kcat is often used instead of k3);
• Assume steady state (steady state assumption: d[ES]/dt= 0):
• d[ES]/dt= 0; Thus: 0 = d[ES]/dt= k1[E][S] - k2[ES] - k3[ES].
So, Which is known as the Michaelis-Menten Equation.
For simple, one-substrate enzymes then, have Michaelis-Menten Equation as a model
for enzyme activity.
Note predicted consequences of model:
• [S] >> KM; then vi = Vmax and get Zero order (r = k)
• [S] << KM; then , and get First order (r = k [S])
• [S] = KM; then vi = Vmax/2 This is definition of KM, the substrate
concentration at half-saturation.
• Note consequences for a plot: start off with approximately linear slope with
y = kx. Then at the limit of high concentrations have a horizontal line. This is
exactly what we expect if we look at the general form of the equation: , the
formula for a rectangular hyperbola: (text Figure 6-12)
Turnover Number. The rate constant (First order) for the breakdown of the [ES]
complex, kcat (k3), is also known as the turnover number, that is the maximum
number of substrate molecules processed/active site (moles substrate/mole active
site): kcat=Vmax / [E]total. Note that this is best determined under saturating
conditions. (text Table 6-08) At very low concentrations of [S] can find the
second-order rate constant for the conversion of E + S E + P: vo = (kcat /
KM)([E][S].
Linear plots for enzyme kinetic studies
Double Reciprocal or Lineweaver-Burke Plot: Need in form: y = ax + b , so take
reciprocals of both sides and have
. (text Box 6-01 figure 6-1)
Other linear plots are also available, and are better in terms of statistics (L-B
one of worst, best quality points [high concentration] have least influence on
slope, while low precision points [low concentration] are more spread out, and
have a large moment, with a strong influence on the slope and the KM intercept ¬
this is not as much of a concern now with computer statistical packages, but you
still have to understand the statistics). We will see others in the laboratory
discussion.
FYI - The Eadie-Hofstee Plot
One common plot is shown below. Note that the data points are distributed much
more evenly over the plot giving better statistics for the slope. In addition the
value of KM is obtained from the slope, giving better precision.
We can model this inhibition with chemical equations, keeping in mind that S & I
are mutually exclusive, E can bind to one OR the other: (text Figure 6-15a)
•
Multi-substrate Enzymes
Look at three common and easily understood types. We will use Cleland Nomenclature
and "Kinetic mechanism diagrams."
• Ordered Sequential Bi Bi mechanism (two on; two off); Note: A must bind
first, Q is released last.
• Ping Pong Bi Bi (one on, one off; one on, one off); Note: have some sort of
modified enzyme intermediate (often covalent intermediate)
• Random Sequential Bi Bi (two on; two off); Note: A or B may bind first, P or
Q may be released last.
Two-substrate Enzyme Product Inhibition Patterns
(Based on: E. B. Cunningham, Biochemistry: Mechanisms of Metabolism. McGraw-Hill
Book Company, New York (1978), and W. Cleland, "Substrate Inhibition: in
Contemporary Enzyme Kinetics and Mechanism. (Daniel L. Purich, ed.) Academic
Press, New york (1983))
Kinetic Mechanism Variable Substrate Product Type of Inhibition
Ordered Sequential Bi Bi
Ordered Sequential Bi Bi A Q Competitive
B Q Noncompetitive
A P Noncompetitive
B P Noncompetitive
Random Sequential Bi Bi
Random Sequential Bi Bi A Q Noncompetitive
B Q Noncompetitive
A P Noncompetitive
B P Noncompetitive
Ping pong Bi Bi
Ping pong Bi Bi A Q Competitive
B Q Noncompetitive
A P Noncompetitive
B P Competitive
Note that in each case we can predict/explain the pattern of inhibition on the
basis of the substrate and inhibitor binding to the same "enzyme form." Thus for
the Ordered Sequential mechanism only the first substrate and last product bind to
the same form, in this case the free enzyme. Similarly for the Ping pong mechanism
the first substrate and last product should be competitive as the both bind the
free enzyme. In this case we also see a competitive inhibition between the second
substrate and the first product, since they both bind to the E-X complex. The
Random Sequential mechanism is a bit more subtle. Here we see across the board
noncompetitive since in each case the substrates (and products) can each bind to
more than one substrate form, so competitive inhibition will not be possible!
(Think of the product as competing with one order of binding but not the other.)
The ping-pong (double displacement) mechanism
________________________________________
The distinguishing feature of these enzymes is that at least one product is
released from the enzyme before all of the substrates have bound. This might seem
slightly unlikely at a first glance, but it's actually easily explained and quite
a common mechanism. Some very familiar enzymes, for instance the serine proteases
(trypsin, chymotrypsin, etc.) and the amino transferases work in this way.
The process starts by binding of the enzyme to the first substrate in the usual
way:
E + A (EA)
Notice that I've used parentheses around the EA complex to indicate that it is a
central complex. The active site is full as this substrate will be converted to
product before the second substrate can bind. The active site has no room for the
second substrate so it is full.
The next reaction is the key to the whole process:
(EA) (FP)
In this reaction a part of the substrate has been removed from substrate A,
converting it to product P. The removed section has become covalently bound to the
enzyme to create a new form of the enzyme, enzyme F.
The first product of the reaction is now released and the second substrate binds:
(FP) F + P
F + B (FB)
Now the stored section of the first substrate is transferred to the second
substrate to create the second product, which is then released:
(FB) (EQ)
(EQ) E + Q
The animation should help to clarify this.
as the first upward arrow (product P) is to the left of the first down arrow
(substrate B).
Now that we're familiar with the principal types of kinetic mechanism we need to
think about experimental techniques to distinguish between them. To start with
we'll examine the effects of changes in substrate concentration on multisubstrate
reactions.
Effects of Substrate Concentration in Multisubstrate Systems
________________________________________
With a multisubstrate enzyme, let's say a typical bi bi enzyme:
A + B P + Q
we can carry out exactly the same experiment. We simply need to keep one substrate
(the fixed substrate) at a constant concentration in all our assays, while we vary
the concentration of the other substrate (the variable substrate). The results
would be exactly the same as you'd expect in a single substrate system and you
could use any of the methods that we've studied to calculate the kinetic
parameters. What would happen though if you repeated the experiment with an
increased concentration of the fixed substrate. Since you're increasing the
concentration of a substrate you would expect the velocity to rise and in fact the
reaction would be faster at any given concentration of the variable substrate than
it was in the previous experiment. So you'd end up with a second set of data which
you could use in your chosen plot. The kinetic parameters would change to reflect
the change in velocity. If you repeated this at a variety of concentrations of the
fixed substrate you would get a series of lines. A typical Lineweaver-Burk plot
obtained as a result of this type of experiment can be seen below. Substrate A was
used as the variable substrate and substrate B as the fixed substrate.
The actual pattern of lines obtained will vary according to the way in which the
enzyme interacts with the two substrates and, as we'll see in the next couple of
pages, enables us to distinguish between sequential and ping-pong enzymes.
In discussing graphs of this type we'll be considering changes in the Vmax and
slope of the line. A change in Vmax indicates the effect that a change in the
concentration of the fixed substrate on the reaction speed at very high
concentrations of the variable substrate. Remember that Vmax is the velocity of
the reaction under those conditions. A change in slope indicates the effect of a
change in concentration of the fixed substrate on the speed at very low
concentrations of the variable substrate. Remember in our discussion of enzyme
inhibition we found that the slope was the rate constant at low substrate
concentrations.
We'll start by considering the expected results of this experiment when carried
out with a sequential enzyme.
Substrate concentration assays with sequential enzymes
________________________________________
Consider a bi bi ordered sequential reaction:
A + B P + Q
The Cleland plot for such a reaction would be:
We'll discuss the results of a set of enzyme assays in which substrate A is used
as the variable substrate and substrate B as the fixed substrate.
At very low A concentrations the rate limiting step of the reaction would be the
binding of A to the enzyme as the substrate is in very short supply. An increase
in the concentration of B would reduce the concentration of the EA complex in the
reaction mixture by binding to it to form EAB complex. Reducing the concentration
of the product of the E + A EA reaction will pull it to the right by the Law of
Mass Action. So the increase in B has increased the speed of the rate limiting
step, and therefore of the overall reaction. As we're looking at effects at low A
concentrations this would be seen as a change in the slope of the Lineweaver-Burk
plot.
At very high A concentrations the rate limiting step would be the EAB EPQ, which
is the inherently slowest reaction, or EA + B EAB at low B levels. An increase in
B would increase the speed of either of these as a reactant in the second reaction
and by the knock on effect of generating more EAB for the central reacton to
occur. This would be seen as a change in Vmax as we are considering effects at
high A concentration.
In summary then, for an ordered sequential reaction, a change in the concentration
of the fixed substrate would bring about a change in both the slope and intercept
of the Lineweaver-Burk plot and the graph would be similar to that suggested on
the previous page.
A similar result would be obtained if the assay was reversed and B used as the
variable substrate or if the enzyme used a random sequential mechanism. You might
like to demonstrate that yourself as an exercise.
Chapter-9
ISOLATION AND PURIFICATION OF ENZYME
INTRODUCTION
ENZYME is isolated and purified to obtain maximum desired product because they are
not utilized during the product formation. And also isolation of enzyme gives the
maximum understanding of the behavior of the enzyme in complex system, its
regulation mechanism. PURIFIED enzyme is needed for laboratory work and less
purified enzyme is needed for commercial purpose. Purifying enzyme is much labor
intensive process and main aim is to separate other protein that are not the part
of the enzyme. Often during purification enzyme yield is decreases many folds.
Purification of enzyme is aimed to get maximum turn over number that is to
increase the activity of enzyme in other world to increase its efficiency of
conversion of per mole substrate into the product. It helps in increasing the
sensitivity of the diagnosis test in the clinics. Other need of the enzyme
purification is the study of kinetics that is rate of enzyme and its specificity
towards the substrate. Inhibition kinetics helps in functional study of the
enzyme. During the disturbance in the metabolic pathway some enzyme may not form
and it results in the formation of unwanted product like in the phenylketonuria
disease homigenistic acid secretion in the urine results. Therefore for the
diagnostic purpose much pure enzyme is needed.
FIGURE 8. 1
strategies for enzyme purification.
source of enzyme
Method of enzyme isolation (cell lysis by osmotic, enzyme, sonication, or
homogenization method)
Method of separation.
[i] Based on size and mass ( centrifugation, GPC gel permeation chromatography,
Dialysis and ultracentrifugation).
[ii] Based on polarity (Ion –exchange, electrophoresis, isoelectric focusing,
hydrophobic interaction chromatography).
[iii] Based on changes in solubility ( by change of pH, change in ionic strength
(Salting in or salting out).
[iv] Based on change in dielectric strength by adding organic solvent.
[v] Based on specific binding site.
Affinity chromatography.
Affinity elution.
Dye –ligand chromatography.
Immuno-adsorption chromatography.
Covalent chromatography.
(4). Test of purification
a). test of purity
b). Test of catalytic activity
c). Active site titration
Test of purity is done by following method
1. Ultrapurification (for impurities < 5%)
2. Electrophoresis (Examining enzyme composed of non identical subunit)
3. SDS-PAGE ( good method for detecting impurities and for detecting damage of
non-identical subunit.)
4. Capillary Electrophoresis
5. Isoelectric –focusing ( very sensitive method)
6. Mass –spectrometry.( power full method )
Source of enzyme
Biologically active enzymes may be extracted from any living organism. A very wide
range of sources are used for commercial enzyme production from Actinoplanes to
Zymomonas, from spinach to snake venom. Of the hundred or so enzymes being used
industrially, over a half are from fungi and yeast and over a third are from
bacteria with the remainder divided between animal (8%) and plant (4%) sources
(Table 8.1). A very much larger number of enzymes find use in chemical analysis
and clinical diagnosis. Non-microbial sources provide a larger proportion of
these, at the present time. Microbes are preferred to plants and animals as
sources of enzymes because:
1. they are generally cheaper to produce.
2. their enzyme contents are more predictable and controllable,
3. reliable supplies of raw material of constant composition are more easily
arranged, and
4. plant and animal tissues contain more potentially harmful materials than
microbes, including phenolic compounds (from plants), endogenous enzyme inhibitors
and proteases.
5. Attempts are being made to overcome some of these difficulties by the use of
animal and plant cell culture.
________________________________________
Table 2.1. Some important industrial enzymes and their sources.
Enzyme a
EC number b
Source Intra/extra
-cellular c
Scale of production d
Industrial use
Animal enzymes
Catalase 1.11.1.6 Liver I - Food
Chymotrypsin 3.4.21.1 Pancreas E - Leather
Lipasee
3.1.1.3 Pancreas E - Food
Rennetf
3.4.23.4 Abomasum E + Cheese
Trypsin 3.4.21.4 Pancreas E - Leather
Plant enzymes
Actinidin 3.4.22.14 Kiwi fruit E - Food
Amylase 3.2.1.1 Malted barley E +++ Brewing
-Amylase 3.2.1.2 Malted barley E +++ Brewing
Bromelain 3.4.22.4 Pineapple latex E - Brewing
Glucanaseg
3.2.1.6 Malted barley E ++ Brewing
Ficin 3.4.22.3 Fig latex E - Food
Lipoxygenase 1.13.11.12 Soybeans I - Food
Papain 3.4.22.2 Pawpaw latex E ++ Meat
Bacterial enzymes
Amylase 3.2.1.1 Bacillus E +++ Starch
-Amylase 3.2.1.2 Bacillus E + Starch
Asparaginase 3.5.1.1 Escherichia coli I - Health
Glucose isomeraseh
5.3.1.5 Bacillus I ++ Fructose syrup
Penicillin amidase 3.5.1.11 Bacillus I - Pharmaceutical
Proteasei
3.4.21.14 Bacillus E +++ Detergent
Pullulanasej
3.2.1.41 Klebsiella E - Starch
Fungal enzymes
Amylase 3.2.1.1 Aspergillus E ++ Baking
Aminoacylase 3.5.1.14 Aspergillus I - Pharmaceutical
Glucoamylasek
3.2.1.3 Aspergillus E +++ Starch
Catalase 1.11.1.6 Aspergillus I - Food
Cellulase 3.2.1.4 Trichoderma E - Waste
Dextranase 3.2.1.11 Penicillium E - Food
Glucose oxidase 1.1.3.4 Aspergillus I - Food
Lactasel
3.2.1.23 Aspergillus E - Dairy
Lipasee
3.1.1.3 Rhizopus E - Food
Rennetm
3.4.23.6 Mucor miehei E ++ Cheese
Pectinasen
3.2.1.15 Aspergillus E ++ Drinks
Pectin lyase 4.2.2.10 Aspergillus E - Drinks
Proteasem
3.4.23.6 Aspergillus E + Baking
Raffinaseo
3.2.1.22 Mortierella I - Food
Yeast enzymes
Invertasep
3.2.1.26 Saccharomyces I/E - Confectionery
Lactasel
3.2.1.23 Kluyveromyces I/E - Dairy
Lipasee
3.1.1.3 Candida E - Food
Raffinaseo
3.2.1.22 Saccharomyces I - Food
a The names in common usage are given. As most industrial enzymes consist of
mixtures of enzymes, these names may vary from the recommended names of their
principal component. Where appropriate, the recommended names of this principal
component is given below.
b The EC number of the principal component.
c I - intracellular enzyme; E - extracellular enzyme.
d +++ > 100 ton year-1; ++ > 10 ton year-1; + > 1 ton year-1; - < 1 ton year-1.
e triacylglycerol lipase;
f chymosin;
g Endo-1,3(4)- -glucanase;
h xylose isomerase;
i subtilisin;
j dextrin endo-1,6- -glucosidase;
k glucan 1,4- -glucosidase;
l -galactosidase;
m microbial aspartic proteinase;
n polygalacturonase;
o -galactosidase;
p -fructofuranosidase.
In practice, the great majority of microbial enzymes come from a very limited
number of genera, of which Aspergillus species, Bacillus species and Kluyveromyces
(also called Saccharomyces) species predominate. Most of the strains used have
either been employed by the food industry for many years or have been derived from
such strains by mutation and selection. There are very few examples of the
industrial use of enzymes having been developed for one task. Shining examples of
such developments are the production of high fructose syrup using glucose
isomerase and the use of pullulanase in starch hydrolysis.
Media for enzyme production
Detailed description of the development and use of fermentors for the large-scale
cultivation of microorganisms for enzyme production is outside the scope of this
volume but mention of media use is appropriate because this has a bearing on the
cost of the enzyme and because media components often find their way into
commercial enzyme preparations. Details of components used in industrial scale
fermentation broths for enzyme production are not readily obtained. This is not
unexpected as manufacturers have no wish to reveal information that may be of
technical or commercial value to their competitors. Also some components of media
may be changed from batch to batch as availability and cost of, for instance,
carbohydrate feedstock change. Such changes reveal themselves in often quite
profound differences in appearance from batch to batch of a single enzyme from a
single producer. The effects of changing feedstock must be considered in relation
to downstream processing. If such variability is likely to significantly reduce
the efficiency of the standard methodology, it may be economical to use a more
expensive defined medium of easily reproducible composition.
Clearly defined media are usually out of the question for large scale use on cost
grounds but may be perfectly acceptable when enzymes are to be produced for high
value uses, such as analysis or medical therapy where very pure preparations are
essential. Less-defined complex media are composed of ingredients selected on the
basis of cost and availability as well as composition. Waste materials and by-
products from the food and agricultural industries are often major ingredients.
Thus molasses, corn steep liquor, distillers soluble and wheat bran is important
components of fermentation media providing carbohydrate, minerals, nitrogen and
some vitamins. Extra carbohydrate is usually supplied as starch, sometimes refined
but often simply as ground cereal grains. Soybean meal and ammonium salts are
frequently used sources of additional nitrogen. Most of these materials will vary
in quality and composition from batch to batch causing changes in enzyme
productivity.
Often the enzyme may be purified several hundred-fold but the yield of the enzyme
may be very poor, frequently below 10% of the activity of the original material
(Table 2.2). In contrast, industrial enzymes will be purified as little as
possible, only other enzymes and material likely to interfere with the process
which the enzyme is to catalyze, will be removed. Unnecessary purification will be
avoided as each additional stage is costly in terms of equipment, manpower and
loss of enzyme activity. As a result, some commercial enzyme preparations consist
essentially of concentrated fermentation broth, plus additives to stabilize the
enzyme's activity.
The content of the required enzyme should be as high as possible (e.g. 10% w/w of
the protein) in order to ease the downstream processing task. This may be achieved
by developing the fermentation conditions or, often more dramatically, by genetic
engineering. It may well be economically viable to spend some time cloning extra
copies of the required gene together with a powerful promoter back into the
producing organism in order to get 'over-producers' (see Chapter protein
engineering).
It is important that the maximum activity is retained during the preparation of
enzymes. Enzyme inactivation can be caused by heat, proteolysis, sub-optimal pH,
oxidation, denaturants, irreversible inhibitors and loss of cofactors or
coenzymes. Of this heat inactivation, this together with associated pH effects is
probably the most significant. It is likely to occur during enzyme extraction and
purification if insufficient cooling is available, but the problem is less when
preparing thermophilic enzymes. Proteolysis is most likely to occur in the early
stages of extraction and purification when the proteases responsible for protein
turnover in living cells are still present. It is also the major reason for enzyme
inactivation by microbial contamination. In their native conformations, enzymes
have highly structured domains which are resistant to attack by proteases because
many of the peptide bonds are mechanically inaccessible and because many proteases
are highly specific. The chances of a susceptible peptide bond in a structured
domain being available for protease attack are low. Single 'nicks' by proteases in
these circumstances may have little immediate effect on protein conformation and,
therefore, activity. The effect, however, may severely reduce the conformational
stability of the enzyme to heat or pH variation so greatly reducing its
operational stability. If the domain is unfolded under these changed conditions,
the whole polypeptide chain may be available for proteolysis and the same,
specific, protease may destroy it. Clearly the best way of preventing proteolysis
is to rapidly remove, or inhibit, protease activity. Before this can be achieved
it is important to keep enzyme preparations cold to maintain their native
conformation and slow any protease action that may occur.
Some intracellular enzymes are used commercially without isolation and
purification but the majority of commercial enzymes is either produced
extracellularly by the microbe or plant or must be released from the cells into
solution and further processed (Figure 2.1). Solid/liquid separation is generally
required for the initial separation of cell mass, the removal of cell debris after
cell breakage and the collection of precipitates. This can be achieved by
filtration, centrifugation or aqueous biphasic partition. In general, filtration
or aqueous biphasic systems are used to remove unwanted cells or cell debris
whereas centrifugation is the preferred method for the collection of required
solid material.
Figure 2.1. Flow diagram for the preparation of enzymes.
This technique is used to investigate the different parameter of the molecule such
as molecular mass, shape, and density. In this process gravity plays most
important role. Therefore, the basis of centrifugation separation techniques
therefore is to exert the lager force than does the gravitational earth, thus
increasing the rate at which the particle settles.
The technique can be divided into two types:
1 preparative centrifugation: for separation of the whole cells, subcellular
organelles, plasma membranes, polysomes, ribosome, chromatin, nucleic acids,
lipoprotein and viruses
2. Analytical centrifugation: it is devoted to study of pure or virtually pure or
macromolecular or particles. They are related with the study of macromolecular
structure rather than the collection of particle fractions.
Principles:
Rate depends on the centrifugal field G directed radially outward (angular
velocity)
G = ωr 2
ω =2π/60 revolution min-1
This method is based upon the difference in the sedimentation rate of particles of
different size and density. In centrifugation the larger particle are sedimented
first. The particle having the same mass but different density, the denser
particle is sedimented first and less dense will sediment later. Particle having
similar density can be separated by the differential centrifugation or the rate
zonal method.
In differentiated centrifugation, the particle to be separated is divided
centrifugally into a number of fractions by increasing the applied centrifugal
field. After the centrifugation, pellet and supernatant are separated, pellet is
washed several time and again centrifugation is done. The particle moves against
respective sedimentation rates. Centrifugation is continued long enough to pellet
all the largest class of particles, the resulting supernatant then being
centrifuged at higher speed to separate medium sized particle and so on. However,
since particles of varying sizes and densities were distributed homogeneously at
the start of centrifugation, so pellet will not be homogeneous but will contain a
mixture of all the sediment components.
Particle separation by the rate zonal technique is based on differences in the
size, shape, and density of the particle. Most of the biological particles having
same size are having narrower density range. So , separation of similar particle
by the rate zonal technique is based mainly upon differences in their sizes and
can not be separated easily like mitochondria, lysosome, peroxisomes. The
technique has been used for the separation of enzymes hormones and RNA and DNA
hybrids, ribosomal subunits, sub cellular organelles.
There are two type of density gradient centrifugation, --1. The rate zonal
technique and the isopycnic (equal density)
Isopycnic centrifugation depends solely upon the buoyant density of the particles
and not its shape or size and is independent of time the size of the particle
affecting only the rate at which it reaches its isopycnic position in the
gradient. The technique is useful in separating the particle of same size but
differing in density.
1Svedberg = 10-13 second
Centrifugation separates on the basis of the particle size and density difference
between the liquid and solid phases. Sedimentation of material in a centrifugal
field may be described by
(2.11)
where v is the rate of sedimentation, d is the particle diameter, rs is the
particle density, rl is the solution density is the angular velocity in radians s-
1, r is the radius of rotation, η is the kinematic viscosity, Fs is a correction
factor for particle interaction during hindered settling and θ is a shape factor
(=1 for spherical particles). Fs depends on the volume fraction of the solids
present; approximately equaling 1, 0.5, 0.1 and 0.05 for 1%, 3%, 12% and 20%
solids volume fraction respectively. Only material which reaches a surface during
the flow through continuous centrifuges will be removed from the centrifuge
feedstock, the efficiency depending on the residence time within the centrifuge
and the distance necessary for sedimentation (D). This residence time will equal
the volumetric throughput (Ф) divide by the volume of the centrifuge (V). The
maximum throughput of a centrifuge for efficient use is given by
(2.12)
The efficiency of the process is seen to depend on the solids volume fraction, the
effective clarifying surface (V/D) and the acceleration factor (ω2r/g, where g is
the gravitational constant, 921 cm s-2; a rotor of radius 25 cm spinning at 1 rev
s-1 has an acceleration factor of approximately 1 G). Low acceleration factors of
about 1 500 g may be used for harvesting cells whereas much higher acceleration
factors are needed to collect enzyme efficiently. The product of these factors
(ω2rV/gD) is called the sigma factor Σ and is used to compare centrifuges and to
assist scale-up.
Laboratory centrifuges using tubes in swing-out or angle head rotors have high
angular velocity ω and radius of rotation (r) but small capacity (V) and
substantial sedimentation distance (D). This type of design cannot be scaled-up
safely, primarily because the mechanical stress on the centrifuge head increases
with the square of the radius, which must increase with increasing capacity.
For large-scale use, continuous centrifuges of various types are employed (Figure
2.2). These allow the continuous addition of feedstock, the continuous removal of
supernatant and the discontinuous, semicontinuous or continuous removal of solids.
Where discontinuous or semicontinuous removal of precipitate occurs, the
precipitate is flushed out by automatic discharge systems which cause its dilution
with water or medium and may be a problem if the precipitate is required for
further treatment. Centrifugation is the generally preferred method for the
collection of enzyme-containing solids as it does not present a great hazard to
most enzymes so long as foam production, with consequent enzymic inactivation, is
minimised.
centrifuges are long and thin enabling rapid acceleration and deceleration,
minimizing the down-time required for the removal of the sedimented solids. Here
the radius and effective liquid thickness are both small allowing a high angular
velocity and hence high centrifugal force; small models can be used at
acceleration factors up to 50,000 g, accumulating 0.1 Kg of wet deposit whereas
large models, designed to accumulate up to 5 Kg of deposit, are restricted to
16,000 g. The capacities of these centrifuges are only moderate.Multichamber disc-
stack centrifuges, originally designed (by Westfalia and Alpha-Laval) for cream
separation, contain multiple coned discs in a stack which are spun and on which
the precipitate collects. They may be operated either semi-continuously or, by
using a centripetal pressurising pump within the centrifuge bowl which forces the
sludge out through a valve, continuously. The capacity and radius of such devices
are large and the thickness of liquid is very small, due to the large effective
surface area. The angular velocity, however, is restricted giving a maximum
acceleration factor of about 2,000 g. A different design which is rather similar
in principle is the solid bowl scroll centrifuge in which an Archimedes' screw
collects the precipitate so that fluid and solids leave at opposite ends of the
apparatus. These can only be used at low acceleration (about 3,000 g) so they are
suitable only for the collection of comparatively large particles.
Although many types of centrifuge are available, the efficient precipitation of
small particles of cell debris can be difficult, sometimes near-impossible.
Clearly from Equation 2.2, the efficiency of centrifugation can be improved if the
particle diameter (d) is increased. This can be done either by coagulating or
flocculating particles. Coagulation is caused by the removal of electrostatic
charges (e.g. by pH change) and allowing particles to adhere to each other.
Flocculation is achieved by adding small amounts of high-molecular-weight charged
materials which bridge oppositely-charged particles to produce a loose aggregate
which may be readily removed by centrifugation or filtration. Flocculation and
coagulation are cheap and effective aids to precipitating or otherwise harvesting
whole cells, cell debris or soluble proteins but, of course, it is essential that
the agents used must not inhibit the target enzymes. It is important to note that
the choice of flocculants is determined by the pH and ionic strength of the
solution and the nature of the particles. Most flocculants have very definite
optimum concentrations above which further addition may be counter-effective. Some
flocculants can be rapidly ruined by shear.
A comparatively recent introduction designed for the removal of cell debris is a
moderately hydrophobic product in which cellulose is lightly derivatised with
diethylaminoethyl functional groups. This material (Whatman CDR; cell debris
remover) is inexpensive (essential as it is not reusable), binds to unwanted
negatively charged cell constituents, acts as a filter aid and may be incinerated
to dispose of hazardous
Figure 2.3. The basic design of the rotary vacuum filter. The suspension is sucked
through a filter cloth on a rotating drum. This produces a filter cake which is
removed with a blade. The filter cake may be rinsed during its rotation. These
filters are generally rather messy and difficult to contain making them generally
unsuitable for use in the production of toxic or recombinant DNA products. There
have been recent developments that improve their suitability, however, such as the
Disposable Rotary Drum Filter.
________________________________________
A simple and familiar filtration apparatus is the perforate bowl centrifuge or
basket centrifuge, in effect a spin drier. Cell debris is collected on a cloth
with, or without, filter aid and can be skimmed off when necessary using a
suitable blade. Such centrifugal filters have a large radius and effective liquid
depth, allowing high volumes. However, safety decrees that the angular velocity
must be low and so only large particles (e.g. plant material) can be removed
satisfactorily.
________________________________________
Figure 2.4. Principles of (a) dead-end filtration and (b) cross-flow filtration.
In dead-end filtration the flow causes the build-up of the filter cake, which may
prevent efficient operation. This is avoided in cross-flow filtration where the
flow sweeps the membrane surface clean.
________________________________________
Chapter-10
Separation in Aqueous biphasic systems
The 'incompatibility' of certain polymers in aqueous solution was first noted by
Beijerinck in 1296. In this case two phases were formed when agar was mixed with
soluble starch or gelatin. Since then, many two phase aqueous systems have been
found; the most thoroughly investigated being the aqueous dextran-polyethylene
glycol system (e.g. 10% polyethylene glycol 4000/2% dextran T500), where dextran
forms the more hydrophilic, denser, lower phase and polyethylene glycol the more
hydrophobic, less dense, upper phase. Aqueous three phase systems are also known.
Phases form when limiting concentrations of the polymers are exceeded. Both phases
contain mainly water and are enriched in one of the polymers. The limiting
concentrations depend on the type and molecular weight of the polymers and on the
pH, ionic strength and temperature of the solution. Some polymers form the upper
hydrophobic phase in the presence of fairly concentrated solutions of phosphates
or sulphate (e.g. 10% polyethylene glycol 4000/12.5% potassium phosphate buffer).
A drawback to the useful dextran/polyethylene glycol system is the high cost of
the purified Dextran used. This has been alleviated by the use of crude
unfractionated dextran preparations, much cheaper hydroxypropyl starch derivatives
and salt-containing biphasic systems.
Aqueous biphasic systems are of considerable value to biotechnology. They provide
the opportunity for the rapid separation of biological materials with little
probability of denaturation. The interfacial tension between the phases is very
low (i.e. about 400-fold less than that between water and an immiscible organic
solvent), allowing small droplet size, large interfacial areas, efficient mixing
under very gentle stirring and rapid partition. The polymers have a stabilizing
influence on most proteins. A great variety of separations have been achieved, by
far the most important being the separation of enzymes from broken crude cell
material. Separation may be achieved in a few minutes, minimizing the harmful
action of endogenous proteases. The systems have also been used successfully for
the separation of different types of cell membranes and organelles, the
purification of enzymes and for extractive bioconversions. Continuous liquid two-
phase separation is easier than continuous solid/liquid separation using equipment
familiar from immiscible solvent systems, for example disc-stack centrifuges and
counter-current separators. Such systems are readily amenable to scale-up and may
be employed in continuous enzyme extraction processes involving some recycling of
the phases.
Cells, cell debris proteins and other material distribute themselves between the
two phases in a manner described by the partition coefficient (P) defined as.
--------------------- (2.14)
Where Ct and Cb represent the concentrations in the top and bottom phases
respectively. The yield and efficiency of the separation is determined by the
relative amounts of material in the two phases and therefore depends on the volume
ratio (Vt/Vb). The partition coefficient is exponentially related to the surface
area (and hence molecular weight) and surface charge of the particles in addition
to the difference in the electrical potential and hydrophobicity of the phases. It
is not generally very sensitive to temperature changes. This means that proteins
and larger particles are normally partitioned into one phase whereas smaller
molecules are distributed more evenly between phases. A partition coefficient of
greater than 3 is required if usable yields are to be achieved by a single
extraction process. Typical partition coefficients for proteins are 0.01-100
whereas the partition coefficients for cells and cell debris are effectively zero.
The influence of pH and salts on protein partition is complex, particularly when
phosphate buffers are present. A given protein distributes differently between the
phases at different pH's and ionic strength but the presence of phosphate ions
affect the partition coefficient in an anomalous fashion because these ions
distribute themselves unequally resulting in electrostatic potential (and pH)
differences. This means that systems may be 'tuned' to enrich an enzyme in one
phase, ideally the upper phase with cell debris and unwanted enzymes in the lower
phase.
An enzyme may be extracted from the upper (polyethylene glycol) phase by the
addition of salts or further polymer, generating a new biphasic system. This stage
may be used to further purify the enzyme. A powerful modification of this
technique is to combine phase partitioning and affinity partitioning. Affinity
ligand (e.g. triazine dyes) may be coupled to either polymer in an aqueous
biphasic system and thus greatly increase the specificity of the extraction.
Phases form when limiting concentrations of the polymers are exceeded. Both phases
contain mainly water (typically 70-90% w/w water) and are enriched in one of the
polymers. The limiting concentrations depend on the type and molecular weight of
the polymers and on the pH, ionic strength and temperature of the solution. Some
polymers form a two-phase system by themselves; PEG forming the upper more-
hydrophobic phase in the presence of fairly concentrated solutions of citrates,
phosphates or sulfates or at higher temperatures (see below). Such aqueous liquid-
liquid two-phase systems are finding increasing use in the extractive separation
of labile biomolecules such as proteins, offering mild conditions due to the low
interfacial tension between the phases (i.e. about 400-fold less than that between
water and an immiscible organic solvent) allowing small droplet size, large
interfacial areas, efficient mixing under very gentle stirring and rapid
partition. The polymers also have a stabilizing influence on most proteins. A
great variety of separations have been achieved, by far the most important being
the separation of enzymes from broken crude cell material. Separation may be
achieved in a few minutes, minimizing the harmful action of endogenous proteases.
The systems have also been used successfully for the separation of different types
of cell membranes, organelles and actinide ions, the purification of enzymes,
extractive bioconversions. Although sometimes perceived as due to polymer
incompatibilities, the properties of these biphasic systems can be mainly
attributed to incompatibility between aqueous pools of low and higher density
water. Each phase may be considered as a different, although aqueous, solvent with
properties determined by its structuring.
PEG usually has a far higher concentration in the upper (low-density) phase of
such solutions in spite of its inherent density being greater than water. These,
together with the properties of this PEG phase encourage the belief that it
creates a predominantly low-density water environment due to its partially
hydrophobic character, in turn mainly determined by the methylene groups. Further
proof of this may be seen by use of microwave dielectric measurements, which show
the water surrounding PEG to be ordered, whereas that surrounding more hydrophilic
polymers is disordered [332]. Also, the dissolution of PEG is exothermic (and
increasingly exothermic with PEG size), in line with a shift in the ES CS
equilibrium towards the more ordered ES structure. It is interesting and perhaps
not simply fortuitous that the diameter (4.9 Å) of the favored PEG helix (formed
by trans, gauche, trans links across the C-O-C-C, O-C-C-O, C-C-O-C bonds) is the
same as the diameter of the spines of the ES water cluster (4.7 Å) formed by
pentagonal boxes, the ether (O-C-C-O) distances (2.22 Å) are close to the O•••O
distances (2.24 Å) in water and the next ether (O-C-C-O-C-C-O) (5.6 Å) distances
are close to the next vertex distance on opposite sides of the pentagonal boxes
(5.4 Å).a Model building shows that optimum hydrogen bonding would tend to distort
this PEG helix, however. The strongly-held hydration, as determined by viscosity,
increases from two molecules of water per PEG monomer at very low polymerization
(tetramer) to 5 molecules of water per PEG monomer for 45-mer , showing that the
extent of water clustering increases with PEG size. The partitioning of proteins
into the hydrophobic PEG phase shows great sensitivity to the protein's surface
hydrophobicity (partition increasing with surface hydrophobicity) and also depends
on the PEG size; increasing with PEG molecular mass , in line with the extent of
water clustering. Increasing PEG size and concentration both increase the
proteins' effective hydration as the PEG is excluded from the proteins' surface.
However, when the PEG phase becomes too ordered (e.g. at higher PEG size)
partitioned proteins are excluded due to the reduced available water content.
An interesting and revealing phenomenon occurs in PEG solutions as the temperature
is raised; the solution at low temperatures separates into two phases (PEG-rich
and PEG-poor) at higher temperature (separating at the cloud-point) and reverts to
a single phase at even higher temperatures. This may be explained as the PEG
creating a low-density water environment with decreased entropy. At low
temperatures a solution is formed due to the enthalpy of hydrogen bonding between
the PEG and the water more than compensating for the entropy lost in forming the
low-density water. This entropy loss is required, due to the hydrophobicity of the
methylene groups, but is not great as the water is somewhat ordered already at
lower temperatures. At the cloud point, the entropy cost is greater as the water
is no longer naturally as structured, and two phases develop. The stronger
hydrogen bonding in D2O, relative to H2O, is expected to raise this cloudpoint. At
higher temperatures still, the water possesses excess energy and cannot be
structured by the PEG. This reduces the entropic cost, so allowing a solution to
form once more.
Anions have a distinct effect on the cloud point in line with the Hofmeister
Series (cloud point lowering: SCN- < I- < Br- < Cl- < F- < OH- < SO42- < HPO42- <
CO32- < PO43-); the greater lowering of the cloud point is in line with greater
surface charge density , stronger hydration, greater tendency to avoid low-density
water and the greater destruction of the natural structuring of the water. A
oppositely-ordered compensating effect on the cloud point has been recognized due
to binding of the anions to the polymer surface. This tends to raise the
cloudpoint at lower salt concentrations as the bound salt increases the polymer
net charge and, hence, solubility. The relative effect of the ions is the reverse
of the Hofmeister series just given with weakly hydrated ions binding best, i.e.
SCN- having the greatest effect and ionic kosmotropes below Cl- having negligible
effect.
Cations have a lesser but opposite effect to anions with chaotropes (e.g. NH4+)
tending to lower the cloud point but kosmotropes (e.g. Li+) raising it.
Exceptionally, however, some di- and trivalent cations such as Mg2+ and Zn2+ act
counter to their normal Hofmeister behavior, due presumably to their specific
chelation to oxygen atoms in the PEG molecules.
Anions and cations distribute themselves differently between the phases depending
on their affinity for low or higher density water but with the requirements that
the phases be electrically neutral and iso-osmotic, so producing an interfacial
potential difference, which may aid the partitioning of charged biomolecules. Thus
sulfate and phosphate ions prefer the bottom phase and, as a consequence,
negatively charged proteins are partitioned into the upper PEG phase, so allowing
more sulfate or phosphate ions to partition into their preferred lower phase.
Preference for the PEG-rich or PEG-poor phase is related to the Hofmeister Series
for the structuring ability of the salts, particularly the anions (e.g. preference
for PEG-rich phase: I- > Br- > Cl- > F- > SO42-; Cs+ > Na+ > Ba2+ > Ca2+;
preference for PEG-poor phase: SO42- > F- > Cl- > Br- > I-). A similar Hofmeister
Series effect is noticed intensifying the incompatibility between two polymers
such as polyethylenimine-PEG, or dextran-PEG, by increasing the concentration of
strongly hydrated (CS-forming) anions, such as sulfate.
a Note that the polymers formed with either one (-O-C-O-C-O-) or three (-O-C-C-C-
O-C-C-C-O-) methylene groups between the oxygen atoms are both insoluble in water.
The reason however is not so much that the O•••O distances (2.12 Å and 4.79 Å
respectively) fit less well with the water cluster spacing but rather that the
molecules form almost-linear extended (rather than helical) chains with a
pronounced hydrophobic character that have strong intra-molecular attraction.
2.9 Preparation of enzymes from clarified solution; Ultrafiltration
In many cases, especially when extracellular enzymes are being prepared for sale,
the clarified solution is simply concentrated, preservative materials added, and
sold as a solution or as a dried preparation. The concentration process chosen
will be the cheapest which is compatible with the retention of enzyme activity.
For some enzymes rotary evaporation can be considered, followed if necessary by
spray drying. The most popular method, though, is ultrafiltration, whereby water
and low molecular weight materials are removed by passage through a membrane under
pressure, enzyme being retained. Ultrafiltration differs from conventional
filtration and microfiltration with respect to the size of particles being
retained (< 50 nm diameter). It uses asymmetric microporous membranes with a
relatively dense but thin skin, containing pores, supported by a coarse strong
substructure. Membranes possessing molecular weight cut-offs from 1000 to 100,000
and usable at pressure up to 2 MPa are available.
There are number types of apparatus available. Stirred cells represent the
simplest configuration of ultrafiltration cell. The membrane rests on a rigid
support at the base of a cylindrical vessel which is equipped with a magnetic
stirrer to combat concentration polarization. It is not suitable for large scale
use but is useful for preliminary studies and for the concentration of laboratory
column eluates. Various large-scale units are available in which membranes are
formed into wide diameter tubes (1 - 2 cm diameter) and the tubes grouped into
cartridges. These are not as compact as capillary systems (area/volume about 25 m-
1) and are very expensive but are less liable to blockage by stray large particles
in the feedstream. Cheaper thin-channel systems are available (area/volume about
500 m-1) which use flat membrane sandwiches in filter press arrangements of
various designs chosen to produce laminar flow across the membrane and minimise
concentration polarization. Capillary membranes represent a relatively cheap and
increasingly popular type of ultrafiltration system which uses micro-tubular
membranes 0.2 - 1.1 mm diameter and provides large membrane areas within a small
unit volume (area/volume about 1000 m-1). Membranes are usually mounted into
modules for convenient manipulation. This configuration of membranes can be scaled
up with ease. Commercial models are available that give ultrafiltration rates of
up to 600 L hr-1.
The steady improvement in the performance, durability and reliability of membranes
has been a boon to enzyme technologists, encouraging wide use of the various
ultrafiltration configurations. Problems with membrane blockage and fouling can
usually be overcome by treatment of membranes with detergents, proteases or, with
care, acids or alkalis. The initial cost of membranes remains considerable but
modern membranes are durable and cost-effective. Ultrafiltration, done
efficiently, results in little loss of enzyme activity. However, some
configurations of apparatus, particularly in which solutions are recycled, can
produce sufficient shear to damage some enzymes.
Chapter-10
Concentration and purification of enzyme
Concentration by precipitation
Precipitation of enzymes is a useful method of concentration and is ideal as an
initial step in their purification. It can be used on a large scale and is less
affected by the presence of interfering materials than any of the chromatographic
methods described later. There are method of salting in and salting out. Salting
in is the method in which ammonium sulphate is used for dissolving the protein.
Note that protein dissolves least at its isoelectric point. On increasing the
ammonium sulphate concentration further proteins starts precipitating this
phenomenon is called as salting out. All this process must be done in the ice cold
solution so that no protein can denature.
Salting out of proteins is done by use of ammonium sulphate, is one of the best
known and used methods of purifying and concentrating enzymes, particularly at the
laboratory scale. Increases in the ionic strength of the solution cause a
reduction in the repulsive effect of like charges between identical molecules of a
protein. It also reduces the forces holding the salvations shell around the
protein molecules. When these forces are sufficiently reduced, the protein will
precipitate; hydrophobic proteins precipitating at lower salt concentrations than
hydrophilic proteins. Ammonium sulphate is convenient and effective because of its
high solubility, cheapness, lack of toxicity to most enzymes and its stabilizing
effect on some enzymes (see Table 2.4). Its large-scale use, however, is limited
as it is corrosive except with stainless steel, it forms dense solutions
presenting problems to the collection of the precipitate by centrifugation, and it
may release gaseous ammonia, particularly at alkaline pH. The practice of using
ammonium sulphate precipitation is more straightforward than the theory.
Reproducible results can only be obtained provided the protein concentration,
temperature and pH are kept constant. The concentration of the salt needed to
precipitate an enzyme will vary with the concentration of the enzyme. However,
fractionation of protein mixtures by the stepwise increase in the ionic strength
can be a very effective way of partly purifying enzymes.
The solubility of an enzyme can be described by the equation
(2.11)
where S is the enzyme solubility, Kintercept is the intercept constant, Ksalt is
the salting out constant and T is the ionic strength which is proportional to the
concentration of a precipitating salt. Kintercept is independent of the salt used
but depends on the pH, temperature, enzyme and the other components in the
solution. Ksalt depends on both the enzyme required and the salt used but is
largely independent of other factors. This equation (2.11) may also be used to
give the minimum salt concentration necessary before enzyme will start to
precipitate; the concentration change necessary to precipitate the enzyme varying
according to the magnitude of the salting out constant.
Some enzymes do not survive ammonium sulphate precipitation. Other salts may be
substituted but the more favored alternative is to use organic solvents such as
methanol, ethanol, propan-2-ol and acetone. These act by reducing the dielectric
of the medium and consequently reducing the solubility of proteins by favoring
protein-protein rather than protein-solvent interactions. Organic solvents are not
widely used on a large scale because of their cost, their flammability, and the
tendency of proteins to undergo rapid denaturation by these solvents if the
temperature is allowed to raise much above 0°C. On safety grounds when organic
solvents are used, special flameproof laboratory areas are used and temperatures
maintained below their flashpoints.
Except when enzymes are presented for sale as ammonium sulphate precipitates, the
precipitating salt or solvent must be removed. This may be done by dialysis,
Ultrafiltration or by using a desalting column of, for instance, Sephadex G-25.
A. Nucleic acid removal
Intracellular enzyme preparations contain nucleic acids which can give rise to
increased viscosity interfering with enzyme purification procedures, in particular
ultrafiltration. Some organisms contain sufficient nuclease activity to eliminate
this problem but, otherwise, the nucleic acids must be removed by precipitation or
degraded by the addition of exogenous nucleases. Ammonium sulphate precipitation
can be effective in removing nucleic acids but will remove some protein at the
same time. Various more specific precipitants have been used, usually positively-
charged materials which form complexes with the negatively-charged phosphate
residues of the nucleic acids. These include, in order of roughly decreasing
effectiveness, polyethyleneimine, the cationic detergent cetyltrimethyl ammonium
bromide, streptomycin sulphate and protamine sulphate. All of these are expensive
and possibly toxic, particularly streptomycin sulphate. Also, they may complex
undesirably with certain enzymes. They may be necessary, however, where possible
contamination of the enzyme product must be avoided, such as in the preparation of
restriction endonucleases. Otherwise, treatment with bovine pancreatic nucleases
is probably the most cost-effective method of nucleic acid removal.
B. Heat treatment
In many cases, unwanted enzyme activities may be removed by heat treatment.
Different enzymes have differing susceptibility to heat denaturation and
precipitation. Where the enzyme required is relatively heat-stable this allows its
easy and rapid purification in terms of enzymic activity. For such enzymes heat-
treatment is always considered as an option at an early stage in their
purification. This method has been particularly successfully applied to the
production of glucose isomerase, where a short incubation at a relatively high
temperature is used (e.g. 60 - 25°C for 10 min). No interfering activity remains
after this treatment and the heat-treated, and hence leaky, cells may be
immobilised and used directly.
1. Enzyme purification by Chromatography
________________________________________
Low molecular weight polyols (e.g. glycerol, sorbitol and mannitol) are also
useful for stabilizing enzymes, by repressing microbial growth, due to the
reduction in the water activity, and by the formation of protective shells which
prevent unfolding processes. Glycerol may be used to protect enzymes against
denaturation due to ice-crystal formation at sub-zero temperatures. Some
hydrophilic polymers (e.g. polyvinyl alcohol, polyvinylpyrrolidone and
hydroxypropylcelluloses) stabilise enzymes by a process of compartmentalisation
whereby the enzyme-enzyme and enzyme-water interactions are somewhat replaced by
less potentially denaturing enzyme-polymer interactions. They may also act by
stabilizing the hydrophobic effect within the enzymes. Many specific chemical
modifications of amino acid side chains are possible which may (or, more commonly,
may not) result in stabilization. A useful example of this is the derivatisation
of lysine side chains in proteases with N-carboxyamino acid anhydrides. These form
polyaminoacylated enzymes with various degrees of substitution and length of
amide-linked side chains. This derivatisation is sufficient to disguise the
proteinaceous nature of the protease and prevent autolysis.
Important lessons about the molecular basis of thermostability have been learned
by comparison of enzymes from mesophilic and thermophilic organisms. A frequently
found difference is the increase in the proportion of arginine residues at the
expense of lysine and histidine residues. This may be possibly explained by noting
that arginine is bidentate and has a higher pKa than lysine or histidine (see
Table 2.1). Consequently, it forms stronger salt links with bidentate aspartate
and glutamate side chains, resulting in more rigid structures. This observation,
among others, has given hope that site-specific mutagenesis may lead to enzymes
with significantly improved stability . In the meantime it remains possible to
convert lysine residues to arginine-like groups by reaction with activated urea.
It should be noted that enzymes stabilised by making them more rigid usually show
lower activity (i.e. Vmax) than the 'natural' enzyme.
Enzymes are more stable in the dry state than in solution. Solid enzyme
preparations sometimes consist of freeze-dried protein. More usually they are
bulked out with inert materials such as starch, lactose, carboxymethylcellulose
and other poly-electrolytes which protect the enzyme during a cheaper spray-drying
stage. Other materials which are added to enzymes before sale may consist of
substrates, thiols to create a reducing environment, antibiotics, benzoic acid
esters as preservatives for liquid enzyme preparations, inhibitors of
contaminating enzyme activities and chelating agents. Additives of these types
must, of course, be compatible with the final use of the enzyme's product.
Chapter-12
Techniques used in Enzyme characterization
Introduction
After salting in and salting out procedure, enzymes are further purified by two
main common techniques 1- Chromatography; 2- Gel electrophoresis. In this chapter
we will focus mainly on choice of these techniques and their broad details of the
application and principles.
A. Chromatography
Principles of chromatography
Mobile phase: This is chosen according to the nature of the biomolecules. Mobile
phase is used to isolate the biomolecules because most of the biomolecules are
present in the solution. Mobile phase is poured in the gel and get separated due
to attachment with the stationary phase.
The basis of all type of chromatography is the partition or distribution
coefficient (Kd). Two immiscible phases are formed after the distribution of
compound in the matrix and is denoted by Kd= concentration of compound in phase A
/ concentration of compound in phase B.
The resolution depends on the beads. The coarser beads are unable to hold the
fluid, so poorer resolution results. For maximum resolution, superfine beads are
used.
The gel is a three dimensional network whose structure is usually random. The gels
acts as molecular sieves consist of cross linked polymers that are generally
inert, do not bind or react with the material that is being analyzed, and are
uncharged. The space within the gel is filled with liquid occupies most of the gel
volume.
The gels currently in use are of three types: ---dextran, agarose, and
polyacrylamide. They are used in the aqueous solution.Dextran is a polysaccharide
composed of glucose residues. It is commercially available in the trade name
“Sephadex”. They can not be used for molecules that have size more than 600, 000.
the alkyl dextran is called as N, N’- methylene bis acrylamide. They made strong
beads. The product is called as Sephacryl S-300.Agarose is a linear polymer of D-
galactose. It forms a gel held together with crosslink of H-bonds. The pore size
is usually much larger than sephadex. This is the reason why they can be used for
the separation of the large macromolecular substance like protein,
DNA.Polyacrylamide gels are produced by cross-linking acrylamide and N, N’-
methylene-bis acrylamide. It is marketed in the name of Bio-Gel –P. Mixed gel of
polyacrylamide and agarose is known as Ultra-Gel.
Beads can be prepared with defined degrees of porosity, average radii, and mean
radii. In general, the porosity of the beads determines the size range of
molecules that can be effectively separated- the fractionation range. The radii of
the beads are more important for determining the capacity of the column to
separate molecules of similar size. Gel permeation chromatography is normally
considered to be a medium- to high resolution chromatographic (polishing)
technique.
Mechanism of separation by size in gel permeation chromatography
For our discussion of the theory of gel permeation chromatography, we will make
the assumption that many proteins have a roughly spherical shape (often called
globular proteins, as opposed to fiber proteins). Access to included volume
(volume that hydrates the inside of the bed) depends on the size of the sphere
(the hydrodynamic radius) that each protein occupies. The pore size of the bead
will determine whether a protein of s Moreover, since proteins have roughly
constant density (mass per volume), the size of this sphere is directly related to
the mass of the globular protein. Thus, gel permeation chromatography is found to
separate globular proteins according to mass. Note, however, that large deviations
from spherical shape can cause a protein to migrate anomalously during gel
permeation chromatography that is with regard to migration versus mass. Void
volume, etc. For chromatography beads of a given porosity, molecules above a
certain size will be completely excluded from the pore structure of the beads.
These excluded molecules elute in the "void volume" (Vo) of the column and are not
fractionated. In contrast, molecules below a certain size for beads of a given
porosity will completely penetrate the pore structure and will elute with the
"included volume" (Vi). Thus, these molecules are not fractionated either. Only
molecules with masses (hydrodynamic radii) that allow them to penetrate the pore
structure of the beads only partially fall within the fractionation range and are
separated according to their molecular size (approximately, as described
above).The use of a gel permeation column as an analytical tool requires the
determination of Vo, Vi, and the elution volumes (Ve) of the proteins of interest.
By comparing the elution volumes of protein standards of known molecular mass, the
molecular mass of an unknown protein can be estimated. In contrast to denaturing
gel electrophoresis, which gives subunit molecular masses for an oligomeric
protein, gel permeation chromatography provides an estimate of mass for the
oligomeric holoprotein. The combination of denaturing gel electrophoresis and gel
permeation chromatography is thus exceedingly powerful for elucidating basic
features of protein structures.
Use of gel permeation chromatography as part of a purification scheme
Most protein purification schemes involve several steps. These can be
characterized as either bulk or polishing steps. Bulk purification steps are
generally useful for samples of low purity and large volume, both of which are
typical of the starting material to be used in a protein purification, such as a
cellular extract. Common bulk purification methods are centrifugation;
precipitation, such as with salt, solvent, acid, or polyethylene glycol;
filtration; and ion-exchange chromatography. Polishing purification steps are
generally useful for samples of higher quality and smaller volume, typical of
partially purified fractions obtained from bulk purification steps. Common
polishing purification methods are ion exchange, affinity, and gel permeation
chromatography. Gel permeation chromatography is a common and often excellent
polishing step during any protein purification; however, it would not be used as a
first step in purification except in unusual circumstances (e.g., high abundance
of the target protein in the starting material).
Table:1
MATERIAL:
POLYMER TRADE NAME FRACTIONATION RANGE
1.DEXTRAN G 10
< 0.7
SEPHADEX G 25
1.0-5
G 50
1.5—3.0
G 100
4--150
G 200
5---600
SEPHYCRYL S 200
5---250
S 300
10---1500
S 400
20—8000
2. AGAROSE 2 B
10-4000
SEPHAROSE 4B
60---20,000
6B
70—40,000
A 5m
10---5000
BIO-GEL A 15m 40---
15,000
A 50
100---50,000
3. POLYACRYLAMIDE BIO-GEL P2
0.1---1.8
P6
1.0—6
P100 5.0---
100.0
Overview of a typical gel permeation chromatography experiment
In a typical gel permeation experiment, a protein sample (often a partially
purified fraction from a previous purification step, see below) is applied onto
the top of the column packing (beads) and allowed to flow into them. As additional
buffer is applied to the top of the column and allowed to flow through the column,
the protein sample migrates through the column. Due to the differential
partitioning of molecules into the pore structure of the beads (as described
above), the protein molecules are separated. As buffer is eluted from the column,
it is collected in fractions until all the components of the original sample have
passed through the column.
Note that all the large M’s come out at nearly the same volume, Vo. This is
because none of the very large polymers ever enter a pore. So they all elute
together at the void volume, Vo. It is customary to plot log(M), not M. Note
that the independent variable is plotted on the y axis by convention.
With such a curve, you are to select a representative sampling of points. For
example, consider point A, indicated by the cross. Starting at VeA read up until
you hit the M vs. Ve trend and then read left to get MA from the left y-axis.
Obtain DRIA similarly from the right ordinate. Repeat for as many points as you
wish! The DRI response is proportional to the concentration of polymer:
DRI c ( in g/mL)
Mw = =
Mn = = = =
Log M
THE plot is between K verses log M (molecular weight). It yields a straight line
except for very small and very large molecule.
The parameter K = Ve---Vo / Vs, where Ve= elution volume, Vo= void volume, Vs=
volume of stationary phase or = Vt---Vo, Vt is the total volume of the column
PAPER CHROMATOGRAPHY
Cellulose has many hydroxyl groups which are polar and bind H2O. The bound H2O is
the Stationary Phase. H2O run across the cellulose paper due to capillary action.
Mobile Phase is mixture of organic solvents (alcohols, ketone, aldehyde etc.) and
possibly water.
The mobile phase solvent will be less polar than H2O; it is usually a mixture of
Solutes partition between H2O in the stationary phase and the solvent of the
mobile phase. One can change the characteristics of separation by changing the
polarity of the mobile phase (i.e. adjust the composition).
Paper Chromatography is the most common form of cellulose chromatography in which
solute is "spotted" on "dry" paper (still contains H2O) encircle by the pencil at
a line mark and chromatograph is "developed by dipping one end in the mobile
phase. There are two modes of chromatography1: Ascending and 2-Descending.The
solvent moves through the paper, drawn by capillary action Solutes move as spots
with a rate depending upon how much time they spend in the stationary phase vs.
the mobile phase--determined by their partition coefficient--measured as an Rf
value. Maximum distance covered by the solvent is noted and the distance covered
by the solute is noted. The ratio of two gives Rf value. This Rf value is fixed
and is generally less than one.
Ion –exchange chromatography
This type of chromatography is used for many biological materials like amino cid
and proteins, which have ionisable groups, i.e. they have either negative or
positive charge. The name ion exchange is given because of exchanging ions for ion
in aqueous solution.
The principle of ion exchange chromatography is that charged molecule adsorb to
ion exchangers reversibly so that molecule can be bound or eluted by changing the
ionic environment. Separation by ion exchange is usually involving two step. First
–the substances to be separated are bound to the exchanger, using the conditions
that make them more stable and tight binding. Ion exchange separation is carried
out mainly in column packed with an ion –exchangers. The column packing for ion
chromatography consist of ion-exchange resins bonded to inert polymeric particles
(typically 10 µm diameter). For cation separation the cation-exchange resin is
usually a sulfonic or carboxylic acid, and for anion separation the anion-exchange
resin is usually a quaternary ammonium group. For cation-exchange with a sulfonic
acid group the reaction is:
-SO3- H+(s) + Mx+(aq) -SO3- Mx+(s) + H+(aq)
where Mx+ is a cation of charge x, (s) indicates the solid or stationary phase,
and (aq) indicates the aqueous or mobile phase. The equilibrium constant for this
reaction is:
[-SO3- Mx+]s [H+]aq
Keq = ------------------------------------------
[-SO3- H+]s [Mx+]aq
Different cations have different values of Keq and are therefore retained on the
column for different lengths of time. The time at which a given cation elutes from
the column can be controlled by adjusting the pH ([H+]aq). Most ion-chromatography
instruments use two mobile phase reservoirs containing buffers of different pH,
and a programmable pump that can change the pH of the mobile phase during the
separation.
Partition Chromatography
In partition chromatography the stationary phase is bonded to inert particles of
3-10 µm of diameter, with the smaller sizes, 3-5 µm, being used in analytical
columns, and the larger particles being used in preparative-scale HPLC. Analyte
separate as they travel through the column due to the differences in their
partitioning between the mobile phase and the stationary phase.
Reverse-phase partition chromatography uses a relatively nonpolar stationary phase
and a polar mobile phase, such as methanol, acetonitrile, water, or mixtures of
these solvents. The most common bonded phases are n-octyldecyl (C18) and n-decyl
(C8) chains, and phenyl groups. Reverse-phase chromatography is the most common
form of liquid chromatography, primarily due to the wide range on analyte that can
dissolve in the mobile phase. Normal-phase partition chromatography uses a polar
stationary phase and a nonpolar organic solvent, such as n-hexane, methylene
chloride, or chloroform, as the mobile phase. The stationary phase is a bonded
siloxane with a polar functional group. The most common functional groups in order
of increasing polarity are:
cyano: -C2H4CN
diol: -C3H6OCH2CHOHCH2OH
amino: -C3H6NH2
dimethylamino: -C3H6N(CH3)2
Chromatographic
Separation principle Commercial name Nature of stationary
Phase Type of support
Adsorption Partisil C8
Corasil
Pellumina
Partisil
Micro Pak Al
Bondapak C18
ULTRA pak TSK ODS Octylsilane
Silica
Alumina
Silica
Alumina Porous
Pellicular
Pellicular
Microporous
Microporous
Pellicular
Porous
Ion exchange Partisil-SAX
MicroPak-NH2
Strong base
Weak base Porous
Porous
Exclusion Bio-glass
Styragel
Superpose
Fractogel TSK Glass
Polystyrene-divenyl benzene
Agarose
Polyvinylchloride Rigid solid
Semi-rigid gel
Soft-gel
Semi-rigid gel
Affinity chromatography
Principle
Affinity chromatography is almost exclusively used for the purification of
biological molecules such as proteins and other macromolecules. The technique has
been known for almost a century, but suitable support materials were not available
until much more recently. With new materials and new demands, the technique became
extremely useful in the 1960s, and it has become essential with the growing demand
of the biotech in the 1980s and 1990s.Biotech research has used affinity
chromatography because of its ability to separate one desired species from a host
of other biological molecules. Specificity based on three aspects of affinity—the
matrix, the ligand, and the attachment of the ligand to the matrix—is the hallmark
of this process and the reason for its success. As the name suggests, it utilizes
the property of biological affinity of the substances to be separated. As a
consequence, it is capable of giving absolute purification, even from complex
mixtures, in a single process.
Affinity chromatography operates on the principle that ligand (as stated in the
Table), attached to a matrix made up of an inert substance, bind to the desired
molecule within a solution to be analyzed . Ideally, the ligand will interact only
with the desired molecule and form a permanent bond. All other compounds in the
solution will elude, leaving the desired product in the column. The desired
molecule is then removed from the column by using a wash (typically changing the
pH) that lowers the dissociation constant and allows recovery of a nearly pure
sample.
Choosing the correct ligand is the first hurdle. The ligand must bind strongly
with the molecule that is to be recovered. Biological systems have millions of
ligand (also known as receptors), and most can be affixed to the matrix and used
to isolate the desired molecule.
If the ligand chosen can bind to more than one molecule in the sample in question,
then a technique called negative affinity, which uses ligand to remove everything
but the target molecule from the solution, may be used. For example, if you were
looking for a molecule from a cell, but the only ligand that binds the molecule
also trapped two additional, different molecules, you could run a normal affinity
column and collect these three molecules. Then, if a ligand were found that
attached to the two unwanted molecules, that ligand could be used in the size
exclusion chromatography and affinity column, allowing the desired molecule to
elute while the other two were retained in the column. Matrix materials simply
hold the active ligand and provide a pore structure to increase the surface area
to which the molecules can bind. Ligand attachment requires that the matrix be
activated and then react with the ligand to fix them onto the matrix. During this
process, the ligand must also remain active toward the target molecule, or all
will be for naught. Substituent groups within the matrix, such as amino, hydroxyl,
carbonyl, and thio groups, are easily activated and can serve as the sites to
which the ligand attach. Matrix materials are often polysaccharides, such as
agarose, that have many hydroxyl groups that can be activated. The matrix, in
addition to requiring activation, must also often stand up to decontamination when
purifying pharmaceutical compounds. Decontamination is typically performed by
rinsing the column with sodium hydroxide or urea. Different matrix materials are
stable in different pH ranges, adding the third aspect of selection for affinity
chromatography. The technique was originally developed for the purification of
enzymes, but it has been extended to nucleotides, nucleic acids, immunoglobulin,
and membrane receptors and even to whole cells and cell fragments.
M + L ML
For the success of the experiment following steps must be kept in mind.
1. Matrix should have broad range of thermal and chemical stability. It should
not absorb any chemical or substance to be purified itself.
2. The ligand should be coupled without altering its binding properties.
3. A ligand must bind tightly.
4. During the elution the matrix should not be destroyed.
The most useful material is the Agarose, and polyacrylamide, since they have broad
range of thermal tolerance, exhibit minimum absorption, maintain good flow
property after coupling, and does not denature after application of extreme pH and
ionic strength.
The choice of ligand depends on the specificity of the substance. For example for
an enzyme ligand must be the substrate, a reversible inhibitor, or an allosteric
activator.
METHOD OF LIGAND IMMOBILIZATION
Linking or coupling of the ligand to matrix material is called as immobilization.
1. CNBR activated agarose
CNBr is negatively charged so they can react strongly with the amino group. It
is extremely useful for coupling enzyme, Co-enzyme, inhibitors, antigen, antibody,
nucleic acid and most protein to agarose.
2. 6-AMINO-HEXENOIC ACID & 1,6 DIAMINO HEXANE.
a) Used mainly for small ligand.
b) They can solve the steric problem
c) Only a Spacer can be attached between matrix and ligand.
d) Spacer can be attached by reacting functional group C00H (by using Agarose)
and NH2 (group of 6AHA).
e) Epoxy –activated Agarose.This is useful for linkage of sugars and
carbohydrate or any material containing OH gp, amino gp, thiol gp.
f) Thiopropyl-Agarose.Can be Used or sulpher containing protein. Before using,
it should be treated with the cysteine.
3. Carbomyl diimidazole activated agarose.
Coupling of N-nucleophile to CNBr. This results in isourea linkage that carries
potential charge and thus can act as an ion-exchanger.
Substance Use
Lectin Polysaccharides and glycoprotein present on the RBC membrane.
Con A Sepharose They selectively can binds to the N-acetyl glucosamine residue.
Therefore they can be used for the lymphocyte separation.
Helix pomatia lectin Used for separation of the pure T-cell
Lactose Caster bean, pea nut can be used for separation of lactose.
Maltose Can be separated by the jack bean.
D-glucosamine Can be separated by clam
NADP+ Can be separated by using 2, 5’ ADP.
Protein A Can be used for separation of IgG (using Fc region)
Poly A Can be separated of m-RNA
Boronate polyacrylamide RNA, sugar, catecholamine
Heparin-Agarose Blood protein, DNA polymerase, Ribosome, androgen receptor
Imino-diacetic acid Zn+2, Cu +2 Can be separated
Octyl –agarose Protein Can be separated
Thio-propul Sepharose Can be separated by clam Protein, Urease, and Papain.
Applications
The applications of affinity chromatography have been numerous, but they are
predominantly in the field of biochemistry. Early applications were in the
separation of biomacromolecules from other biological compounds, such as molecules
from an entire cell. This continues to be the primary and extremely important
field for affinity chromatography. For example, S. Loukas and colleagues studied
the existence of one type of suspected opiate receptor in the brain (1994). They
separated the ( -opioid binding protein by using an opioid receptor antagonist
that was specific to the ( -opioid binding protein. These studies may one day lead
to a better understanding of how drugs such as opium affect our brains.
In addition to using small ligand to separate large molecules, researchers have
immobilized large molecules on the matrix and used them to separate the small
molecules that bind to them. In addition to biological separation, affinity
chromatography can be used to determine dissociation constants of ligand and
molecules. The longer a molecule stays on the column, the broader the
chromatographic peak, indicating that the molecule is more tightly bound to the
ligand. This quantitative information can be used in further studies of the ligand
or molecule.
A thin layer of about .25 mm thick slurry is prepared in water is applied to glass
with the help of plate spreader.
CaSO4 is mixed to facilitate adhesion of the adsorbent to the plate.
The plate is dried at 100—1200C. This is also helpful in the activation of the
plate. Sample is applied to the plate 2—2.5 cm from edge by means of micropipette
or microsyringe.
The TLC plate is dipped in the developing phase to depth of about 1.5 cm it is
left for one hour.
Detection is done by the several methods. For e.g. fluorescent dye (this can be
absorbed by the UV light.
For investigating the unsaturated compound I2 vapour can be used. For radiolabel
led compound autoradiography can be used.
Movement of compound can be observed by the specific Rf values.
IT has great resolving power and greater speed of separation. A wider range of
sorbant can be used and also due to easy detection of spot and separation of
chromatogram. Two factor that affect the TLC has, High surface to volume ratio and
the weight ratio, If necessary 2D gels electrophoresis can be used in the TLC
plate this can be used by placing the plate in the buffer at right angle to first
separation. Commonly used separating agent is the Ninhydrin for detection of the
amino acid. Rhodamine B is used for the detection of the lipid; SbCl2 for steroid
and tarpenoid; H2SO4 for organic acid, H2SO4 and KMN03 for hydrocarbon. Br2 vapour
is used for olefins detection.
HPTLC and HPPLC
Thin-layer chromatography (TLC) gets the high-performance (HP) treatment through
several optimization steps leading to improved efficiency and automation. The
layers are made smaller (0.02 mm instead of 0.25 mm), they have smaller mean grain
sizes of the coating particles (down to 7 µm instead of 12–30 µm), and the grain
size is more uniform. Equally if not more important, HPTLC shows better optical
properties than standard TLC, allowing for easy densitometry studies. Better
resolution as well as a 10-fold improvement in detection limits are key to HPTLC’s
increasing popularity.
By using a forced-flow mobile phase and a sealing chamber, researchers can
transform HPTLC into high-pressure planar liquid chromatography (HPPLC), gaining
the added benefits that pressure provides, especially to the speed of the run.
HPTLC can also be used with centrifugation to force the sample outward in what is
known as rotational planar chromatography (RPC). These adaptations are
collectively responsible for what is known as modern TLC, which relies heavily on
instrumental analysis.
Applications of these modern forms are extensive, including routine use in the
pharmaceutical industry and clinical analysis, in food analysis, natural products
analysis (including a variety of botanicals and herbals), and in environmental
analysis for determining such things as pesticides in drinking water.
F= qv/ velocity
q-= charge and V is the potential difference. Electrophoretic mobility (μ) is
defined as ratio of velocity to field strength.
IF this free radical is represented as R’. Oxygen can be used for the removal of
the free radicals. Free radical generation can be done by the photo
polymerization. Low percentage gel can be used for the separation of the DNA. For
protein separation SDS –PAGE can be used the usual percentage lies between the 3
to 30 % of acrylamide. Since protein separation done in the two steps: first it is
separated in the stalking gel, and size exclusion chromatography on it is resolved
by the resolving gel. Stalking gel generally uses lower percentage of the gel that
provides the larger pore size. It allows the free movement of the protein so that
one type of protein either same in the molecular weight or charge can stalk at one
position. After this process the protein is separated in the gel having smaller
pore size. All these process can be done by the vertical slabs.
c. SDS-PAGE
SDS is an anionic detergent (CH3—(CH2)10 –CH2OSO3-Na+). With β mercaptoethanol and
SDS, protein can be denatured into the simple protein. It helps in the better
separation of the protein. And thus protein is analyzed in qualitative way. On
average it has seen that one SDS can binds to the two amino acid. Problem arises
during the electrophoresis is the settling of sample and exact tracking of the
protein position in the gel. For settling problem sucrose solution is used, and
for tracking the protein bromo-phenol blue is used. The protein first of all
loaded in the stalking gel. In this master mix, glycine is added. This is done to
sharpen the protein band. But note that glycinate ion have a lower electrophoretic
mobility than protein –SDS complex, which have lower mobility than chloride ion of
the loading buffer and the stacking gel
Cl- > PROTEIN-SDS > GLYCINATE
So protein SDS band lies in between the Cl- and glycinate ion. PH of the stacking
gel is generally 6.8 and resolving gel has pH about 8.8. The negatively charged
protein is attracted toward the anode. After the protein is reaches the bottom,
the gel is removed and placed in stain more generally the Coomassie blue. The gel
is then placed in the destain solution. Staining of gel is done for 2-3 hrs. And
destaining requires overnight. Generally 15 % polyacrylamide gel is used in the
separating gel. This can allow separation of the protein in the range of 100,000
to 10, 000. For protein of molecular weight more than 150, 000 7.5% gel is used.
Molecular weight of protein Mr can be determined by the comparing its mobility
with those of a number of protein used as standard. By plotting a graph of
distance moved against log Mr for each of standard proteins, a calibration curve
can be
constructed. The distance moved by the protein of unknown Mr is then measured and
its log Mr and hence Mr can be determined from calibration curve. A protein
generally have single band in the protein unless it has two same subunit.
d. Native (buffer) gel
In this method SDS is not used for the separation of the protein subunit prior to
loading. Here protein is separated according to the native charge of protein at pH
of the gel (normally pH 8.7) and according to the different electrophoretic
nobilities and the sieving effect of the gel. The method is generally used for
the enzyme –substrate reaction and total protein content.
e. Gradient gel
The protein is separated according to the gradient formed by the different
concentration of the gel. Generally 5% at the top, while 15% gel is used at the
bottom. The main advantage is that – very similar molecular weight can be
resolved.
f. Iso-electric focusing: IEF gel:
It utilizes the horizontal gels and separates the protein according to the iso-
electric point of the protein. As we know that protein is the ampholytes, it can
be separated easily. Here riboflavin is used for initiation of the polymerization
of the gel. Protein having pH lower than iso-electric point will be positively
charged, and will initially migrate towards the cathode. As they proceed further,
the charge on the protein decreases slowly and at one point protein stops where IP
is equal to the charge. For determining the IP of the protein, a standard IP of
known protein can be determined and with the help of this calibration curve, IP of
unknown protein can be determined. IEF is highly sensitive technique and used for
studying heterogeneity of the protein.
g. Chromatofocussing
Is suitable for the protein separation. This is based on forming a pH gradient.
The ion-exchanger is fixed in the column and set to a particular temperature and
pH. The difference of pH lies between 3-4 unit from upper and bottom. On adding
protein at top of column the protein moves at its isoelectric point. Just beyond
the isoelectric point the protein is bind to the positive charge of the ion-
exchange column. Chromatofocussing gives a good resolution of quit complex mixture
of protein provided that there is close difference in their isoelectric point, it
gives poor resolution of compound having same isoelectric point.
2D-PAGE
This technique utilizes the technique of both IEF and the SDS-PAGE. In the first
dimension –isoelectric focusing is done in polyacrylamide gel in narrow tubes in
the presence of ampholytes, 8M urea and non-ionic detergent. Denatured protein is
separated in the gel according to the isoelectric point. In another step the
protein is run in presence of SDS. Generally the technique is used in the
translational product of the gene or mRNA. It also helps in isolating the extra
protein in the expression. Now a days to reduce so much of the labor, computerized
2D is done.
Figure 6.2. Schematic diagram showing the effect of soluble enzyme concentration
on the activity of enzyme immobilised by adsorption to a suitable matrix. The
amount adsorbed depends on the incubation time, pH, ionic strength, surface area,
porosity, and the physical characteristics of both the enzyme and the support.
________________________________________
Table 6.1 Preparation of immobilised invertase by adsorption (Woodward 1985)
Support type
% bound at DEAE-Sephadex
anion exchanger CM-Sephadex
cation exchanger
pH 2.5 0 100
pH 4.7 100 75
pH 7.0 100 34
________________________________________
Covalent coupling
This involves the formation of a covalent bond between the enzyme and the carrier
material. The bond is normally formed between functional groups on the carrier and
the enzyme. Those on the enzymes are usually amino acid residues such as amino
(NH2) group from Lys or Arg, carboxyl (COOH) group from Asp, Glu, hydroxyl (OH)
group from Ser, Thr, and sulfhydryl (SH) group from Cys. Tests must be run to
ensure the formation of covalent bonds will not inactivate the enzyme. Through
chemical modifications, functional groups on the carriers can be altered to
different forms to accommodate different kinds of covalent bonds to be formed with
the enzyme. For example, chemical modification of -OH group can give rise to AE-
cellulose (aminoethyl), CM- cellulose (carboxymethyl), and DEAE-cellulose
(diethylaminoethyl). This increases the range of immobilization methods that can
be used for a given carrier.
While many supports exist, an important factor for enzyme immobilization appears
to be hydrophilicity, which helps to maintain enzyme activity in a hydrophilic
milieu. Immobilisation of enzymes by their covalent coupling to insoluble matrices
is an extensively researched technique. Only small amounts of enzymes may be
immobilised by this method (about 0.02 gram per gram of matrix) although in
exceptional cases as much as 0.3 gram per gram of matrix has been reported. The
strength of binding is very strong, however, and very little leakage of enzyme
from the support occurs.
Functional groups that affects the covalent coupling
The relative usefulness of various groups, found in enzymes, for covalent link
formation depends upon their availability and reactivity (nucleophilicity), in
addition to the stability of the covalent link, once formed (Table 3.2). The
reactivity of the protein side-chain nucleophiles is determined by their state of
protonation (i.e. charged status) and roughly follows the relationship -S- > -SH >
-O- > -NH2 > -COO- > -OH >> -NH3+where the charges may be estimated from a
knowledge of the pKa values of the ionising groups (Table 1.1) and the pH of the
solution. Lysine residues are found to be the most generally useful groups for
covalent bonding of enzymes to insoluble supports due to their widespread surface
exposure and high reactivity, especially in slightly alkaline solutions. They also
appear to be only very rarely involved in the active sites of enzymes.
________________________________________
Table 6.2 Relative usefulness of enzyme residues for covalent coupling
Residue Content Exposure Reactivity Stability
of couple Use
Aspartate + ++ + + +
Arginine + ++ - ± -
Cysteine - ± ++ - -
Cystine + - ± ± -
Glutamate + ++ + + +
Histidine ± ++ + + +
Lysine ++ ++ ++ ++ ++
Methionine - - ± - -
Serine ++ + ± + ±
Threonine ++ ± ± + ±
Tryptophan - - - ± -
Tyrosine + - + _+ +
C terminus - ++ + + +
N terminus - ++ ++ ++ +
Carbohydrate - ~ ++ ++ + + ±
Others - ~ ++ - - - ~ ++ -
The most commonly used method for immobilising enzymes on the research scale (i.e.
using less than a gram of enzyme) involves Sepharose, activated by cyanogen
bromide. This is a simple, mild and often successful method of wide applicability.
Sepharose is a commercially available beaded polymer which is highly hydrophilic
and generally inert to microbiological attack. Chemically it is an agarose (poly-
{β1,3-D-galactose-α-1,4-(3,6-anhydro)-L-galactose}) gel. The hydroxyl groups of
this polysaccharide combine with cyanogen bromide to give the reactive cyclic
imido-carbonate. This reacts with primary amino groups (i.e. mainly lysine
residues) on the enzyme under mildly basic conditions (pH 9 - 11.5, Figure 3.3a).
The high toxicity of cyanogen bromide has led to the commercial, if rather
expensive, production of ready-activated Sepharose and the investigation of
alternative methods, often involving chloroformates, to produce similar
intermediates (Figure 3.3b).
Carbodiimides (Figure 13.3c) are very useful bifunctional reagents as they allow
the coupling of amines to carboxylic acids. Careful control of the reaction
conditions and choice of carbodiimide allow a great degree of selectivity in this
reaction.
Glutaraldehyde is another bifunctional reagent which may be used to cross-link
enzymes or link them to supports (Figure 13.3d). It is particularly useful for
producing immobilised enzyme membranes, for use in biosensors, by cross-linking
the enzyme plus a non-catalytic diluent protein within a porous sheet (e.g. lens
tissue paper or nylon net fabric). The use of trialkoxysilanes allows even such
apparently inert materials as glass to be coupled to enzymes (Figure 13.3e). There
are numerous other methods available for the covalent attachment of enzymes (e.g.
the attachment of tyrosine groups through diazo-linkages, and lysine groups
through amide formation with acyl chlorides or anhydrides).
________________________________________
A. cyanogen bromide
Figure 6.3. (e) The use of trialkoxysilane to derivatise glass. The reactive glass
may be linked to enzymes by a number of methods including the use thiophosgene, as
shown.
________________________________________
It is clearly important that the immobilised enzyme retains as much catalytic
activity as possible after reaction. This can, in part, be ensured by reducing the
amount of enzyme bound in non-catalytic conformations (Figure 3.4). Immobilisation
of the enzyme in the presence of saturating concentrations of substrate, product
or a competitive inhibitor ensures that the active site remains unreacted during
the covalent coupling and reduces the occurrence of binding in unproductive
conformations. The activity of the immobilised enzyme is then simply restored by
washing the immobilised enzyme to remove these molecules.
________________________________________
Chapter-14
Introduction to Industrial biotechnology
Figure 7.10. Diagram showing the production rate of a seven-column PBR facility on
start -up, assuming exponential decay of reactor activity. The columns are brought
into use one at a time. At any time a maximum of six PBRs are operating in
parallel, whilst the seventh, exhausted, reactor is being refilled with fresh
biocatalyst. ——— PBR activities allowed to decay through three half-lives (to
12.5% initial activity) before replacement. The final average productivity is 2.51
times the initial productivity of one column. - - -- - - - PBR activities
allowed to decay through two half-lives (to 25% initial activity) before
replacement. The final average productivity is 3.23 times the initial productivity
of one column. It may be seen that the final average production rate is higher
when the PBRs are individually operated for shorter periods but this 29% increase
in productivity is achieved at a cost of 50% more enzyme, due to the more rapid
replacement of the biocatalyst in the PBRs. A shorter PBR operating time also
results in a briefer start-up period and a more uniform productivity.
________________________________________
After isomerisation, the pH of the syrup is lowered to 4 - 5 and it is purified by
ion-exchange chromatography and treatment with activated carbon. Then, it is
normally concentrated by evaporation to about 70% dry solids.For many purposes a
42% fructose syrup is perfectly satisfactory for use but it does not match the
exacting criteria of the quality soft drink manufacturers as a replacement for
sucrose in acidic soft drinks. For use in the better colas, 55% fructose is
required. This is produced by using vast chromatographic columns of zeolites or
the calcium salts of cation exchange resins to adsorb and separate the fructose
from the other components. The fractionation process, although basically very
simple, is only economic if run continuously. The fructose stream (90% (w/w)
fructose, 9% glucose) is blended with 42% fructose syrups to give the 55% fructose
(42% glucose) product required. The glucose-rich 'raffinate' stream may be
recycled but if this is done undesirable oligosaccharides build up in the system.
Immobilised glucoamylase is used in some plants to hydrolyse oligosaccharides in
the raffinate; here the substrate concentration is comparatively low (around 20%
dry solids) so the formation of isomaltose by the enzyme is insignificant.Clearly
the need for a second large fructose enrichment plant in addition to the glucose
isomerase plant is undesirable and attention is being paid to means of producing
55% fructose syrups using only the enzyme. The thermodynamics of the system favour
fructose production at higher temperatures and 55% fructose syrups could be
produced directly if the enzyme reactors were operated at around 95°C. The use of
miscible organic co -solvents may also produce the desired effect. Both these
alternatives present a more than considerable challenge to enzyme technology!
The present world market for HFCS is over 5 million tonnes of which about 60% is
for 55% fructose syrup with most of the remainder for 42% fructose syrup. This
market is still expanding and ensures that HFCS production is the major
application for immobilised-enzyme technology.The high-fructose syrups can be used
to replace sucrose where sucrose is used in solution but they are inadequate to
replace crystalline sucrose. Another ambition of the corn syrup industry is to
produce sucrose from starch. This can be done using a combination of the enzymes
phosphorylase (EC 2.4.1.1), glucose isomerase and sucrose phosphorylase (EC
2.4.1.7), but the thermodynamics do not favour the conversion so means must be
found of removing sucrose from the system as soon as it is formed. This will not
be easy but is achievable if the commercial pull (i.e. money available) is
sufficient:
phosphorylase
starch (Gn) + orthophosphate starch (Gn-1) + α-glucose-1-phosphate [7.1]
glucose isomerase
glucose fructose [7.2]
sucrose phosphorylase
-glucose-1 -phosphate + fructose sucrose + orthophosphate [7.3]
A further possible approach to producing sucrose from glucose is to supply glucose
at high concentrations to microbes whose response to osmotic stress is to
accumulate sucrose intracellularly. Provided they are able to release sucrose
without hydrolysis when the stress is released, such microbes may be the basis of
totally novel processes.
3-Use of immobilised raffinase
The development of a raffinase (α-D-galactosidase) suitable for commercial use is
another triumph of enzyme technology. Plainly, it would be totally unacceptable to
use an enzyme preparation containing invertase to remove this material during
sucrose production. It has been necessary to find an organism capable of producing
an -galactosidase but not an invertase. A mould, Mortierella vinacea var.
raffinoseutilizer, fills the requirements. This is grown in a particulate form and
the particles harvested, dried and used directly as the immobilised-enzyme
preparation. It is stirred with the sugar beet juice in batch stirred tank
reactors. When the removal of raffinose is complete, stirring is stopped and the
juice pumped off the settled bed of enzyme. Enzyme, lost by physical attrition, is
replaced by new enzyme added with the next batch of juice. The galactose released
is destroyed in the alkaline conditions of the first stages of juice purification
and does not cause any further problems while the sucrose is recovered. This
process results in a 3% increase in productivity and a significant reduction in
the costs of the disposal of waste molasses.
Immobilised raffinase may also be used to remove the raffinose and stachyose from
soybean milk. These sugars are responsible for the flatulence that may be caused
when soybean milk is used as a milk substitute in special diets.
4-Use of immobilised Invertase
Invertase was probably the first enzyme to be used on a large scale in an
immobilised form (by Tate & Lyle). In the period 1941 -1946 the acid, previously
used in the manufacture of Golden Syrup, was unavailable, so yeast invertase was
used instead. Yeast cells were autolysed and the autolysate clarified by
adjustment to pH 4.7, followed by filtration through a bed of calcium sulphate and
adsorption into bone char. A layer of the bone char containing invertase was
included in the bed of bone char already used for decolourising the syrup. The
scale used was large, the bed of invertase-char being 2 ft (60 cm) deep in a bed
of char 20 ft (610 cm) deep. The preparation was very stable, the limiting factors
being microbial contamination or loss of decolourising power rather than loss of
enzymic activity. The process was cost-effective but, not surprisingly, the
product did not have the subtlety of flavour of the acid-hydrolysed material and
the immobilised enzyme process was abandoned when the acid became available once
again. Recently, however, it has been relaunched using BrimacTM, where the
invertase -char mix is stabilised by cross-linking and has a half-life of 90 days
in use (pH 5.5, 50°C). The revival is due, in part, to the success of HFCS as a
high-quality low-colour sweetener. It is impossible to produce inverted syrups of
equivalent quality by acid hydrolysis. Enzymic inversion avoids the high-colour,
high salt-ash, relatively low conversion and batch variability problems of acid
hydrolysis. Although free invertase may be used (with residence times of about a
day), the use of immobilised enzymes in a PBR (with residence time of about 15
min) makes the process competitive; the cost of 95% inversion (at 50% (w/w)) being
no more than the final evaporation costs (to 75% (w/w)). A productivity of 16
tonnes of inverted syrup (dry weight) may be achieved using one litre of the
granular enzyme.
5-Production of amino acids
Another early application of an immobilised enzyme was the use of the aminoacylase
from Aspergillus oryzae to resolve racemic mixtures of amino acids.
[7.8]
[7.10] Many other potential and proven antibiotics have been synthesised in this
manner, using a variety of synthetic β-lactams and activated carboxylic acids.
Preparation of acrylamide
Acrylamide is an important monomer needed for the production of a range of
economically useful polymeric materials. It may be produced by the addition of
water to acrylonitrile.
CH2=CHCN + H2O CH2=CHCONH2 [14.11]
This process may be achieved by the use of a reduced copper catalyst (Cu+);
however, the yield is poor, unwanted polymerisation or conversion to acrylic acid
(CH2=CHCOOH) may occur at the relatively high temperatures involved (80 -140°C)
and the catalyst is difficult to regenerate. These problems may be overcome by the
use of immobilised nitrile hydratase (often erroneously called a nitrilase). The
enzyme from Rhodococcus has been used by the Nitto Chemical Industry Co. Ltd, as
it contains only very low amidase activity which otherwise would produce unwanted
acrylic acid from the acrylamide.
Immobilised nitrile hydratase is simply prepared by entrapping the intact cells in
a cross-linked 10% (w/v) polyacrylamide/dimethylaminoethylmethacrylate gel and
granulating the product. It is used at 10°C and pH 8.0-8.5 in a semibatchwise
process, keeping the substrate acrylonitrile concentration below 3% (w/v). Using
1% (w/v) immobilised-enzyme concentration (about 50,000 U l-1) the process takes
about a day. Product concentrations of up to 20% (w/v) acrylamide have been
achieved, containing negligible substrate and less than 0.02% (w/w) acrylic acid.
Acrylamide production using this method is about 4000 tonnes per year.
The closely related enzymes cyanidase and cyanide hydratase are used to remove
cyanide from industrial waste and in the detoxification of feeds and foodstuffs
containing amygdalin (see equation [7.12]).
HCN + 2H2O HCOO- + NH4+ [7.12]
HCN + H2O HCONH2 [7.13]
Alkaline phosphates
This enzyme is detected in the obstructive jaundice. It is also useful in the
detection of bone disease like ostomalacia, rickets and hyperparathyroidism. This
enzyme is normally found in the serum. This enzyme concentration also increases
during the pregnancy.
Acid phosphatase.
This enzyme is found in highest concentration in the prostrate carcinoma.
In Treatment of cancer
A major potential therapeutic application of enzymes is in the treatment of
cancer. Asparaginase has proved to be particularly promising for the treatment of
acute lymphocytic leukemia. Its action depends upon the fact that tumour cells are
deficient in aspartate-ammonia ligase activity, which restricts their ability to
synthesise the normally non-essential amino acid L-asparagine. Therefore, they are
forced to extract it from body fluids. The action of the asparaginase does not
affect the functioning of normal cells which are able to synthesize enough for
their own requirements, but reduce the free exogenous concentration and so induces
a state of fatal starvation in the susceptible tumour cells. A 60% incidence of
complete remission has been reported in a study of almost 6000 cases of acute
lymphocytic leukemia. The enzyme is administered intravenously. It is only
effective in reducing asparagine levels within the bloodstream, showing a half-
life of about a day (in a dog). This half-life may be increased 20-fold by use of
polyethylene glycol-modified asparaginase.
Enzyme deficiencies
Phenylketonuria is detected by presence of phenylalanine in the urine. Some inborn
error of metabolism is also detected are relatively harmless e.g. albinism ,
alkaptonuria,
Table 8.1 showing List of defective enzyme and their diseases
Alkaptonuria
Phenylketonuria
Maple syrup disease
Galactosomia
uridyltransferasae
Glycogen storage
Fructosuria
Gaucher disease
Tay Sachs
Wilson disease
Acetalasaemia
Xerderma pigmentosa
homogenistate 1 oxidase
phenylalanine 4 monooxygenase
oxo acid decorboxylase
galactose-1 phosphate
glucose 6 phosphate
fructokinase
glucocerbrosidase
β-NAcetykll –D-hexosaminidase
P-type ATPase
catalase
DNA binding protein helicases
Enzyme inhibitors and drug design
Inhibition of hydroxymethylglutaryl Co-A reductase (HMGCo-A), during
hypercholesterolemia. Other competitive inhibitors of HMGCo-A is namely mevinolin,
compactin and monacol K which inhibits the enzyme.
Inhibition of HIV protease.The replication of HIV-1 is the cause of AIDS. The HIV-
1 protease catalyses this protein sequence. HIV protease is an aspartyl protease
having a sequence Asp-thr-Gly at its active site. It resemble pepsin, and other
retroviral protease. Many inhibitors have been designed that are analogous like
rennin. Figure below showing structure of HIV protease.
There are number of enzymatic advantage method estimate the metabolite in presence
of many other substances an inhibitor present in serum may completely inhibit
enzyme activity. For the estimation of certain metabolite e.g. glucose, and plasma
glycerides enzyme methods are now used almost exclusively e.g. serum creatine and
non-enzymic method are still being used in clinical chemistry.
Blood glucose
In the investigation of diabetes there are three enzymatic method that are
available; hexokinase couple with glucose 6-phosphate dehydrogenase, glucose
oxidase coupled with peroxidase. The second method is glucose oxidase is more
commonly used.
________________________________________
Table 8.2 Some important therapeutic enzymes
Enzyme EC number Reaction Use
Asparaginase 3.5.1.1 L-Asparagine H2O L-aspartate + NH3 Leukaemia
Collagenase 3.4.24.3 Collagen hydrolysis Skin ulcers
Glutaminase 3.5.1.2 L-Glutamine H2O L-glutamate + NH3 Leukaemia
Hyaluronidasea
3.2.1.35 Hyaluronate hydrolysis Heart attack
Lysozyme 3.2.1.17 Bacterial cell wall hydrolysis Antibiotic
Rhodanaseb
2.8.1.1 S2O32- + CN- SO32- + SCN-
Cyanide poisoning
Ribonuclease 3.1.26.4 RNA hydrolysis Antiviral
β-Lactamase 3.5.2.6 Penicillin penicilloate
Penicillin allergy
Streptokinasec
3.4.22.10 Plasminogen plasmin
Blood clots
Trypsin 3.4.21.4 Protein hydrolysis Inflammation
Uricased
1.7.3.3 Urate + O2 allantoin
Gout
Urokinasee
3.4.21.31 Plasminogen plasmin
Blood clots
a Hyaluronoglucosaminidase, b thiosulphate sulfurtransferase,c streptococcal
cysteine proteinase
d urate oxidase,e plasminogen activator
________________________________________
Disadvantages of Using Enzyme as Therapeutic Agents
As enzymes are specific biological catalysts, they should make the most desirable
therapeutic agents for the treatment of metabolic diseases. Unfortunately a number
of factors severely reduce this potential utility:
a) They are too large to be distributed simply within the body's cells. This is
the major reason why enzymes have not yet been successful applied to the large
number of human genetic diseases. A number of methods are being developed in order
to overcome this by targeting enzymes; as examples, enzymes with covalently
attached external α-galactose residues are targeted at hepatocytes and enzymes
covalently coupled to target-specific monoclonal antibodies are being used to
avoid non-specific side-reactions.
b) Being generally foreign proteins to the body, they are antigenic and can
elicit an immune response which may cause severe and life-threatening allergic
reactions, particularly .on continued use. It has proved possible to circumvent
this problem, in some cases, by disguising the enzyme as an apparently non-
proteinaceous molecule by covalent modification.
Asparaginase, modified by covalent attachment of polyethylene glycol, has been
shown to retain its anti-tumour effect whilst possessing no immunogenicity.
Clearly the presence of toxins, pyrogens and other harmful materials within a
therapeutic enzyme preparation is totally forbidden. Effectively, this encourages
the use of animal enzymes, in spite of their high cost, relative to those of
microbial origin.
Their effective lifetime within the circulation may be only a matter of minutes.
This has proved easier than the immunological problem to combat, by disguise using
covalent modification. Other methods have also been shown to be successful,
particularly those involving entrapment of the enzyme within artificial
liposome’s, synthetic microspheres and red blood cell ghosts. However, although
these methods are efficacious at extending the circulatory lifetime of the
enzymes, they often cause increased immunological response and additionally may
cause blood clots.
In contrast to the industrial use of enzymes, therapeutically useful enzymes are
required in relatively tiny amounts but at a very high degree of purity and
(generally) specificity. The favoured kinetic properties of these enzymes are low
Km and high Vmax in order to be maximally efficient even at very low enzyme and
substrate concentrations. Thus the sources of such enzymes are chosen with care to
avoid any possibility of unwanted contamination by incompatible material and to
enable ready purification. Therapeutic enzyme preparations are generally offered
for sale as lyophilised pure preparations with only biocompatible buffering salts
and mannitol diluent added.
The costs of such enzymes may be quite high but still comparable to those of
competing therapeutic agents or treatments. As an example, urokinase (a serine
protease, see Table 4.4) is prepared from human urine (some genetically engineered
preparations are being developed) and used to dissolve blood clots. The cost of
the enzyme is about Rs. 5000 mg-1, with the cost of treatment in a case of lung
embolism being about Rs. 50000 for the enzyme alone. In spite of this, the market
for the enzyme is worth about Rs 350M year-1.
INDUSTRIAL ENZYME PROCESS AT HIGH TEMPERATURE 8.3
Enzyme operating temperature 0C Major
applications
alpha amylase (bacterial) 90-100 starch hydroysis, brewing baking detergents
Gluco amylase 50-60 Maltodextrin hydrolysis
alpha amylase (fungal) 50-60 Maltose
Pullulanase 50-60 high glucose syrups
Xylose isomerase 45-55 High fructose syrups
Pectinase 20-50 clarification of juices
/wines
Cellulose 45-55 cellulose hydrolysis
Lactase 30-50 lactose hydrolysis ,
food processing
Acid protease 30-50 food processing
fungal protease 40-60 baking ,brewing,food
processing
Alkaline proteases 40-60 Detergents
Lipases 30-70 Detergents, food
processing
Enzyme used in Industries
Thermozymes
Thermozymes are thermostable enzymes that function optimally at 60 0C and 125 0C.
these extremozymes are extremely valuable tools for study of protein stability
Thermozymes are used in the molecular biology experiments for example taq
polymerase and in the detergents (e.g.) proteases and starch processing (e.g.
alpha amylase, glucsoe isomerases) various lipase and proteases oxidoreductase are
used in the diagnostics, waste treatment and pulp and paper manufacture.
Thermozymes are more stable because they are active against denaturing condition
Hyperthermophiles have good potential for use in novel biotechnological processes
including oil coal and waste gas desulphurization, heavy metal leaching and
bioconversion of crude oils. Thermostable enzymes such as DNA polymerase,
amylases, xylanases proteases and lipase are required in basic research and
biotechnology.
Organic solvent tolerant bacteria that exhibit the ability to degrade crude oil,
polyaromatic hydrocarbons, or cholesterol or can utilize sulphure compounds have
been isolated. e.g. Strain Y-40 degrades hydrocarbons and belongs to Candida. It
can grow well in the presence of solvents such as n-octane, isooctane, cyclo-
octane, or kerosene at a concentration of 50 % (v/v) the first strain that
isolated for organic solvent tolerant bacterium e.g. Pseudomonas putida can grow
in more than 50% toluene.
Obligate extremophiles such as thiobacillus thiooxidans and thiobacillus
ferrooxidanse occur in highly acidic environments. T. ferroxidans reduces sulphure
compounds as well as ferrous ion to ferric. This leads to production of acids.
Currently these bacteria are utilized in the Biomining used in minerals leaching
for example. T. ferroxidans used to isolate sulphure from the coal.
Many extremophiles are used for craft industry for leather tanning (B. subtilis
and B. licheniformis) with the help of various alkalophiles. Alkalophiles such as
bacillus strains N-4 are used for cellulose digestion in the waste water treatment
to digest cellulose. xylanases are produced by the alkalophiles Aeromonas strain
212 that can hydrolyze the beta 1.-4 linkage in the xylan polysaccharides in the
crop plant. They show good activity and stability at pH 9. Neutral
metalloproteases from B. amyloliquifaciens can be used in the brewing industry,
when substituting malt with unmlated barley to increase the amount of free amino
acids.
The large-scale use of enzymes in solution
Several enzymes, especially those used in starch processing, high-fructose syrup
manufacture, textile desizing and detergent formulation, are now traded as
commodity products on the world's markets. Although the cost of enzymes for use at
the research scale is often very high, where there is a clear large-scale need for
an enzyme its relative cost reduces dramatically with increased production.
Relatively few enzymes, notably those in detergents, meat tenderizers and garden
composting agents, are sold directly to the public. Most are used by industry to
produce improved or novel products, to bypass long and involved chemical synthetic
pathways or for use in the separation and purification of isomeric mixtures. Many
of the most useful, but least-understood, uses of free enzymes are in the food
industry. Here they are used, together with endogenous enzymes, to produce or
process foodstuffs, which are only rarely substantially refined. Their action,
however apparently straightforward, is complicated due to the effect that small
amounts of by-products or associated reaction products have on such subjective
effects as taste, smell, colour and texture.
The use of enzymes in the non-food (chemicals and pharmaceuticals) sector is
relatively straightforward. Products are generally separated and purified and,
therefore, they are not prone to the subtleties available to food products. Most
such enzymic conversions benefit from the use of immobilised enzymes or biphasic
systems
The use of enzymes in detergents
The use of enzymes in detergent formulations is now common in developed countries,
with over half of all detergents presently available containing enzymes. In spite
of the fact that the detergent industry is the largest single market for enzymes
at 25 - 30% of total sales. details of the enzymes used and the ways in which they
are used, have rarely been published.
Dirt comes in many forms and includes proteins, starches and lipids. In addition,
clothes that have been starched must be freed of the starch. Using detergents in
water at high temperatures and with vigorous mixing, it is possible to remove most
types of dirt but the cost of heating the water is high and lengthy mixing or
beating will shorten the life of clothing and other materials. The use of enzymes
allows lower temperatures to be employed and shorter periods of agitation are
needed, often after a preliminary period of soaking. In general, enzyme detergents
remove protein from clothes soiled with blood, milk, sweat, grass, etc. far more
effectively than non-enzyme detergents. However, using modern bleaching and
brightening agents, the difference between looking clean and being clean may be
difficult to discern. At present only proteases and amylases are commonly used.
Although a wide range of lipases is known, it is only very recently that lipases
suitable for use in detergent preparations have been described.
Detergent enzymes must be cost-effective and safe to use. Early attempts to use
proteases foundered because of producers and users developing hypersensitivity.
This was combatted by developing dust-free granulates (about 0.5 mm in diameter)
in which the enzyme is incorporated into an inner core, containing inorganic salts
(e.g. NaCI) and sugars as preservative, bound with reinforcing, fibres of
carboxymethyl cellulose or similar protective colloid. This core is coated with
inert waxy materials made from paraffin oil or polyethylene glycol plus various
hydrophilic binders, which later disperse in the wash. This combination of
materials both prevents dust formation and protects the enzymes against damage by
other detergent components during storage.
Enzymes are used in surprisingly small amounts in most detergent preparations,
only 0.4 - 0.8% crude enzyme by weight (about 1% by cost). It follows that the
ability to withstand the conditions of use is a more important criterion than
extreme cheapness. Once released from its granulated form the enzyme must
withstand anionic and non-ionic detergents, soaps, oxidants such as sodium
perborate which generate hydrogen peroxide, optical brighteners and various less-
reactive materials (Table 15.4), all at pH values between 8.0 and 10.5. Although
one effect of incorporating enzymes is that lower washing temperatures may be
employed with consequent savings in energy consumption, the enzymes must retain
activity up to 60°C.
________________________________________
Table 15.4 Compositions of an enzyme detergent
Constituent Composition (%)
Sodium tripolyphosphate (water softener, loosens dirt)a
38.0
Sodium alkane sulphonate (surfactant) 25.0
Sodium perborate tetrahydrate (oxidising agent)25.0
Soap (sodium alkane carboxylates) 3.0
Sodium sulphate (filler, water softener) 2.5
Sodium carboxymethyl cellulose (dirt-suspending agent) 1.6
Sodium metasilicate (binder, loosens dirt) 1.0
Bacillus protease (3% active) 0.8
Fluorescent brighteners 0.3
Foam-controlling agents Trace
Perfume Trace
Water to 100%
a A recent trend is to reduce this phosphate content for environmental reasons. It
may be replaced by sodium carbonate plus extra protease.
________________________________________
The enzymes used are all produced using species of Bacillus, mainly by just two
companies. Novo Industri A/S produce and supply three proteases, Alcalase, from B.
licheniformis, Esperase, from an alkalophilic strain of a B. licheniformis and
Savinase, from an alkalophilic strain of B. amyloliquefaciens (often mistakenly
attributed to B. subtilis). GistBrocades produce and supply Maxatase, from B.
licheniformis. Alcalase and Maxatase (both mainly subtilisin) are recommended for
use at 10-65°C and pH 7-10.5. Savinase and Esperase may be used at up to pH 11 and
12, respectively. The -amylase supplied for detergent use is Termamyl, the
enzyme from B. licheniformis which is also used in the production of glucose
syrups. -Amylase is particularly useful in dish-washing and de-starching
detergents.
In addition to the granulated forms intended for use in detergent powders, liquid
preparations in solution in water and slurries of the enzyme in a non-ionic
surfactant are available for formulating in liquid 'spotting' concentrates, used
for removing stubborn stains. Preparations containing both Termamyl and Alcalase
are produced, Termamyl being sufficiently resistant to proteolysis to retain
activity for long enough to fulfil its function.
It should be noted that all the proteolytic enzymes described are fairly non-
specific serine endoproteases, giving preferred cleavage on the carboxyl side of
hydrophobic amino acid residues but capable of hydrolysing most peptide links.
They convert their substrates into small, readily soluble fragments which can be
removed easily from fabrics. Only serine protease; may be used in detergent
formulations: thiol proteases (e.g. papain) would be oxidised by the bleaching
agents, and metalloproteases (e.g. thermolysin) would lose their metal cofactors
due to complexing with the water softening agents or hydroxyl ions.
The enzymes are supplied in forms (as described above) suitable for formulation by
detergent manufacturers. Domestic users are familiar with powdered preparations
but liquid preparations for home use are increasingly available. Household
laundering present’s problems quite different from those of industrial laundering:
the household wash consists of a great variety of fabrics soiled with a range of
materials and the user requires convenience and effectiveness with less
consideration of the cost. Home detergents will probably include both an amylase
and a protease and a lengthy warm-water soaking time will be recommended.
Industrial laundering requires effectiveness at minimum cost so heated water will
be re-used if possible. Large laundries can separate their 'wash' into categories
and thus minimise the usage of water and maximise the effectiveness of the
detergents. Thus white cotton uniforms from an abattoir can be segregated for
washing, only protease being required. A pre-wash soaking for 10-20 min at pH up
to 11 and 30-40°C is followed by a main wash for 10-20 min at pH 11 and 60-65°C.
The water from these stages is discarded to the sewer. A third wash includes
hypochlorite as bleach which would inactivate the enzymes rapidly. The water from
this stage is used again for the pre-wash but, by then, the hypochlorite
concentration is insufficient to harm the enzyme. This is essentially a batch
process: hospital laundries may employ continuous washing machines, which transfer
less-initially-dirty linen from a pre-rinse initial stage, at 32°C and pH 8.5,
into the first wash at 60°C and pH 11, then to a second wash, containing hydrogen
peroxide, at 71°C and pH 11, then to a bleaching stage and rinsing. Apart from the
pre-soak stage, from which water is run to waste, the process operates counter-
currently. Enzymes are used in the pre-wash and in the first wash, the levels of
peroxide at this stage being insufficient to inactivate the enzymes.
There are opportunities to extend the use of enzymes in detergents both
geographically and numerically. They have not found widespread use in developing
countries which are often hot and dusty, making frequent washing of clothes
necessary. The recent availability of a suitable lipase may increase the
quantities of enzymes employed very significantly. There are, perhaps,
opportunities for enzymes such as glucose oxidase, lipoxygenase and glycerol
oxidase as means of generating hydrogen peroxide in situ. Added peroxidases may
aid the bleaching efficacy of this peroxide.
A recent development in detergent enzymes has been the introduction of an
alkaline-stable fungal cellulase preparation for use in washing cotton fabrics.
During use, small fibres are raised from the surface of cotton thread, resulting
in a change in the 'feel' of the fabric and, particularly, in the lowering of the
brightness of colours. Treatment with cellulase removes the small fibres without
apparently damaging the major fibres and restores the fabric to its 'as new'
condition. The cellulase also aids the removal of soil particles from the wash by
hydrolyzing associated cellulose fibres.
15.12 Applications of proteases in the food industry
Certain proteases have been used in food processing for centuries and any record
of the discovery of their activity has been lost in the mists of time. Rennet
(mainly chymosin), obtained from the fourth stomach (abomasum) of unweaned calves
has been used traditionally in the production of cheese. Similarly, papain from
the leaves and unripe fruit of the pawpaw (Carica papaya) has been used to
tenderize meats. These ancient discoveries have led to the development of various
food applications for a wide range of available proteases from many sources,
usually microbial. Proteases may be used at various pH values, and they may be
highly specific in their choice of cleavable peptide links or quite non-specific.
Proteolysis generally increases the solubility of proteins at their isoelectric
points.
15.13 Rennet in cheese making
The action of rennet in cheese making is an example of the hydrolysis of a
specific peptide linkage, between phenylalanine and methionine residues (-Phe105-
Met106-) in the κ-casein protein present in milk . The κ-casein acts by
stabilizing the colloidal nature of the milk, its hydrophobic N-terminal region
associating with the lipophilic regions of the otherwise insoluble - and β-
casein molecules, whilst its negatively charged C-terminal region associates with
the water and prevents the casein micelles from growing too large. Hydrolysis of
the labile peptide linkage between these two domains, resulting in the release of
a hydrophilic glycosylated and phosphorylated oligopeptide (caseino macropeptide)
and the hydrophobic para-κ-casein, removes this protective effect, allowing
coagulation of the milk to form curds, which are then compressed and turned into
cheese (Figure 4.1). The coagulation process depends upon the presence of Ca2+ and
is very temperature dependent (Q10 = 11) and so can be controlled easily. Calf
rennet, consisting of mainly chymosin with a small but variable proportion of
pepsin, is a relatively expensive enzyme and various attempts have been made to
find cheaper alternatives from microbial sources These have ultimately proved to
be successful and microbial rennets are used for about 70% of US cheese and 33% of
cheese production world-wide.
________________________________________
Figure 15. 3 The use of enzymes in processing starch. Typical conditions are
given.
________________________________________
Of the two components of starch, amylopectine presents the great challenge to
hydrolytic enzyme systems. This is due to the residues involved in α-1,6-
glycosidic branch points which constitute about 4 - 6% of the glucose present.
Most hydrolytic enzymes are specific for α-1,4-glucosidic links yet the -1,6-
glucosidic links must also be cleaved for complete hydrolysis of amylopectin to
glucose. Some of the most impressive recent exercises in the development of new
enzymes have concerned debranching enzymes.
It is necessary to hydrolyse starch in a wide variety of processes which may be
condensed into two basic classes:
Processes in which the starch hydrolysate is to be used by microbes or man, and
Processes in which it is necessary to eliminate starch.
In the former processes, such as glucose syrup production, starch is usually the
major component of reaction mixtures, whereas in the latter processes, such as the
processing of sugar cane juice, small amounts of starch which contaminate non-
starchy materials are removed. Enzymes of various types are used in these
processes. Although starches from diverse plants may be utilised, corn is the
world's most abundant source and provides most of the substrate used in the
preparation of starch hydrolysates.
There are three stages in the conversion of starch (Figure 15.3):
gelatinization, involving the dissolution of the nano-gram-sized starch granules
to form a viscous suspension;
liquefaction, involving the partial hydrolysis of the starch, with concomitant
loss in viscosity; and
Saccharification, involving the production of glucose and maltose by further
hydrolysis.
a. Gelatinization is achieved by heating starch with water, and occurs necessarily
and naturally when starchy foods are cooked. Gelatinized starch is readily
liquefied by partial hydrolysis with enzymes or acids and saccharified by further
acidic or enzymic hydrolysis.
The starch and glucose syrup industry uses the expression dextrose equivalent or
DE, similar in definition to the DH units of proteolysis, to describe its
products, where:
(15 .3)
In practice, this is usually determined analytically by use of the closely
related, but not identical, expression:
(15.4)
Thus, DE represents the percentage hydrolysis of the glycosidic linkages present.
Pure glucose has a DE of 100, pure maltose has a DE of about 50 (depending upon
the analytical methods used; see equation (15.4)) and starch has a DE of
effectively zero. During starch hydrolysis, DE indicates the extent to which the
starch has been cleaved. Acid hydrolysis of starch has long been used to produce
'glucose syrups' and even crystalline glucose (dextrose monohydrate). Very
considerable amounts of 42 DE syrups are produced using acid and are used in many
applications in confectionery. Further hydrolysis using acid is not satisfactory
because of undesirably coloured and flavoured breakdown products. Acid hydrolysis
appears to be a totally random process which is not influenced by the presence of
α-1,6-glucosidic linkages.
________________________________________
Table 15.5 Enzymes used in starch hydrolysis
Enzyme EC number Source Action
α-Amylase 3.2.1.1 Bacillus amyloliquefaciens Only α-1,4-oligosaccharide
links are cleaved to give α-dextrins and predominantly maltose (G2), G3, G6 and G7
oligosaccharides
B. licheniformis Only α1,4-oligosaccharide links are cleaved to give
α-dextrins and predominantly maltose, G3, G4 and G5 oligosaccharides
Aspergillus oryzae, A. niger Only α-1,4 oligosaccharide links are
cleaved to give α-dextrins and predominantly maltose and G3 oligosaccharides
Saccharifying α-amylase 3.2.1.1 B. subtilis (amylosacchariticus) Only
α-1,4-oligosaccharide links are cleaved to give α-dextrins with maltose, G3, G4
and up to 50% (w/w) glucose
β-Amylase 3.2.1.2 Malted barley Only α-1,4-links are cleaved, from non-
reducing ends, to give limit dextrins and β-maltose
Glucoamylase 3.2.1.3 A. niger α-1,4 and α1,6-links are cleaved, from
the nonreducing ends, to give α-glucose
Pullulanase 3.2.1.41 B. acidopullulyticus Only α-1,6-links are cleaved
to give straight-chain maltodextrins
________________________________________
The nomenclature of the enzymes used commercially for starch hydrolysis
The nomenclature of the enzymes used commercially for starch hydrolysis is
somewhat confusing and the EC numbers sometimes lump together enzymes with subtly
different activities (Table 15.5). For example, α-amylase may be subclassified as
liquefying or saccharifying amylases but even this classification is inadequate to
encompass all the enzymes that are used in commercial starch hydrolysis. One
reason for the confusion in the nomenclature is the use of the anomeric form of
the released reducing group in the product rather than that of the bond being
hydrolysed; the products of bacterial and fungal -amylases are in the -
configuration and the products of β-amylases are in the β-configuration, although
all these enzymes cleave between α-1,4-linked glucose residues.
The α-amylases (1,4-α-D-glucan glucanohydrolases) are endohydrolases which cleave
1,4-α-D-glycosidic bonds and can bypass but cannot hydrolyze 1,6-α-D-glucosidic
branch points. Commercial enzymes used for the industrial hydrolysis of starch are
produced by Bacillus amyloliquefaciens (supplied by various manufacturers) and by
B. licheniformis (supplied by Novo Industri A/S as Termamyl). They differ
principally in their tolerance of high temperatures, Termamyl retaining more
activity at up to 110°C, in the presence of starch, than the B. amyloliquefaciens
α-amylase. The maximum DE obtainable using bacterial α-amylases is around 40 but
prolonged treatment leads to the formation of maltulose (4-α-D-glucopyranosyl-D-
fructose), which is resistant to hydrolysis by glucoamylase and α-amylases. DE
values of 8-12 are used in most commercial processes where further
saccharification is to occur. The principal requirement for liquefaction to this
extent is to reduce the viscosity of the gelatinised starch to ease subsequent
processing.
Different approaches for starch liquefaction
Various manufacturers use different approaches to starch liquefaction using α-
amylases but the principles are the same. Granular starch is slurried at 30-40%
(w/w) with cold water, at pH 6.0-6.5, containing 20-80 ppm Ca2+ (which stabilizes
and activates the enzyme) and the enzyme is added (via a metering pump). The α-
amylase is usually supplied at high activities so that the enzyme dose is 0.5-0.6
kg tonne-1 (about 1500 U kg-1 dry matter) of starch. When Termamyl is used, the
slurry of starch plus enzyme is pumped continuously through a jet cooker, which is
heated to 105°C using live steam. Gelatinization occurs very rapidly and the
enzymic activity, combined with the significant shear forces, begins the
hydrolysis. The residence time in the jet cooker is very brief. The partly
gelatinized starch is passed into a series of holding tubes maintained at 100-
105°C and held for 5 min to complete the gelatinization process. Hydrolysis to the
required DE is completed in holding tanks at 90-100°C for 1 to 2 h. These tanks
contain baffles to discourage backmixing. Similar processes may be used with B.
amyloliquefaciens α-amylase but the maximum temperature of 95°C must not be
exceeded. This has the drawback that a final 'cooking' stage must be introduced
when the required DE has been attained in order to gelatinize the recalcitrant
starch grains present in some types of starch which would otherwise cause
cloudiness in solutions of the final product.
Saccharification
The liquefied starch is usually saccharified but comparatively small amounts are
spray-dried for sale as 'maltodextrins' to the food industry mainly for use as
bulking agents and in baby food. In this case, residual enzymic activity may be
destroyed by lowering the pH towards the end of the heating period.
Fungal α-amylase also finds use in the baking industry. It often needs to be added
to bread-making flours to promote adequate gas production and starch modification
during fermentation. This has become necessary since the introduction of combine
harvesters. They reduce the time between cutting and threshing of the wheat, which
previously was sufficient to allow a limited sprouting so increasing the amounts
of endogenous enzymes. The fungal enzymes are used rather than those from bacteria
as their action is easier to control due to their relative heat lability,
denaturing rapidly during baking. The liquefied starch at 8 -12 DE is suitable for
saccharification to produce syrups with DE values of from 45 to 98 or more. The
greatest quantities produced are the syrups with DE values of about 97. At present
these are produced using the exoamylase, glucan 1,4-α-glucosidase (1,4-α-D-glucan
glucohydrolase, commonly called glucoamylase but also called amyloglucosidase and
γ-amylase), which releases β-D-glucose from 1,4-α-, 1,6-α- and 1,3-α-linked
glucans. In theory, carefully liquefied starch at 8 -12 DE can be hydrolysed
completely to produce a final glucoamylase reaction mixture with DE of 100 but, in
practice, this can be achieved only at comparatively low substrate concentrations.
The cost of concentrating the product by evaporation decreases that a substrate
concentration of 30% is used. It follows that the maximum DE attainable is 96 - 98
with syrup composition 95 - 97% glucose, 1 - 2% maltose and 0.5 - 2% (w/w)
isomaltose (α-D-glucopyranosyl-(1,6)-D-glucose). This material is used after
concentration, directly for the production of high-fructose syrups or for the
production of crystalline glucose.
Whereas liquefaction is usually a continuous process, saccharification is most
often conducted as a batch process. The glucoamylase most often used is produced
by Aspergillus niger strains. This has a pH optimum of 4.0 - 4.5 and operates most
effectively at 60°C, so liquefied starch must be cooled and its pH adjusted before
addition of the glucoamylase. The cooling must b rapid, to avoid retrogradation
(the formation of intractable insoluble aggregates of amylose; the process that
gives rise to the skin on custard). Any remaining bacterial -amylase will be
inactivated when the pH is lowered; however, this may be replaced later by some
acid-stable -amylase which is normally present in the glucoamylase preparations.
When conditions are correct the glucoamylase is added, usually at the dosage of
0.65 - 0.80 litre enzyme preparation.tonne-1 starch (200 U kg-1). Saccharification
is normally conducted in vast stirred tanks, which may take several hours to fill
(and empty), so time will be wasted if the enzyme is added only when the reactors
are full. The alternatives are to meter the enzyme at a fixed ratio or to add the
whole dose of enzyme at the commencement of the filling stage. The latter should
give the most economical use of the enzyme.
________________________________________
Figure 15. 4. The % glucose formed from 30% (w/w) 12 DE maltodextrin, at 60°C and
pH 4.3, using various enzyme solutions. ———200 U kg-1 Aspergillus niger
glucoamylase; -----------400 U kg-1 A. niger glucoamylase; ••••••••• 200 U kg-1 A.
niger glucoamylase plus 200 U kg-1 Bacillus acidopullulyticus pullulanase. The
relative improvement on the addition of pullulanase is even greater at higher
substrate concentrations.
________________________________________
The saccharification process takes about 72 h to complete but may, of course, be
speeded up by the use of more enzyme. Continuous saccharification is possible and
practicable if at least six tanks are used in series. It is necessary to stop the
reaction, by heating to 85°C for 5 min, when a maximum DE has been attained.
Further incubation will result in a fall in the DE, to about 90 DE eventually,
caused by the formation of isomaltose as accumulated glucose re-polymerises with
the approach of thermodynamic equilibrium (Figure 15.4).
Final step in syrup formation
The saccharified syrup is filtered to remove fat and denatured protein released
from the starch granules and may then be purified by passage through activated
charcoal and ion-exchange resins. It should be remembered that the dry substance
concentration increases by about 11 % during saccharification, because one
molecule of water is taken up for each glycosidic bond hydrolysed (molecule of
glucose produced).
Although glucoamylase catalyses the hydrolysis of 1,6-α-linkages, their breakdown
is slow compared with that of 1,4-α-linkages (e.g. the rates of hydrolyzing the
1,4-α, 1,6-α and 1,3-α-links in tetrasaccharides are in the proportions 300 : 6 :
1). It is clear that the use of a debranching enzyme would speed the overall
saccharification process but, for industrial use such an enzyme must be compatible
with glucoamylase. Two types of debranching enzymes are available: pullulanase,
which acts as an exo hydrolase on starch dextrins; and isoamylase (EC.3.2.1.68),
which is a true endohydrolase. Novo Industri A/S have recently introduced a
suitable pullulanase, produced by a strain of Bacillus acidopullulyticus. The
pullulanase from Klebsiella aerogenes which has been available commercially to
some time is unstable at temperatures over 45°C but the B. acidopullulyticus
enzymes can be used under the same conditions as the Aspergillus glucoamylase
(60°C, pH 4.0-4.5). The practical advantage of using pullulanase together with
glucoamylase is that less glucoamylase need be used This does not in itself give
any cost advantage but because less glucoamylase is used and fewer branched
oligosaccharides accumulate toward the end of the saccharification, the point at
which isomaltose production becomes significant occurs at higher DE (Figure 4.3).
It follows that higher DE values and glucose contents can be achieved when
pullulanase is use (98 - 99 DE and 95 - 97% (w/w) glucose, rather than 97 - 98 DE)
and higher substrate concentrations (30 - 40% dry solids rather than 25 - 30%) may
be treated. The extra cost of using pullulanase is recouped by savings in
evaporation and glucoamylase costs. In addition, when the product is to be used to
manufacture high-fructose syrups, there is a saving in the cost of further
processing.
The development of the B. acidopullulyticus pullulanase is an excellent example of
what can be done if sufficient commercial pull exists for a new enzyme. The
development of a suitable α-D-glucosidase, in order to reduce the reversion, would
be an equally useful step for industrial glucose production. Screening of new
strains of bacteria for a novel enzyme of this type is a major undertaking. It is
not surprising that more details of the screening procedures used are not readily
available.
15.17 Production of syrups containing maltose
Traditionally, syrups containing maltose as a major component have been produced
by treating barley starch with barley β-amylase. β-Amylases (1,4-β-D-glucan
maltohydrolases) are exohydrolases which release maltose from 1,4-α-linked glucans
but neither bypass nor hydrolyse 1,6-α-linkages. High-maltose syrups (40 - 50 DE,
45-60% (w/w) maltose, 2 - 7% (w/w) glucose) tend not to crystallise, even below
0°C and are relatively non-hygroscopic. They are used for the production of hard
candy and frozen deserts. High conversion syrups (60 - 70 DE, 30 - 37% maltose, 35
- 43% glucose, 10% maltotriose, 15% other oligosaccharides, all by weight) resist
crystallisation above 4°C and are sweeter (Table 4.3). They are used for soft
candy and in the baking, brewing and soft drinks industries. It might be expected
that β-amylase would be used to produce maltose-rich syrups from corn starch,
especially as the combined action of β-amylase and pullulanase give almost
quantitative yields of maltose. This is not done on a significant scale nowadays
because presently available β-amylases are relatively expensive, not sufficiently
temperature stable (although some thermostable β-amylases from species of
Clostridium have recently been reported) and are easily inhibited by copper and
other heavy metal ions. Instead fungal β-amylases, characterised by their ability
to hydrolyse maltotriose (G3) rather than maltose (G2) are employed often in
combination with glucoamylase. Presently available enzymes, however, are not
totally compatible; fungal α-amylases requiring a pH of not less than 5.0 and a
reaction temperature not exceeding 55°C.
High-maltose syrups (see Figure 15.3) are produced from liquefied starch of around
11 DE at a concentration of 35% dry solids using fungal -amylase alone.
Saccharification occurs over 48 h, by which time the fungal -amylase has lost
its activity. Now that a good pullulanase is available, it is possible to use this
in combination with fungal -High-conversion syrups are produced using
combinations of fungal α-amylase and glucoamylase. These may be tailored to
customers' specifications by adjusting the activities of the two enzymes used but
inevitably, as glucoamylase is employed, the glucose content of the final product
will be higher than that of high-maltose syrups. The stability of glucoamylase
necessitates stopping the reaction, by heating, when the required composition is
reached. It is now possible to produce starch hydrolysates with any DE between 1
and 100 and with virtually any composition using combinations of bacterial α-
amylases, fungal α-amylases, glucoamylase and pullulanase.
________________________________________
Table 15.6 The relative sweetness of food ingredients
Food ingredient Relative sweetness (by weight, solids)
Sucrose 1.0
Glucose 0.7
Fructose 1.3
Galactose 0.7
Maltose 0.3
Lactose 0.2
Raffinose 0.2
Hydrolysed sucrose 1.1
Hydrolysed lactose 0.7
Glucose syrup 11 DE <0.1
Glucose syrup 42 DE 0.3
Glucose syrup 97 DE 0.7
Maltose syrup 44 DE 0.3
High-conversion syrup 65 DE 0.5
HFCS (42% fructose)a
1.0
HFCS (55% fructose) 1.1
Aspartame 180
a HFCS, high-fructose corn syrup.
15.18 Enzymes in the sucrose industry
The sucrose industry is a comparatively minor user of enzymes but provides few
historically significant and instructive examples of enzyme technology The
hydrolysis ('inversion') of sucrose, completely or partially, to glucose and
fructose provides sweet syrups that are more stable (i.e. less likely crystallise)
than pure sucrose syrups. The most familiar 'Golden Syrup' produced by acid
hydrolysis of one of the less pure streams from the cane sugar refinery but other
types of syrup are produced using yeast (Saccharomyces cerevisiae) invertase.
Although this enzyme is unusual in that it suffers from substrate inhibition at
high sucrose levels ( > 20% (w/w)), this does not prevent its commercial use at
even higher concentrations:
Figure 15. 6 Outline of the relationship between the enzyme activities in the
hydrolysis of cellulose. || represents inhibitory effects. Endo-1,4-β-glucanase is
the rate-controlling activity and may consist of a mixture of enzymes acting on
cellulose of different degrees of crystallinity. It acts synergistically with both
exo-1,4-β-glucosidase and exo-cellobiohydrolase. Exo-1,4-β-glucosidase is a
product-inhibited enzyme. Exo-cellobiohydrolase is product inhibited and
additionally appears to be inactivated on binding to the surface of crystalline
cellulose.
________________________________________
Proper economic analysis reveals that cheap sources of cellulose prove to be
generally more expensive as sources of glucose than apparently more expensive
starch. Relatively pure cellulose is valuable in its own right, as a paper pulp
and chipboard raw material, which currently commands a price of over twice that of
corn starch. With the increasing world shortage of pulp it cannot be seen
realistically as an alternative source of glucose in the foreseeable future.
Knowledge of enzyme systems capable of degrading lignocellulose is advancing
rapidly but it is unlikely that lignocellulose will replace starch as a source of
glucose syrups for food use. It is, however, quite possible that it may be used,
in a process involving the simultaneous use of both enzymes and fermentative
yeasts, to produce ethanol; the utilisation of the glucose by the yeast removing
its inhibitory effect on the enzymes. It should be noted that cellobiose is a non-
fermentable sugar and must be hydrolysed by additional β-glucosidase (EC 3.2.1.21,
also called cellobiase for maximum process efficiency (Figure 15.6).
15.20 The use of lactases in the dairy industry
Lactose is present at concentrations of about 4.7% (w/v) in milk and the whey
(supernatant) left after the coagulation stage of cheese-making. Its presence in
milk makes it unsuitable for the majority of the world's adult population,
particularly in those areas which have traditionally not had a dairy industry.
Real lactose tolerance is confined mainly to peoples whose origins lie in Northern
Europe or the Indian subcontinent and is due to 'lactase persistence'; the young
of all mammals clearly are able to digest milk but in most cases this ability
reduces after weaning. Of the Thai, Chinese and Black American populations, 97%,
90% and 73% respectively, are reported to be lactose intolerant, whereas 84% and
96% of the US White and Swedish populations, respectively, are tolerant.
Additionally, and only very rarely some individuals suffer from inborn metabolic
lactose intolerance or lactase deficiency, both of which may be noticed at birth.
The need for low-lactose milk is particularly important in food-aid programmes as
severe tissue dehydration, diarrhoea and even death may result from feeding
lactose containing milk to lactose-intolerant children and adults suffering from
protein-calorie malnutrition. In all these cases, hydrolysis of the lactose to
glucose and galactose would prevent the (severe) digestive problems.
Another problem presented by lactose is its low solubility resulting in crystal
formation at concentrations above 11 % (w/v) (4°C). This prevents the use of
concentrated whey syrups in many food processes as they have a unpleasant sandy
texture and are readily prone to microbiological spoilage. Adding to this problem,
the disposal of such waste whey is expensive (often punitively so) due to its high
biological oxygen demand. These problems may be overcome by hydrolysis of the
lactose in whey; the product being about four times as sweet (see Table 15.6),
much more soluble and capable of forming concentrated, microbiologically secure,
syrups (70% (w/v)).
Commercially, it may be prepared from the dairy yeast Kluyveromyces fragilis (K.
marxianus var. marxianus), with a pH optimum (pH 6.5-7.0) suitable for the
treatment of milk, or from the fungi Aspergillus oryzae or A. niger, with pH
optima (pH 4.5-6.0 and 3.0-4.0, respectively) more suited to whey hydrolysis.
These enzymes are subject to varying degrees of product inhibition by galactose.
In addition, at high lactose and galactose concentrations, lactase shows
significant transferase ability and produces β-1,6-linked galactosyl
oligosaccharides.
Lactases are now used in the production of ice cream and sweetened flavoured and
condensed milks. When added to milk or liquid whey (2000 U kg-1) and left for
about a day at 5°C about 50% of the lactose is hydrolysed, giving a sweeter
product which will not crystallise if condensed or frozen. This method enables
otherwise-wasted whey to replace some or all of the skim milk powder used in
traditional ice cream recipes. It also improves the 'scoopability' and creaminess
of the product. Smaller amounts of lactase may be added to long-life sterilised
milk to produce a relatively inexpensive lactose-reduced product (e.g. 20 U kg-1,
20°C, 1 month of storage). Generally, however, lactase usage has not reached its
full potential, as present enzymes are relatively expensive and can only be used
at low temperatures.
15.21 Enzymes in the fruit juice, wine, brewing and distilling industries
One of the major problems in the preparation of fruit juices and wine is
cloudiness due primarily to the presence of pectins. These consist primarily of α-
1,4-anhydrogalacturonic acid polymers, with varying degrees of methyl
esterification. They are associated with other plant polymers and, after
homogenisation, with the cell debris. The cloudiness that they cause is difficult
to remove except by enzymic hydrolysis. Such treatment also has the additional
benefits of reducing the solution viscosity, increasing the volume of juice
produced (e.g. the yield of juice from white grapes can be raised by 15%), subtle
but generally beneficial changes in the flavour and, in the case of wine-making,
shorter fermentation times. Insoluble plant material is easily removed by
filtration, or settling and decantation, once the stabilising effect of the
pectins on the colloidal haze has been removed.
Commercial pectolytic enzyme preparations are produced from Aspergillus niger and
consist of a synergistic mixture of enzymes:
polygalacturonase (EC 3.2.1.15), responsible for the random hydrolysis of 1,4- -
D-galactosiduronic linkages;
pectinesterase (EC 3.2.1.11), which releases methanol from the pectyl methyl
esters, a necessary stage before the polygalacturonase can act fully (the increase
in the methanol content of such treated juice is generally less than the natural
concentrations and poses no health risk);
pectin lyase (EC 4.2.2.10), which cleaves the pectin, by an elimination reaction
releasing oligosaccharides with non-reducing terminal 4-deoxymethyl-α-D-galact-4-
enuronosyl residues, without the necessity of pectin methyl esterase action; and
hemicellulase (a mixture of hydrolytic enzymes including: xylan endo-1,3-β-
xylosidase, EC 3.2.1.32; xylan 1,4-β-xylosidase, EC 3.2.1.37; and α-L-
arabinofuranosidase, EC 3.2.1.55), strictly not a pectinase but its adventitious
presence is encouraged in order to reduce hemicellulose levels.
The optimal activity of these enzymes is at a pH between 4 and 5 and generally
below 50°C. They are suitable for direct addition to the fruit pulps at levels
around 20 U l-1 (net activity). Enzymes with improved characteristics of greater
heat stability and lower pH optimum are currently being sought.
In brewing, barley malt supplies the major proportion of the enzyme needed for
saccharification prior to fermentation. Often other starch containing material
(adjuncts) are used to increase the fermentable sugar and reduce the relative
costs of the fermentation. Although malt enzyme may also be used to hydrolyse
these adjuncts, for maximum economic return extra enzymes are added to achieve
their rapid saccharification. It not necessary nor desirable to saccharify the
starch totally, as non-fermentable dextrins are needed to give the drink 'body'
and stabilise its foam 'head'. For this reason the saccharification process is
stopped, by boiling the 'wort', after about 75% of the starch has been converted
into fermentable sugar.
The enzymes used in brewing are needed for saccharification of starch (bacterial
and fungal α-amylases), breakdown of barley β-1,4- and β-1,3- linked glucan (β-
glucanase) and hydrolysis of protein (neutral protease) to increase the (later)
fermentation rate, particularly in the production of high-gravity beer, where
extra protein is added. Cellulases are also occasionally used, particularly where
wheat is used as adjunct but also to help breakdown the barley β-glucans. Due to
the extreme heat stability of the B. amyloliquefaciens α-amylase, where this is
used the wort must be boiled for a much longer period (e.g. 30 min) to inactivate
it prior to fermentation. Papain is used in the later post-fermentation stages of
beer-making to prevent the occurrence of protein- and tannin-containing 'chill-
haze' otherwise formed on cooling the beer. Recently, 'light' beers, of lower
calorific content, have become more popular. These require a higher degree of
saccharification at lower starch concentrations to reduce the alcohol and total
solids contents of the beer. This may be achieved by the use of glucoamylase
and/or fungal -amylase during the fermentation.
A great variety of carbohydrate sources are used world wide to produce distilled
alcoholic drinks. Many of these contain sufficient quantities of fermentable sugar
(e.g. rum from molasses and brandy from grapes), others contain mainly starch and
must be saccharified before use (e.g. whiskey from barley malt, corn or rye). In
the distilling industry, saccharification continues throughout the fermentation
period. In some cases (e.g. Scotch malt whisky manufacture uses barley malt
exclusively) the enzymes are naturally present but in others (e.g. grain spirits
production) the more heat-stable bacterial -amylases may be used in the
saccharification.
15.22 Glucose oxidase and catalase in the food industry
Glucose oxidase is a highly specific enzyme, from the fungi Aspergillus niger and
Penicillium, which catalyses the oxidation of β-glucose to glucono-1,5-lactone
(which spontaneously hydrolyses non-enzymically to gluconic acid) using molecular
oxygen and releasing hydrogen peroxide. It finds uses in the removal of either
glucose or oxygen from foodstuffs in order to improve their storage capability.
Hydrogen peroxide is an effective bacteriocide and may be removed, after use, by
treatment with catalase (derived from the same fungal fermentations as the glucose
oxidase) which converts it to water and molecular oxygen:
catalase
2H2O2 2H2O + O2 [4.4]
For most large-scale applications the two enzymic activities are not separated.
Glucose oxidase and catalase may be used together when net hydrogen peroxide
production is to be avoided.
A major application of the glucose oxidase/catalase system is in the removal of
glucose from egg-white before drying for use in the baking industry. A mixture of
the enzymes is used (165 U kg-1) together with additional hydrogen peroxide (about
0.1 % (w/w)) to ensure that sufficient molecular oxygen is available, by catalase
action, to oxidise the glucose. Other uses are in the removal of oxygen from the
head-space above bottled and canned drinks and reducing non-enzymic browning in
wines and mayonnaises.
Chapter-16 Enzyme Reactors
Introduction
An enzyme reactor consists of a vessel, or series of vessels, used to perform a
desired conversion by enzymic means. There are several important factors that
determine the choice of reactor for a particular process. In general, the choice
depends on the cost of a predetermined productivity within the product's
specifications. This must be inclusive of the costs associated with substrate(s),
downstream processing, labour, depreciation, overheads and process development, in
addition to the more obvious costs concerned with building and running the enzyme
reactor. Other contributing factors are the form of the enzyme of choice (i.e.
free or immobilised), the kinetics of the reaction and the chemical and physical
properties of an immobilization support including whether it is particulate,
membranous or fibrous, and its density, compressibility, robustness, particle size
and regenerability. Attention must also be paid to the scale of operation, the
possible need for pH and temperature control, the supply and removal of gases and
the stability of the enzyme, substrate and product. These factors will be
discussed in more detail with respect to the different types of reactor.
There are two type of Reactor 1. Batch Reactor; 2. Continuous reactor
Stirred tank batch reactor (STR).
Batch membrane reactor (MR).
Packed bed reactor (PBR).
continuous flow stirred tank reactor (CSTR.
continuous flow membrane reactor (CMR)
fluidised bed reactor (FBR)
16.1 Batch Reactor
Batch reactors generally consist of a tank containing a stirrer (stirred tank
reactor, STR). Note that a batch reactor is one in which all of the product is
removed, as rapidly as is practically possible, after a fixed time. The tank is
normally fitted with fixed baffles that improve the stirring efficiency. Generally
this means that the enzyme and substrate molecules must have identical residence
times within the reactor, although in some circumstances there may be a need for
further additions of enzyme and/or substrate (i.e. fed -batch operation).
a. Disadvantage of using batch reactor
1. The operating costs of batch reactors are higher than for continuous processes
due to the necessity for the reactors to be emptied and refilled both regularly
and often. This procedure is not only expensive in itself but means that there are
considerable periods when such reactors are not productive; it also makes uneven
demands on both labour and services.
2. STRs can be used for processes involving non-immobilised enzymes, if the
consequences of these contaminating the product are not severe.
3. Batch reactors also suffer from pronounced batch-to-batch variations, as the
reaction conditions change with time, and may be difficult to scale-up, due to the
changing power requirements for efficient fixing.
b. Advantage of using Batch Bioreactor
They do, however, have a number of advantageous features. Primary amongst these is
their simplicity both in use and in process development. For this reason they are
preferred for small-scale production of highly priced products, especially where
the same equipment is to be used for a number of different conversions. They offer
a closely controllable environment that is useful for slow reactions, where the
composition may be accurately monitored, and conditions (e.g. temperature, pH,
coenzyme concentrations) varied throughout the reaction. They are also of use when
continuous operation of a process proves to be difficult due to the viscous or
intractable nature of the reaction mix.
________________________________________
Figure 16. 2 This figure shows two related behaviours. (a) The change in substrate
and product concentrations with time, in a batch reactor. The reaction S P is
assumed, with the initial condition [S]0/Km = 10. The concentrations of substrate
(——— and product (-----------) are both normalised with respect to [S]0. The
normalised time (i.e. t° = t Vmax/[S]0) is relative to the time (t° = 1) that
would be required to convert all the substrate if the enzyme acted at Vmax
throughout, the actual time for complete conversion being longer due to the
reduction in the substrate concentration at the reaction progresses. The dashed
line also indicates the variation of the fractional conversion (X) with t°. (b)
The change in substrate and product concentrations with reactor length for a PBR.
The reaction S P is assumed with the initial condition, [S]0/Km = 10. The
concentrations of substrate (———) and product (-----------) are both normalised
with respect to [S]". The normalised reactor length (i.e. I° = lVmax/F, where Vmax
is the maximum velocity for unit reactor length and I is the reactor length) is
relative to the length (i.e. when I° = 1) that contains sufficient enzyme to
convert all the substrate at the given flow rate if the enzyme acted at its
maximum velocity throughout; the actual reactor length necessary for complete
conversion being longer due to the reduction in the substrate concentration as the
reaction progresses. P may be considered as the relative position within a PBR or
the reactor's absolute length.
________________________________________
16.2 Membrane reactors
The main requirement for a membrane reactor (MR) is a semipermeable membrane which
allows the free passage of the product molecules but contains the enzyme
molecules. A cheap example of such a membrane is the dialysis membrane used for
removing low molecular weight species from protein preparations. The usual choice
for a membrane reactor is a hollow-fibre reactor consisting of a preformed module
containing hundreds of thin tubular fibres each having a diameter of about 200
m and a membrane thickness of about 50 m.
Advantage of using Membrane reactor
[1] Membrane reactors may be used in either batch or continuous mode and [2] they
allow the easy separation of the enzyme from the product. [3] They are normally
used with soluble enzymes, avoiding the costs and problems associated with other
methods of immobilization and some of the diffusion limitations of immobilized
enzymes. If the substrate is able to diffuse through the membrane, it may be
introduced to either side of the membrane with respect to the enzyme; otherwise it
must be within the same compartment as the enzyme, a configuration that imposes a
severe restriction on the flow rate through the reactor, if used in continuous
mode.[4] Due to the ease with which membrane reactor systems may be established,
they are often used for production on a small scale (g to kg), especially where a
multi-enzyme pathway or coenzyme regeneration is needed.[5] They allow the easy
replacement of the enzyme in processes involving particularly labile enzymes and
can also be used for biphasic reactions.
The major disadvantage of these reactors concerns the cost of the membranes and
their need to be replaced at regular intervals.
16.3 The kinetics of membrane reactors
The kinetics of membrane reactors are similar to those of the batch STR, in batch
mode, or the CSTR, in continuous mode (see later). Deviations from these models
occur primarily in configurations where the substrate stream is on the side of the
membrane opposite to the enzyme and the reaction is severely limited by its
diffusion through the membrane and the products' diffusion in the reverse
direction. Under these circumstances the reaction may be even more severely
affected by product inhibition or the limitations of reversibility than is
indicated by these models.
16.4 Packed bed reactors (PBR)
The most important characteristic of a PBR is that; they are also called plug flow
reactors (PFR) because material flows through the reactor as a plug. Ideally, all
of the substrate stream flows at the same velocity, parallel to the reactor axis
with no back -mixing. All material present at any given reactor cross -section has
had an identical residence time. The longitudinal position within the PBR is,
therefore, proportional to the time spent within the reactor; all product emerging
with the same residence time and all substrate molecule having an equal
opportunity for reaction. The conversion efficiency of a PBR, with respect to its
length, behaves in a manner similar to that of a well -stirred batch reactor with
respect to its reaction time (Figure 5.2(b)) Each volume element behaves as a
batch reactor as it passes through the PBR. Any required degree of reaction may be
achieved by use of an idea PBR of suitable length.
The flow rate (F) is equivalent to VolS/t for a batch reactor. Therefore equation
(16.5) may be converted to represent an ideal PBR, given the assumption, not often
realised in practice, that there are no diffusion limitations:
(16.6)
In order to produce ideal plug -flow within PBRs, a turbulent flow regime is
preferred to laminar flow, as this causes improved mixing and heat transfer normal
to the flow and reduced axial back-mixing. Achievement of high enough Re may,
however, be difficult due to unacceptably high feed rates. Consequent upon the
plug -flow characteristic of the PBR is that the substrate concentration is
maximised, and the product concentration minimised, relative to the final
conversion at every point within the reactor; the effectiveness factor being high
on entry to the reactor and low close to the exit. This means that PBRs are the
preferred reactors, all other factors being equal, for processes involving product
inhibition, substrate activation and reaction reversibility. At low Re the flow
rate is proportional to the pressure drop across the PBR. This pressure drop is,
in turn, generally found to be proportional to the bed height, the linear flow
rate and dynamic viscosity of the substrate stream and (1 - ε)2/ε3 (where ε is
the porosity of the reactor; i.e. the fraction of the PBR volume taken up by the
liquid phase), but inversely proportional to the cross-sectional area of the
immobilised enzyme pellets. In general PBRs are used with fairly rigid
immobilised-enzyme catalysts (1 -3 mm diameter), because excessive increases in
this flow rate may distort compressible or physically weak particles. Particle
deformation results in reduced catalytic surface area of particles contacting the
substrate-containing solution, poor external mass transfer characteristics and a
restriction to the flow, causing increased pressure drop. A vicious circle of
increased back-pressure, particle deformation and restricted flow may eventually
result in no flow at all through the PBR.
PBRs behave as deep-bed filters with respect to the substrate stream. It is
necessary to use a guard bed if plugging of the reactor by small particles is more
rapid than the biocatalysts' deactivation. They are also easily fouled by
colloidal or precipitating material. The design of PBRs does not allow for control
of pH, by addition of acids or bases, or for easy temperature control where there
is excessive heat output, a problem that may be particularly noticeable in wide
reactors (> 15 cm diameter).
Deviations from ideal plug-flow are due to back-mixing within the reactors, the
resulting product streams having a distribution of residence times. In an extreme
case, back-mixing may result in the kinetic behaviour of the reactor approximating
to that of the CSTR (see below), and the consequent difficulty in achieving a high
degree of conversion. These deviations are caused by channeling, where some
substrate passes through the reactor more rapidly, and hold-up, which involves
stagnant areas with negligible flow rate. Channels may form in the reactor bed due
to excessive pressure drop, irregular packing or uneven application of the
substrate stream, causing flow rate differences across the bed. The use of a
uniformly sized catalyst in a reactor with an upwardly flowing substrate stream
reduces the chance and severity of non-ideal behavior.
16.5 Continuous flow stirred tank reactors (CSTIR)
This reactor consists of a well -stirred tank containing the enzyme, which is
normally immobilised. The substrate stream is continuously pumped into the reactor
at the same time as the product stream is removed. This is the example of
continous reactor. If the reactor is behaving in an ideal manner, there is total
back-mixing and the product stream is identical with the liquid phase within the
reactor and invariant with respect to time. Some molecules of substrate may be
removed rapidly from the reactor, whereas others may remain for substantial
periods. The distribution of residence times for molecules in the substrate stream
is shown in Figure 16.2
Advantages
The CSTR is an easily constructed, versatile and cheap reactor, which allows
simple catalyst charging and replacement.
Its well -mixed nature permits straightforward control over the temperature and
pH of the reaction and the supply or removal of gases.
CSTRs tend to be rather large as the: need to be efficiently mixed. Their volumes
are usually about five to ten time the volume of the contained immobilised enzyme.
This, however, has the advantage that there is very little resistance to the flow
of the substrate stream, which may contain colloidal or insoluble substrates, so
long as the insoluble particles are not able to sweep the immobilised enzyme from
the reactor.
The mechanical nature of the stirring limits the supports for the immobilised
enzymes to materials which do not easily disintegrate to give 'fines' which may
enter the product stream. However, fairly small particle (down to about 10 m
diameter) may be used, if they are sufficiently dense to stay within the reactor.
This minimises problems due to diffusional resistance.
An ideal CSTR has complete back -mixing resulting in a minimisation of the
substrate concentration, and a maximisation of the product concentration, relative
to the final conversion, at every point within the reactor the effectiveness
factor being uniform throughout. Thus, CSTRs are the preferred reactors,
everything else being equal, for processes involving substrate inhibition or
product activation. They are also useful where the substrate stream contains an
enzyme inhibitor, as it is diluted within the reactor. This effect is most
noticeable if the inhibitor concentration is greater than the inhibition constant
and [S]0/Km is low for competitive inhibition or high for uncompetitive
inhibition, when the inhibitor dilution has more effect than the substrate
dilution. Deviations from ideal CSTR behaviour occur when there is a less
effective mixing regime and may generally be overcome by increasing the stirrer
speed, decreasing the solution viscosity or biocatalyst concentration or by more
effective reactor baffling.
Kinetics of CSTR
The rate of reaction within a CSTR can be derived from a simple mass balance to be
the flow rate (F) times the difference in substrate concentration between the
reactor inlet and outlet. Hence:
(16.7)
Therefore:
(16.8)
from equation (5.4):
(16.9)
Therefore:
(16.10)
This equation should be compared with that for the PBR (equation (16.6)). Together
these equations can be used for comparing the productivities of the two reactors
(Figures 16.4 and 16.5).
________________________________________
Figure 16. 3Figure 5.4. The residence time distribution of a CSTR. The relative
number of molecules resident within the reactor for a particular time N, is
plotted against the normalised residence time (i.e. t F/V, where V is the reactor
volume, and F is the flow rate; it is the time relative to that required for one
reactor volume to pass through the reactor). The residence time distribution of
non -reacting media molecules ( ----------- which obeys the relationship , where
[M] is the concentration of media molecules, giving a half-life for remaining in
the reactor of , product (——— ) and substrate (•••••••••) are shown. The reaction
S P is assumed, and substrate molecules that have long residence times are
converted into product, the average residence time of the product being greater
than that for the substrate. The composition of the product stream is identical
with that of the liquid phase within the reactor. This composition may be
calculated from the relative areas under the curves and, in this case, represents
a 90% conversion. Under continuous operating conditions (operating time > 4V/F),
the mean residence time within the reactor is V/F. However, it may be noted from
the graph that only a few molecules have a residence time close to this value
(only 7% between 0.9V/F and 1.1 V/F) whereas 20% of the molecules have residence
times of less than 0.1 V/F or greater than 2.3V/F. It should be noted that 100% of
the molecules in an equivalent ideal PBR might be expected to have residence times
equal to their mean residence time.
________________________________________
Figure 16. 4Figure 5.5. Comparison of the changes in fractional conversion with
flow rate between the PBR (———) and CSTR (-----------) at different values of
[S]0/Km (10,1 and 0.1, higher [S]0/Km giving the higher curves). The flow rate is
normalised with respect to the reactor's volumetric enzyme content ( = FKm/Vmax.
It can be seen that there is little difference between the two reactors at faster
flow rates and lower conversions, especially at high values of [S]0/Km.
________________________________________
Figure 16. 5 Figure 5.6. Comparison of the changes in fractional conversion with
residence time between the PBR (———) and CSTR (-----------) at different values of
[S]0/Km (10, 1 and 0.1; higher [S]0/Km values giving the lower curves). The
residence time is the reciprocal of the normalised flow rate (see Figure 5.5). If
the flow rate is unchanged then the 'normalised residence time' may be thought of
as the reactor volume needed to produce the required degree of conversion.
________________________________________
Equations describing the behaviour of CSTRs and PBRs utilising reversible
reactions or undergoing product or substrate inhibition can be derived in a
similar manner, using equations (1.68), (1.85) and (1.96) rather than (1.8):
a. Substrate -inhibited PBR
(16.11)
Substrate -inhibited CSTR
(16.12)
b. Product -inhibited PBR
(16.13)
Product -inhibited CSTR
(16.14)
Reversible reaction in a PBR
(16.15)
Reversible reaction in a CSTR
(16.16)
X in equations (5.15) and (5.16) is the fractional conversion for a reversible
reaction.
(16.17)
These equations may be used to compare the size of PBR and CSTR necessary to
achieve the same conversion under various conditions (Figure 16.6).
The productivity
Another useful parameter for comparing these reactors is the productivity. This
can be derived for each reactor assuming a first-order inactivation of the enzyme
(equation (1.26)). Combined with equation (5.6) for PBR, or (5.10) for CSTR, the
following relationships are obtained on integration:
PBR (16.18)
CSTR (16.19)
where kd is the first -order inactivation constant (i.e. kd1, in equation (1.25))
and the fractional conversion subscripts refer to time = 0 or t. The change in
productivity (Figure 16.7) and fractional conversion (Figure 16.8) of these
reactors with time can be compared using these equations.
These reactors may be operated for considerably longer periods than that
determined by the inactivation of their contained immobilised enzyme, particularly
if they are capable of high conversion at low substrate concentrations (Figure
16.8). This is independent of any enzyme stabilisation and is simply due to such
reactors initially containing large amounts of redundant enzyme.
________________________________________
Figure 16. 6Figure 5.7. Comparison of the ratio, of the enzyme content in a CSTR
to that in a PBR, necessary to achieve various degrees of conversion for a range
of process conditions. The actual size of the CSTR will be five to ten times
greater than indicated due to the necessity of maintaining stirring within the
vessel. ———Uninhibited reaction; •••••••••••• product inhibited; ---------
substrate inhibited. (curve a) [S]0/Km = 100; (curve b) [S]0/Km = 1; (curve c)
[S]0/Km < 0.01; (curve d) [S]0/Km = 1, product inhibited KP/Km = 0.1 ; (curve e)
[S]0/Km = 1, product inhibited KP/Km = 0.01; (curve f) [S]0/Km = 1, substrate
inhibited [S]0/KS = 10; (curve g) [S]0/Km = 100; substrate inhibited [S]0/KS = 10.
The size of a CSTR becomes prohibitively large at high conversions (e.g. using
curve b, a CSTR contains three times the enzyme in a PBR to achieve a 90%
conversion, but this increases to 18 times for 99% conversion. The difference
between the two types of reactor is increased if the effectiveness factor (η) is
less than one due to diffusional effects.
________________________________________
Figure 16. 7Figure 5.8. The change in productivity of a PBR (---------) and CSTR
(———) with time, assuming an initial fractional conversion (X0) = 0.99 and [S]0/Km
= 100. The units of time are half -lives of the free enzyme ( ) and the
productivity is given in terms of (FXt1/2). Although the overall productivity is
1.6 times greater for a CSTR than a PBR, it should be noted that the CSTR contains
1.9 times more enzyme.
________________________________________
In general, there is little or no back -pressure to increased flow rate through
the CSTR. Such reactors may be started up as batch reactors until the required
degree of conversion is reached, when the process may be made continuous. CSTRs
are not generally used in processes involving high conversions but a chain of
CSTRs may approach the PBR performance. This chain may be a number (greater than
three) of reactors connected in series or a single vessel divided into
compartments, in order to minimise back-mixing CSTRs may be used with soluble
rather than immobilised enzyme if an ultrafiltration membrane is used to separate
the reactor output stream from the reactor contents. This causes a number of
process difficulties, including concentration polarization or inactivation of the
enzyme on the membrane but may be preferable in order to achieve a combined
reaction and separation process or where a suitable immobilised enzyme is not
readily available.
________________________________________
Figure 16. 8Figure 5.9. The change in fractional conversion of PBRs and CSTRs with
time, assuming initial fractional conversion (X0) of 0.99 or 0.80. ————CSTR,
[S]o/Km = 0.01; - - - - - - CSTR, [S]0/Km = 100; •••••••••••• PBR [S]0/Km =
0.01; •-•-•-•-•-•-•-• PBR [S]0/Km = 100. The time is given in terms of the half
-life of the free enzyme ( ). Although the CSTR maintains its fractional
conversion for a longer period than the PBR, particularly at high X0. It should be
noted that a CSTR capable of X0 = 0.99 at a substrate feed concentration of
[S]0/Km = 0.01 contains 22 times more enzyme than an equivalent PBR, but yields
only 2.2 times more product. The initial stability in the fractional conversion
over a considerable period of time, due to the enzyme redundancy, should not be
confused with any effect due to stabilisation of the immobilised enzyme.
5. Fluidised bed reactors
These reactors generally behave in a manner intermediate between CSTRs and PBRs.
They consist of a bed of immobilised enzyme which is fluidised by the rapid
upwards flow of the substrate stream alone or in combination with a gas or
secondary liquid stream, either of which may be inert or contain material relevant
to the reaction. A gas stream is usually preferred as it does not dilute the
product stream. There is a minimum fluidisation velocity needed to achieve bed
expansion, which depends upon the size, shape, porosity and density of the
particles and the density and viscosity of the liquid. This minimum fluidisation
velocity is generally fairly low (about 0.2 -I.0 cm s-1) as most immobilised-
enzyme particles have densities close to that of the bulk liquid. In this case the
relative bed expansion is proportional to the superficial gas velocity and
inversely proportional to the square root of the reactor diameter. Fluidising the
bed requires a large power input but, once fluidised, there is little further
energetic input needed to increase the flow rate of the substrate stream through
the reactor (Figure 16.2). At high flow rates and low reactor diameters almost
ideal plug -flow characteristics may be achieved. However, the kinetic performance
of the FBR normally lies between that of the PBR and the CSTR, as the small fluid
linear velocities allowed by most biocatalytic particles causes a degree of back-
mixing that is often substantial, although never total. The actual design of the
FBR will determine whether it behaves in a manner that is closer to that of a PBR
or CSTR (see Figures 5.5 -5.9). It can, for example, be made to behave in a manner
very similar to that of a PBR, if it is baffled in such a way that substantial
backmixing is avoided. FBRs are chosen when these intermediate characteristics are
required, e.g. where a high conversion is needed but the substrate stream is
colloidal or the reaction produces a substantial pH change or heat output. They
are particularly useful if the reaction involves the utilisation or release of
gaseous material.
The FBR is normally used with fairly small immobilised enzyme particles (20-40 m
diameter) in order to achieve a high catalytic surface area. These particles must
be sufficiently dense, relative to the substrate stream, that they are not swept
out of the reactor. Less-dense particles must be somewhat larger. For efficient
operation the particles should be of nearly uniform size otherwise a non-uniform
biocatalytic concentration gradient will be formed up the reactor. FBRs are
usually tapered outwards at the exit to allow for a wide range of flow rates. Very
high flow rates are avoided as they cause channelling and catalyst loss.
The major disadvantage of development of FBR process is the difficulty in scaling-
up these reactors. PBRs allow scale-up factors of greater than 50000 but, because
of the markedly different fluidisation characteristics of different sized
reactors, FBRs can only be scaled-up by a factor of 10 -100 each time. In
addition, changes in the flow rate of the substrate stream causes complex changes
in the flow pattern within these reactors that may have consequent unexpected
effects upon the conversion rate.
Chapter-17 Protein Engineering
Introduction
Protein engineering is the branch of science in which novel enzymes are being
designed and produce by genetic engineering methods to improve the stability of an
enzyme (stability with respect to chemical oxidation, temperature, and pH).
Therefore protein engineering includes two parts one large scale production of
genes by modification in the gene by gene cloning methods and other modification
in the structure of protein to improve the substrate specificity, the cofactor
requirement (NADPH to NADH) or imparting novel properties to a protein (eg. adding
a Mn binding site into horse heart myoglobin at UBC).In the genetic engineering
methods the availability of a cloned gene is important. Cloned gene is expressed
in the expression vector to obtain the 3-D structure of the enzyme, resolved by X-
ray crystallography. In the absence of detailed 3-D structure, one can do random
mutagenesis and/or directed evolution. There are many directions in which enzyme
technologists are currently applying their art and which are at the forefront of
biotechnological research and development. At present, relatively few enzymes are
available on a large scale (i.e. > kg) and are suitable for industrial
applications. These shortcomings are being addressed in a number of ways:
New enzymes are being sought in the natural environment and by strain selection.
Established industrial enzymes are being used in as wide a variety of ways as can
be conceived.
novel enzymes are being designed and produce by genetic engineering;
New organic catalysts are being designed and synthesized.
More complex enzyme systems are being utilised.
The development of genetically improved enzymes is generally undertaken by
molecular biologists and the design and synthesis of novel enzyme-like catalysts
is done by the organic chemists. Both groups of workers will, however, base their
science on data provided by the enzyme technologist. Space requirements in this
volume do not allow the full treatment of these related areas but will be
discussed briefly here.
17.1 Enzyme engineering
A most exciting development over the last few years is the application of genetic
engineering techniques to enzyme technology. There are a number of properties
which may be improved or altered by genetic engineering for example, the yield and
kinetics of the enzyme, the ease of downstream processing and various safety
aspects. Enzymes from dangerous or unapproved microorganisms and from slow growing
or limited plant or animal tissue may be cloned into safe high-production
microorganisms. In the future, enzymes may be redesigned to fit more appropriately
into industrial processes; for example, making glucose isomerase less susceptible
to inhibition by the Ca2+ present in the starch saccharification processing
stream.
17.2 Enzyme production can be increased by cloning of gene
The amount of enzyme produced by a microorganism may be increased by increasing
the number of gene copies that code for it by inserting a portion of gene for
specific enzyme into the suitable vector. If the vector is expression type then
large amount of protein will be obtained after the translation of vector. The
product can be tested by its specific function. The DNA having gene of interest
for specific enzyme can be isolated by partial digestion of gene or complete
digestion of gene (incomplete or complete fragmentation of gene) and selection of
specific gene can be done with the help of probe. This principle has been used to
increase the activity of penicillin-G-amidase in Escherichia coli. The cellular
DNA from a producing strain is selectively cleaved by the restriction endonuclease
Hind III. This hydrolyses the DNA at relatively rare sites containing the
5'-AAGCTT-3' base sequence to give identical 'staggered' ends.
Figure 17. 1 figure showing staggered cut of DNA double strand by the restriction
endonuclease. Note that single stranded DNA is rarely cut by the Restriction
enzyme.
R.E.
Intact DNA cleaved DNA
Figure 17. 2 showing structure of vector and their site containing antibiotic
resistance gene as the marker of the gene for selection of recombinant gene.
The total DNA is cleaved into about 10000 fragments, only one of which contains
the required genetic information. These fragments are individual cloned into a
cosmid vector and thereby returned to E. coli. These colonies containing the
active gene are identified by their inhibition of a 6-amino-penicillanic acid-
sensitive organism. Such colonies are isolated and the penicillin-G-amidase gene
transferred on to pBR322 plasmids and recloned back into E. coli. The engineered
cells, aided by the plasmid amplification at around 50 copies per cell, produce
penicillin-G-amidase constitutively and in considerably higher quantities than
does the fully induced parental strain. Such increased yields are economically
relevant not just for the increased volumetric productivity but also because of
reduced downstream processing costs, the resulting crude enzyme being that much
purer. Another extremely promising area of genetic engineering is protein
engineering. New enzyme structures may be designed and produced in order to
improve on existing enzymes or create new activities. An outline of the process of
protein engineering is shown in Figure 17.1. Such factitious enzymes are produced
by site-directed mutagenesis (Figure 17.2). Unfortunately from a practical point
of view, much of the research effort in protein engineering has gone into studies
concerning the structure and activity of enzymes chosen for their theoretical
importance or ease of preparation rather than industrial relevance. This emphasis
is likely to change in the future.
Figure 17. 3 showing structure and location of plasmid DNA inside the E.coli
vector.
Figure 17. 7 The protein engineering cycle. The process starts with the isolation
and characterization of the required enzyme. This information is analyzed together
with the database of known and putative structural effects of amino acid
substitutions to produce a possible improved structure. This factitious enzyme is
constructed by site-directed mutagenesis, isolated and characterised. The results,
successful or unsuccessful, are added to the database, and the process repeated
until the required result is obtained.
________________________________________
Protein engineering, therefore, is presently rather a hit or miss process which
may be used with only little realistic likelihood of immediate success. Apparently
quite small sequence changes may give rise to large conformational alterations and
even affect the rate-determining step in the enzymic catalysis. However it is
reasonable to suppose that, given a sufficiently detailed database plus suitable
software, the relative probability of success will increase over the coming years
and the products of protein engineering will make a major impact on enzyme
technology.
17.2 Application of Enzyme Engineering
17.2.1 Subtilisin
Much protein engineering has been directed at subtilisin (from Bacillus
amyloliquefaciens), the principal enzyme in the detergent enzyme preparation,
Alcalase. This has been aimed at the improvement of its activity in detergents by
stabilising it at even higher temperatures, pH and oxidant strength. Most of the
attempted improvements have concerned alterations to:
The P1 cleft, which holds the amino acid on the carbonyl side of the targeted
peptide bond; 2. The oxyanion hole (principally Asn155), which stabilises the
tetrahedral intermediate; 3. the neighborhood of the catalytic histidyl residue
(His64), which has a general base role; and 4.the methionine residue (Met222)
which causes subtilisin's lability to oxidation.
It has been found that the effect of a substitution in the P1 cleft on the
relative specific activity between substrates may be fairly accurately predicted
even though predictions of the absolute effects of such changes are less
successful. Many substitutions, particularly for the glycine residue at the bottom
of the P1 cleft (Gly166), have been found to increase the specificity of the
enzyme for particular peptide links whilst reducing it for others. These effects
are achieved mainly by corresponding changes in the Km rather than the Vmax.
Increases in relative specificity may be useful for some applications. They should
not be thought of as the usual result of engineering enzymes, however, as native
subtilisin is unusual in being fairly non-specific in its actions, possessing a
large hydrophobic binding site which may be made more specific relatively easily
(e.g. by reducing its size). The inactivation of subtilisin in bleaching solutions
coincides with the conversion of Met222 to its sulfoxide, the consequential
increase in volume occluding the oxyanion hole. Substitution of this methionine by
serine or alanine produces mutants that are relatively stable, although possessing
somewhat reduced activity.
________________________________________
Figure 17. 8
Introduction
A biosensor is an analytical device which converts a biological response into an
electrical signal (Figure 19.1). The term 'biosensor' is often used to cover
sensor devices used in order to determine the concentration of substances.
Clark and Lyons first demonstrated the modern concept of biosensors, in which an
enzyme was immobilized into an electrode to form a biosensor. When the biological
component of biosensor is a component of the immune system then it is referred to
as Immunosensors. The emphasis of this Chapter concerns enzymes as the
biologically responsive material, but it should be recognised that other
biological systems may be utilised by biosensors, for example, whole cell
metabolism, ligand binding and the antibody-antigen reaction.
19.1 The use of enzymes in analysis
Figure 19. 1 Schematic diagram showing the main components of a biosensor. The
biocatalyst (a) converts the substrate to product. This reaction is determined by
the transducer (b) which converts it to an electrical signal. The output from the
transducer is amplified (c), processed (d) and displayed (e).
________________________________________
A biosensor is a device that detects, transmits and records information regarding
a physiological or biochemical change. Technically, it is a probe that integrates
a biological component with an electronic transducer thereby converting a
biochemical signal into a quantifiable electrical response. The sensor works by
converting the signal produced by the biological sensing element on response to a
specific analyte to a measurable electrical signal with the help of the
transducer. The amplifier increases the intensity of the signal so that it can be
readily measured. The digital display then displays the reading in a suitable
unit. All these components are generally integrated onto a single probe to make
the handling easier.
Biosensor is device that on matching with appropriate biological sample gives
signal to electrical components. Biological component is bound or immobilized on
the electronic component called as transducer.
Figure 19. 2
The electrical signal from the transducer is often low and superimposed upon a
relatively high and noisy (i.e. containing a high frequency signal component of an
apparently random nature, due to electrical interference or generated within the
electronic components of the transducer) baseline. The signal processing normally
involves subtracting a 'reference' baseline signal, derived from a similar
transducer without any biocatalytic membrane, from the sample signal, amplifying
the resultant signal difference and electronically filtering (smoothing) out the
unwanted signal noise. The relatively slow nature of the biosensor response
considerably eases the problem of electrical noise filtration. The analogue signal
produced at this stage may be output directly but is usually converted to a
digital signal and passed to a microprocessor stage where the data is processed,
converted to concentration units and output to a display device or data store.
19.4 Classification of Biosensor
There are several type of Biosensor depends on the physical characteristic like
heat , electrical signal . light, electron ,charge, and mass. Biosensors may be
classified according to several criteria, such as transducers, bioactive
components, or immobilization techniques used.
The heat output (or absorbed) by the reaction (calorimetric biosensors),
changes in the distribution of charges causing an electrical potential to be
produced (potentiometric biosensors),
movement of electrons produced in a redox reaction (amperometric biosensors),
light output during the reaction or a light absorbance difference between the
reactants and products (optical biosensors), or
Effects due to the mass of the reactants or products (piezo-electric biosensors).
There are three so-called 'generations' of biosensors
First generation biosensors where the normal product of the reaction diffuses to
the transducer and causes the electrical response.
Second generation biosensors which involve specific 'mediators' between the
reaction and the transducer in order to generate improved response.
Third generation biosensors where the reaction itself causes the response and no
product or mediator diffusion is directly involved.
A typical biosensor has got two main parts
Biological component which can be enzyme, antibody, nucleic acid, microorganism,
tissue, cell, etc.
Electronic device, i.e., transducer which can be electrochemical, optical,
piezoelectric, thermal, etc.
The biological component is generally immobilized near or onto the transducer
surface in order to facilitate reuse, to minimize interference and to maximize
response. In each case it is the ability of the biological component to react or
respond specifically to an analyte (or a group of analytes) that makes the
biomolecule suitable for use as the sensing element of a biosensor. For example,
an antibody will only bind to the specific antigen under suitable conditions. The
biological signal that is produced is converted by means of a suitable transducer
into a quantifiable electrical signal.Biosensors are suitable for detecting a wide
variety of analytes including pollutants, explosives, viruses, biochemical &
pharmaceutical products, vitamins, amino acids, heavy metals, ions, gases etc . In
fact, every single analyte, be it simple or complex can be detected provided a
biomolecule that response specifically to it is identified.
1. Transducers
This is the component of biosensor which converts the biological signal to a
quantifiable electrical signal.
Electrochemical: In this configuration, sensing molecules are either coated onto
or covalently bonded to a probe surface. A membrane holds the sensing molecule in
place, excluding interfering species from the analyte solution. The sensing
molecule reacts specifically with compounds to be detected, sparking an electrical
signal proportional to the concentration of the analyte. The most common detection
method for electrochemical biosensors involves measurement of current, voltage,
capacitance, conductance and impedance.
Among such sensors, amperometric (e.g. Oxygen or hydrogen peroxide) and
potentiometric (e.g. pH and carbon dioxide) transducers have found the widest
applications.
Optical: In optical biosensors, the optical fibers allow detection of analytes on
the basis of absorption, fluorescence or light scattering. Since they are non-
electrical, optical biosensors have the advantages of lending themselves to in
vivo applications and allowing multiple analytes to be detected by using different
monitoring wave-lengths. The versatility of fiber optics probes is due to their
capacity to transmit signals that reports on changes in wavelength, wave
propagation, time, intensity, distribution of the spectrum or polarity of light.
Piezoelectric: In this mode, sensing molecules are attached to a piezoelectric
surface-a mass to frequency transducer-in which interactions between the analyte
and the sensing molecules set up mechanical vibrations that can be translated into
an electrical signal proportional to the analyte. Example of such sensor is quartz
crystals.
Thermal: In this mode, the biocomponent is immobilized in proximity to the heat
sensing transducer, generally a thermister. Most of the enzymatic or microbial
reactions are accompanied by considerable heat evolution making this sensor
applicable to a very wide range of detection. However the use of sophisticated and
expensive instrumentation is the major drawback of this technique.
2. Bioactive components
This is the biological part of the biosensor which specifically reacts with the
analyte of interest sparking a signal that is detectable by the attached
transducer.
Enzymes: Purified enzymes have been commonly used in the construction of
biosensors due to their high specific activities as well as high analytical
specificity. They are mostly used in catalytic type biosensors. Purified enzymes,
however, are expensive and unstable, thus limiting their application sin the field
of biosensors. As most of the enzymes being employed are intracellular, isolation
and purification becomes tough.
Antibodies: The binding between an antigen and its corresponding antibody is very
specific. This property of antibody is exploited while designing biosensors based
on antibodies. The binding reaction between the antibody and antigen can be
monitored as a time dependent change of fluorescence signal which is proportional
to the reaction ratio of antibody to analyte.
Cells: Either whole microorganisms or tissues can be used as the biocomponent.
Whole cells can be used either in a viable or non-viable form. Viable microbes
metabolize various organic compounds either anaerobically or aerobically resulting
in various end products like ammonia, carbon dioxide, acids etc that can be
monitored using a variety of transducers. Viable cells are mainly used when the
overall substrate assimilation capacity of microorganism is taken as an index of
respiratory metabolic activity, as in the case of estimation of BOD, vitamins,
sugars, organic acids, etc. Another mechanism used for the viable microbial
biosensor involves the inhibition of microbial respiration by the analyte of
interest, like environmental pollutants. The major limitation to the use of whole
cells is the diffusion of substrate and products through the cell wall resulting
in a slow response as compared to enzyme-based sensors.
Nucleic acids: The ability of a single stranded nucleic acid to hybridize with
another fragment of DNA by complementary base pairing is the principle behind the
nucleic acid sensors. Technological innovation is introduced in the manner in
which the nucleic acid oligomer is attached to the surface of the detector and the
manner in which the hybridized nucleic acid is detected and transduced into a
measurable signal. Ammonia derivetised oligonucleotides can be detected by
attaching to glass surfaces such as fiber-optics cables, glass beads or
microscopic slides through covalent bonding with a chemical linker.
Lipids: An active biological receptor can be immobilized and stabilized in a
polymeric film for determining an analyte of interest in a sample.
3. Immobilization techniques for the bio-component:
The biological material should bring the physico-chemical changes in close
proximity of a transducer. Immobilization not only helps in forming the required
close proximity between the biomaterial and the transducer, but also helps in
stabilizing it for reuse.The selection of a technique and/or support material
would depend on the nature of the biomaterial and the substrate and configuration
of the transducer used.
Covalent binding, a commonly used technique for the immobilization of enzymes and
antibodies, has not been useful for the immobilization of cells. On the other
hand, cross-linking using bifunctional reagents like glutaraldehyde has been
successfully used for the immobilization of cells in various supports. Thus cross-
linking technique will be useful in obtaining immobilized non-viable cell
preparations containing active intracellular enzymes. Entrapment and adsorption
techniques are more useful when viable cells are used. The synthetic polymers used
for microbial biosensor applications include polyacrylamide, polyurethane-based
hydrogels, photo cross-linkable resins and polyvinyl alcohol. Natural polymers
used for the entrapment of the cells include alginate, carrageenam, low-melting
agarose, chitosan, etc. But entrapment technique adds another diffusional
barrier.Passive trapping of cells into the pores or adhesion onto the surfaces of
cellulose or other synthetic membranes has the major advantage of direct contact
between the liquid phase and the cell, thus reducing or eliminating the problem of
mass transfer
Figure 19. 4
An alternative method for determining the rate of this reaction is to measure the
production of hydrogen peroxide directly by applying a potential of +0.68 V to the
platinum electrode, relative to the Ag/AgCl electrode, and causing the reactions:
Pt anode H2O2 O2 + 2H+ + 2e- [19.6]
Ag cathode 2AgCl + 2e- 2Ag0 + 2Cl-[19.7]
The major problem with these biosensors is their dependence on the dissolved
oxygen concentration. This may be overcome by the use of 'mediators' which
transfer the electrons directly to the electrode bypassing the reduction of the
oxygen co-substrate. In order to be generally applicable these mediators must
possess a number of useful properties.
They must react rapidly with the reduced form of the enzyme.
They must be sufficiently soluble, in both the oxidised and reduced forms, to be
able to rapidly diffuse between the active site of the enzyme and the electrode
surface. This solubility should, however, not be so great as to cause significant
loss of the mediator from the biosensor's microenvironment to the bulk of the
solution. However soluble, the mediator should generally be non-toxic.
The overpotential for the regeneration of the oxidised mediator, at the electrode,
should be low and independent of pH.
The reduced form of the mediator should not readily react with oxygen.
The ferrocenes represent a commonly used family of mediators (Figure 19.5 a).
Their reactions may be represented as follows,
Figure 19. 9 Schematic diagram of the section across the width of an ENFET. The
actual dimensions of the active area is about 500 m long by 50 m wide by 300 m
thick. The main body of the biosensor is a p-type silicon chip with two n-type
silicon areas; the negative source and the positive drain. The chip is insulated
by a thin layer (0.1 m thick) of silica (SiO2) which forms the gate of the FET.
Above this gate is an equally thin layer of H+-sensitive material (e.g. tantalum
oxide), a protective ion selective membrane, the biocatalyst and the analyte
solution, which is separated from sensitive parts of the FET by an inert
encapsulating polyimide photopolymer. When a potential is applied between the
electrodes, a current flows through the FET dependent upon the positive potential
detected at the ion-selective gate and its consequent attraction of electrons into
the depletion layer. This current (I) is compared with that from a similar, but
non-catalytic ISFET immersed in the same solution. (Note that the electric
current is, by convention, in the opposite direction to the flow of electrons).
Figure 19. 10. Schematic diagram of a calorimetric biosensor. The sample stream
(a) passes through the outer insulated box (b) to the heat exchanger (c) within an
aluminium block (d). From there, it flows past the reference thermistor (e) and
into the packed bed bioreactor (f, 1ml volume), containing the biocatalyst, where
the reaction occurs. The change in temperature is determined by the thermistor (g)
and the solution passed to waste (h). External electronics (l) determines the
difference in the resistance, and hence temperature, between the thermistors.
________________________________________
The thermistors, used to detect the temperature change, function by changing their
electrical resistance with the temperature, obeying the relationship
(19.26)
therefore:
(19.27)
Where R1 and R2 are the resistances of the thermistors at absolute temperatures T1
and T2 respectively and B is a characteristic temperature constant for the
thermistor. When the temperature change is very small, as in the present case,
B(1/T1) - (1/T2) is very much smaller than one and this relationship may be
substantially simplified using the approximation when x<<1 that exÅ1 + x (x here
being B(1/T1) - (1/T2),
(19.28)
As T1 Δ T2, they both may be replaced in the denominator by T1.
(19.29)
The relative decrease in the electrical resistance (ΔR/R) of the thermistor is
proportional to the increase in temperature (ΔT). A typical proportionality
constant (-B/T12) is -4%°C-1. The resistance change is converted to a proportional
voltage change, using a balanced Wheatstone bridge incorporating precision wire-
wound resistors, before amplification. The expectation that there will be a linear
correlation between the response and the enzyme activity has been found to be
borne out in practice. A major problem with this biosensor is the difficulty
encountered in closely matching the characteristic temperature constants of the
measurement and reference thermistors. An equal movement of only 1°C in the
background temperature of both thermistors commonly causes an apparent change in
the relative resistances of the thermistors equivalent to 0.01°C and equal to the
full-scale change due to the reaction. It is clearly of great importance that such
environmental temperature changes are avoided, which accounts for inclusion of the
well-insulated aluminium block in the biosensor design .
The sensitivity (10-4 M) and range (10-4 - 10-2 M) of thermistor biosensors are
both quite low for the majority of applications although greater sensitivity is
possible using the more exothermic reactions (e.g. catalase). The low sensitivity
of the system can be increased substantially by increasing the heat output by the
reaction. In the simplest case this can be achieved by linking together several
reactions in a reaction pathway, all of which contribute to the heat output. Thus
the sensitivity of the glucose analysis using glucose oxidase can be more than
doubled by the co-immobilisation of catalase within the column reactor in order to
disproportionate the hydrogen peroxide produced. An extreme case of this
amplification is shown in the following recycle scheme for the detection of ADP.
Figure 19. 11
ADP is the added analyte and excess glucose, phosphoenol pyruvate, NADH and oxygen
are present to ensure maximum reaction. Four enzymes (hexokinase, pyruvate kinase,
lactate dehydrogenase and lactate oxidase) are co-immobilised within the packed
bed reactor. In spite of the positive enthalpy of the pyruvate kinase reaction,
the overall process results in a 1000 fold increase in sensitivity, primarily due
to the recycling between pyruvate and lactate. Reaction limitation due to low
oxygen solubility may be overcome by replacing it with benzoquinone, which is
reduced to hydroquinone by flavo-enzymes. Such reaction systems do, however, have
the serious disadvantage in that they increase the probability of the occurrence
of interference in the determination of the analyte of interest. Reactions
involving the generation of hydrogen ions can be made more sensitive by the
inclusion of a base having a high heat of protonation. For example, the heat
output by the penicillinase reaction may be almost doubled by the use of Tris
(tris-(hydroxymethyl)aminomethane) as the buffer.In conclusion, the main
advantages of the thermistor biosensor are its general applicability and the
possibility for its use on turbid or strongly coloured solutions. The most
important disadvantage is the difficulty in ensuring that the temperature of the
sample stream remains constant (± 0.01°C).
19.5.5 Immunosensors
Chapter-19
Abstract:-
I Definition of Stability
Before entering into a discussion of stability in proteins, we must define exactly
what we mean by stability. The word is used in different ways by different people.
For example, a physical biochemist and a biotechnologist may each mean something
different when they speak of stability.
The physical biochemist, on the one hand, would probably discuss protein stability
primarily in terms of the thermodynamic stability of a protein that unfolds and
refolds rapidly, reversibly, cooperatively, and with a simple, two-state
mechanism:
The Gibbs free energy, G, is made up the two terms enthalpy (H) and entropy (S),
related by the equation:
Where T is the temperature in Kelvin.
The folding free energy difference, Gu, is typically small, of the order of 5- 15
kcal/mol for a globular protein (compared to e.g. ~30 - 100 kcal/mol for a
covalent bond).
The biotechnologist, on the other hand, is more concerned with the practical
utility of the definition: Is the protein stable enough to function under harsh
conditions of temperature or solvent? While the answer to this question may lie in
thermodynamic stability (discussed above); it may also lie either simply in
reversibility or, for irreversibly or slowly unfolding proteins, in kinetic
stability.
If a protein unfolds reversibly it may be fully unfolded and inactive at high
temperatures, but once it cools to room temperature, it will refold and fully
recover activity. From a functional standpoint this may be all that is required
for it to be classified as thermostable. However, from a thermodynamic standpoint
(and in terms of this dissertation) it is classified as non-thermostable.
In the case of irreversible or slowly unfolding proteins, it is kinetic stability
or the rate of unfolding that is important. A protein that is kinetically stable
will unfold more slowly than a kinetically unstable protein. In a kinetically
stable protein, a large free energy barrier to unfolding is required and the
factors affecting stability are the relative free energies of the folded (Gf) and
the transition state (Gts) for the first committed step on the unfolding pathway.
Kinetic stability is discussed in more detail in its own section; see Kinetic
Stability. Irreversible loss of protein folded structure is represented by:
Although both these interactions have small free energies per residue, they are
important because there are so many of them. The same is true for those
interactions which stabilize the unfolded state. The most important of which is
conformational entropy. Thus, the overall free energy of a folded protein is given
by the small difference between two large numbers. This is a major reason for the
difficulty of quantitative computational calculation of protein stability. In a
recent analysis of the factors contributing to the stability of RNase T1, the
stabilizing and destabilizing interactions were estimated at 271 and 286 kcal/mol,
respectively (Pace et al., 1996). Hydrogen bonding and hydrophobic interactions
were estimated to contribute 260 kcal/mol to the stabilizing interactions, while
the bulk of the destabilizing factors were attributed to loss of conformational
entropy on folding, and unfavourable burial of peptide and polar groups. See
table.
At room temperature, the enthalpy of transfer from organic solution into aqueous
solution is negligible; the interaction enthalpies are the same in both cases.
The entropy however is negative. Water tends to form ordered cages around the non-
polar molecule and this leads to a decrease in entropy. At high temperatures (~
110°C) these cages are no longer any stronger than bulk water, and the entropy
contribution tends to zero. The enthalpy of transfer, however, is now positive
(unfavourable). Because the temperature dependence of entropy and enthalpy are not
the same, there is some temperature at which the hydrophobic effect is strongest,
and the effect decreases at temperatures above and below this temperature. The
decrease in the strength of the hydrophobic effect with decreasing temperatures is
probably the major cause of cold-denaturation in proteins.
The contribution of the hydrophobic effect to globular protein stability has been
estimated empirically both by measuring the thermodynamics of transfer of model
compounds (e.g. blocked amino acids, cyclic peptides...) from organic solvents to
water, and by site directed mutagenesis studies on proteins. The number arrived at
is usually given as a function of the change in the solvent accessible non-polar
surface area upon going from the unfolded to the folded state.
The model compound studies predict that the hydrophobic effect of exposing one
buried methylene group to bulk water is 0.8 kcal/mol (in Pace, 1995). The site
directed mutagenesis studies yielded a larger number with greater statistical
variation: the average hydrophobic effect estimated by SDM for a buried methylene
group is about 1.3 kcal/mol. However, when the SDM results for methylene were
plotted against the size of the cavity created by the residue substitution, and
extrapolated to zero, the result at zero cavity size is 0.8 kcal/mol - in
agreement with the value found for the transfer of model compounds from octanol to
water (Pace et al., 1996 and references therein). In the SDM studies, cavities
created by residue substitution have an additional destabilizing effect: the loss
of favourable VDWs interactions (as compared to the wild-type). Thus, the
"hydrophobic effect" measured by SDM includes both an entropic component due to
solvent ordering and a (primarily) enthalpic component due to loss of VDWs
contacts within the protein.
Such an SDM study of T4 lysozyme replaced the 80% buried Ile3 residue by Val
(Eriksson et al, 1992): the loss of this methyl group gave rise to a decrease in
stability of 0.6 kcal/mol (corrected to 100% burial). This is smaller than
expected (c.f. 0.8 kcal/mol for methylene) and suggests that the mutation
introduced some smaller stabilizing influence, perhaps such as the alleviation of
strain within the protein.
Correlation between the number of side chain methylene and methyl groups, in a
radius of 6 Å of the group deleted from wild-type, and the changes in the free
energy of unfolding for mutations of hydrophobic residues in barnase. (Taken from
Serrano et al, 1992. with permission)
The average free energy decrease for removal of a completely buried methylene
group was found to be 1.5±0.6 kcal/mol. This is additive, such that Ile or Leu to
Ala can destabilize a protein by up to 5 kcal/mol. (Remember that many mesophilic
proteins are stable by <10 kcal/mol, so two deletions such as this would be enough
to destabilize a protein completely).
Hydrogen Bonds
A hydrogen bond occurs when two electronegative atoms, such as nitrogen and
oxygen, interact with the same hydrogen. The hydrogen is normally covalently
attached to one atom, the donor, but interacts electrostatically with the other,
the acceptor. This interaction is due to the dipole between the electronegative
atoms and the proton.
There is a geometric component involved in hydrogen bonds, and for single donor
acceptor systems, such as N-H---O, the strongest hydrogen bonds are collinear
(Creighton, 1993 and references therein). Electrostatic calculations suggest that
deviation of 20° from linearity leads to a decrease in binding energy of
approximately 10% (Pimentel & McClellan, 1960).
In double acceptor systems, bifurcated hydrogen bonds with non-linear angles are
preferred. The occurrence of hydrogen bonds in protein structure has been
extensively reviewed by Baker & Hubbard (1984), albeit before the pdb database was
as large as it is today. They found that 90% of N-H---O bonds in proteins lie
between 140 and 180°, and that they are centred around 158°C. For C=O---H, the
range is more broadly distributed between 90° and 160° and centred around 129°.
The strength of a hydrogen bond is between 2 and 10 kcal/mol, and one might think
that this is the amount of energy one hydrogen bond contributes towards
stabilization of a folded protein. However, in the unfolded state, all potential
hydrogen bonding partners in the extended polypeptide chain are satisfied by
hydrogen bonds to water. When the protein folds, these protein-to-water H-bonds
are broken, and only some are replaced by (often sub-optimal) intra-protein H-
bonds. McDonald & Thornton (1994) showed that while only 1.3% of backbone amino
groups and 1.8% of carbonyl groups in proteins fail to H-bond (without any
obviously compensating interactions), 80% of main chain carbonyls fail to form a
second hydrogen bond. Thus, if one considers enthalpy terms alone, it would appear
that hydrogen bonding is destabilizing to folded protein structure.
However, one must also consider entropy. When a protein folds, and those hydrogen
bonds that the protein made to bulk water are broken, the entropy of the solvent
increases. The balance between the entropy and enthalpy terms are close, and in
the recent past it was considered that H-bonds made no contribution overall to
protein stability. But, it is now generally accepted that H-bonds make a positive
contribution to protein stabilisation (reviewed in Pace et al., 1996).
Estimation of the contribution of hydrogen bonding to protein stability has been
made by a combination of experiments on model compounds and site-directed
mutational (SDM) studies. The difficulty with the SDM studies is that when a
smaller residue replaces a larger one, a cavity is created. For example, mutating
Asn to Ala creates a cavity of 37.4 Å3 (Harpaz et al , 1994). This cavity may then
be filled by water, replacing the hydrogen bonding of the asparagine NH group.
Even in more conservative mutations such as Thr to Val (which is isosteric) or Ser
to Ala, one must take into account the contribution of side chain entropy and the
hydrophobic effect to the ( G) values. Dissection of the latter contributions
from those due only to hydrogen bonds is not trivial. An estimation has been made
of a positive contribution of 1.5±1.0 kcal/mol (Pace et al., 1996, Fersht, 1987)
from the formation of a buried intramolecular uncharged hydrogen bond. However, in
order to form, the unfavourable interaction energy from burial of a polar group
must be overcome. Thus, the net energy gain for formation of a buried H-bond is
approximately 0.6 kcal/mol.
Despite the small contribution made to protein stability by hydrogen bonds, we
must remember that if we break or delete an intramolecular hydrogen bond in a
protein without the possibility of forming a compensating H-bond to solvent, that
protein will be destabilized. In globular proteins, much of the H-bonding
potential of the backbone amide and carbonyl groups is satisfied by the formation
of regular structure such as alpha helix and beta sheet (links to PPS); regular
structure comprises 80 - 90% of globular protein structure.
There is evidence that hydrogen bonds contribute to stability in hyper-
thermostable proteins. A comparison of glyceraldehyde-3-phosphate dehydrogenase
(GADH) from four organisms with a range of thermostabilities and more than 50%
sequence identity found that the strongest correlation to thermostability was with
the number of buried charged residues H-bonded to buried neutral residues (Tanner
et al, 1996). The rationalization given for this preference of charged-to-neutral
over neutral-to-neutral or charged-to-charged residue H-bonding was as follows:
The enthalpy of H-bond formation is in the order, charged-to-charged > charged-to-
neutral > neutral-to-neutral, but the entropic cost of desolvation is in the
inverse order. The greatest overall free energy benefit is proposed to be for the
charged-to-neutral H-bonds.
Salt Bridges
Salt bridges or ion-pairs are a special form of particularly strong hydrogen bonds
made up of the interaction between two charged residues.
The contribution of salt bridges to protein stability is a somewhat contentious
issue in the literature. On the one hand is the observation that thermophilic and
hyper-thermophilic analogues of mesophilic proteins tend to have increased numbers
of salt-bridges (Tanner et al., 1996; Perutz & Raidt, 1975; Perutz, 1978; Dekker
et al., 1991). On the other hand are mutational studies showing that the
contribution of salt bridges to stability is small. Perhaps at higher temperatures
salt bridges make more of a contribution to stability.
Horovitz et al . (1990) measured the stability of a surface salt bridge triad
between Asp8, Asp12 and Arg110 on the surface of barnase by construction of a
thermodynamic cycle of all possible combinations of 1, 2, or 3 alanine mutants.
The free energy contribution to the stability of the protein is only 1.25 kcal/mol
for the Asp12/Arg110 pair and 0.98 kcal/mol for the Asp8/Arg110 pair. Removal of
Arg 110 has no effect on stability!
Other studies have had similar results (Akke & Forsen, 1990). One reason that
these contributions are not as large as might be expected from the strength of
such an ion pair is that, in order form a salt bridge, strong hydrogen bonds with
water have to be broken. In fact, it is possible that most of the energy of
stabilization comes from the increase in solvent entropy upon formation of the ion
pair.
In contrast to surface salt bridges, removal of one partner from a buried salt
bridge leads to destabilization of 3-4 kcal/mol. However, it has been found that
replacing a buried salt-bridge triad by well packed hydrophobic residues (found by
random mutagenesis at the three charged residue positions) leads to an increase in
stability of 4.5 kcal/mol in the arc repressor (Waldburger et al., 1995). Thus,
hydrophobic interactions contribute more to stability than a salt bridge triad.
This is illustrated below and is presumably due to the cost of desolvating the
charged groups on going from the unfolded to the folded state. The mutant is R31M,
E36Y, R40L.
Interestingly, it was also shown that the wild-type arc repressor folds between 10
and 1250 more slowly than the mutant (Waldburger et al., 1996). This is proposed
to be due to the high energy barrier to burying charged residues. The transition
state would have a particularly high energy if one charged residue had to be
buried before the other. Even if the salt bridge had formed prior to the
transition state, the geometry of the salt bridge might well be sub-optimal until
that part of the protein attained its native conformation. Hydrophobic
interactions have less of a steric requirement.
Aromatic-Aromatic Interactions
About 60% of the aromatic side chains (Phe, Tyr, and Trp), found in proteins are
involved in aromatic pairings. Studies with model compounds suggest that the
optimal geometry is perpendicular, such that the partially positively charged
hydrogens on the edge of one ring can interact favourably with the pi electrons
and partially negatively charged carbons of the other. From these observations, it
might be expected that such interactions make a contribution to protein stability.
This has been tested on the solvent exposed Tyr13 / Tyr17 pair on the surface of
barnase (Serrano et al., 1991). Tyr13 and Tyr17 were mutated to both Ala and Phe.
Mutation of the Tyr13 or Tyr17 to Phe leads to a decrease in stability of 0.30 or
0.41 kcal/mol, and 0.61 kcal/mol in the double mutant. As both hydroxyl groups are
exposed to solvent (as they would be in the unfolded state), it is unclear as to
the source of this small destabilization. However, mutation to the double alanine
mutant leads to a decrease in stability of 4.6 kcal/mol. Most of this
destabilization can be explained in terms of the loss of interactions between the
tyrosine residues and the rest of the protein; however, analysis of the data using
thermodynamic cycles (Carter, 1984; Horovitz & Fersht, 1990) indicates that the
interaction energy between the two aromatic groups contributes only 1.3 kcal/mol
to the protein stability. This is only very slightly higher than the stabilization
expected from the hydrophobic contribution from burying surface area between them.
In this case, therefore, there is little apparent extra stabilization due to the
aromatic pair.
Metal Binding
Another method by which the folded state of proteins can be stabilized is metal
binding, in which metal ions are coordinated, usually by lone pair donation from
oxygen or nitrogen atoms.
Experiments have shown that metal binding can contribute 6 - 9 kcal/mol (Braxton,
1996 and references therein) to stability. However, this is a little misleading as
the comparisons made are between the apo- and the holo- enzyme; in the apo-enzyme
there is often a destabilising cluster of negative charge from coordinating acidic
side chains. Perhaps a fairer estimation of the contribution of metal binding to
protein stability comes from an experiment in which a metal chelating site was
introduced into an alpha helix of iso-cytochrome c and gave rise to a 1 kcal/mol
increase in stability in the presence of saturating Cu(II) (Kellis et al., 1991).
Another interesting study was that of Kuroki et al. (1989). They observed that the
sequence and tertiary structure of alpha-lactalbumin (Ca2+ binding) and c-type
lysozymes (non-Ca2+ binding) are homologous.
They recruited the binding site from alpha-lactalbumin into human c-type lysozyme
(Q86D/A92D). The mutant protein binds one mole of calcium ions and has optimal
activity at about 10°C higher than the wild-type. Interestingly, the apo-enzyme is
about 5 °C less stable than wild-type.
Disulphide Bonds
Disulphide bonds are formed by the oxidation of two cysteine residues to form a
covalent sulphur-sulphur bond which can be intra- (examples are shown in Jane
Richardson's Protein Tourist kinamage) or inter- (exemplified by insulin at this
PPS link) molecular bridges.
One might imagine that as the enthalpy of a covalent disulphide bond is very high,
it contributes a great deal to stability. However, this bond is present in both
the folded and the unfolded state, thus its enthalpic contribution to the free
energy difference is negligible. All of the stabilizing effect of a disulphide
bond is proposed to come from the decrease in conformational entropy of the
unfolded state, as described in Conformational Entropy of Unfolding, above.
Calculations suggest that a disulphide bond should give rise to 2.5 - 3.5 kcal/mol
of stabilization, depending on the primary sequence separation between the
crosslinks (Braxton, 1996). Experiments in which naturally occurring disulphides
are either mutated to alanine, or chemically reduced and blocked, lead to
decreased stability ranging from 2 - 8 kcal/mol (Betz, 1993 and references
therein). Unfortunately, because these experiments also leave cavities, or buried
polar groups, or otherwise have more consequences than just removal of the
disulphide bridge, it is hard to estimate the stabilization due to crosslinks
alone.
Introduction of novel disulphides into proteins has also had mixed results. Five
disulphides have been introduced into T4 lysozyme (which has no disulphides in the
wild-type). Two are destabilizing, and three are stabilizing relative to their
reduced form, but all five are destabilized relative to wild-type (Betz, 1993)!
However, there have been successful stabilizations by introduction of disulphides:
The stability of RNase Hn is increased by 2.8 kcal/mol upon introduction of a
disulphide. Engineering disulphides into the ribonuclease barnase gave rise to
increased stability of 1.2 and 4.1 kcal/mol (Clarke et al., 1995). Interestingly,
the former disulphide encompasses a loop of 34 residues, while the latter
encompasses 17.
If the stabilization is purely due to conformational entropy, the magnitude of
stabilization would be the opposite way round; further, the degree of
stabilization observed for the 17 residue loop (4.1 kcal/mol) is higher than would
be predicted by the theory (Betz, 1993 ). Thus, it is clear that we are still far
from understanding the role of disulphides in protein structure.
It is worth noting that small proteins are often naturally rich in disulphide
bonds, perhaps, when the geometry is optimal, they compensate for the small number
of non-covalent interactions.
Disulphide linkages are rare in hyper-thermostable proteins, presumably because
they are chemically labile at high temperatures .
Disulphides can also contribute a great deal to Kinetic Stability .
V Chemical Degradation
It should be mentioned that however stable a protein can be made by stabilizing
the folded state, the ultimate limit of protein stability must come from covalent
degradation. At high temperatures (80 - 120 °C) Asn and Gln are susceptible to
deamidation, Asp-Xaa peptide bonds are susceptible to hydrolysis, disulphides
bonds rupture, and Xaa-Pro peptide bonds undergo cis-trans isomerisation (where
Xaa is any amino acid).
Interestingly, the upper limit for protein chemical thermostability may be higher
than one would calculate from studies involving model mesophilic enzymes. Apart
from the trivial response of just avoiding these residues (disulphides are absent
and Asn/Gln content is reduced in hyper-thermophiles), it is observed that the
deamidation rate of Gln and Asn residues is reduced, presumably by steric
constraint, in fully folded hyper-thermophilic structures (Vielle & Zeikus, 1996
and references therein).
VI Conclusions
This dissertation has discussed some of the many forces that make small and
conflicting contributions to protein stability. It is the sum of these various
stabilising and destabilising interactions that gives rise to the final stability
of a protein. The total destabilising and the total stabilising energies are both
large, and their difference is small. This is one of the reasons that current
computational methods struggle to predict protein stability from structure.
Furthermore, our understanding of these many forces is incomplete; as often as not
mutations have the opposite effect to that which had been predicted. In addition,
the activation energy for folding is an important determinant of both kinetic
stability and whether a protein will fold to a global minimum. However, it also
clear that great strides have been made, and the search for the solution to The
Folding Problem, one of the great remaining questions in biology, is and continues
to be, an exciting one.
Chapter -20
Study of drug stratgies
INTRODUCTION
DNA is the carrier of all genetic information in most organisms and thus a
biological molecule of paramount importance. DNA replication and transcription are
the basic steps in the processes of cell division and gene expression. DNA
replication and transcription are regulated by several small DNA binding proteins
such as transcription factors and polymerases. A number of molecules have been
artificially created that mimic the interactions between the DNA and these
regulatory proteins. These molecules have served as useful drugs that can be used
to inibit, activate or modulate the processes of DNA replication and
transcription by binding to the DNA instead of the regulatory proteins. Though the
actions of activation and modulation are possible, mostly DNA is targeted in an
inhibitory mode, to destroy cells for antitumor and antibiotic action.
We are already aware of the Watson and Crick model of DNA double helix in which
there are two sugar phosphate backbone strands running spirally around each other
in an antiparallel fashion and between them base pairs stacked one above the
other. DNA binding drugs interact with DNA either non-covalently or covalently.
NON COVALENT INTERACTIONS
Non covalent interactions are generally reversible. Drugs that undergo non
covalent interactions with the DNA can be classified into two main classes:
• Minor Groove binders
• Intercalators
Minor groove binding drugs are usually shaped such that they easily fit into
the groove. The binding mainly is promoted by van der Waals interactions. These
drugs can also form hydrogen bonds with N-3 of adenine and O-2 of thymine.
Generally minor groove binding has negligible influence on the conformation of
DNA. Most minor groove binding drugs bind to A/T rich sequences.
Example: Berenil.
Recently, a few synthetic polyamides like lexitropsins and imidazole-pyrrole
polyamides specific forG-C and C-G regions in the grooves have been designed.
These polyamides are linked systems that recognize DNA base pairs through specific
orientation of imidazole (Im) and pyrrole (Py) rings.
Example: The eight ring hairpin polyamide ImPyPyPy-g-ImPyPyPy-b-Dp (Dp
dimethylamino propylamide) has been found to inhibit the expression of 5S RNA in
fibroblast cells (skin cancer cells) by blocking the transcription factor IIIA-
binding site.
INTERCALATORS
COVALENT INTERACTIONS
It platinates N-7 of guanine on the major groove site of DNA double helix. This
leads to the cross-linking of two adjacent guanines on the same DNA strand
hindering the mobility of DNA polymerases.
COUNTER IONS
DNA carries a large negative charge because of the phosphate backbone.
Therefore, small positively charged counter ions such as Na+, or Ca++ and Mg++
ions may be present around the DNA. The counter ions can effectively screen the
negative backbone surface thereby allowing non electrolytes as well as positively
charged drug ligands to interact more strongly with the target base pairs.
SOLVENT
In the process of drug DNA binding, a displacement of solvent from the binding
site on both the DNA and drug takes place. There also occurs a partial
compensation of charges as the DNA and drug are oppositely charged which causes
some partially solvated counterions to be released into the bulk solvent and
become fully solvated.
STRUCTURAL MODIFICATIONS
So that the DNA and the drug molecule can accommodate each other, some structural
deformation/adaptation occurs in both.
Cancer cells exhibit rapid cell division. They lose the property of contact
inhibition and do not undergo appoptosis. Chemotherapy makes use of DNA binding
drugs to kill cancerous cells. The chemotherepeutic drugs bind to the DNA of the
cancer cells and halt the cell division. When the cancer cells fail to divide they
die, ultimately causing the entire tumor to shrink. Some of the important DNA
binding drugs used in chemotherapy are cisplatin, amifosatine and mitomycin C.
Hair loss
Nausea
Low RBC count
Decreased immunity
Faliure of certain organs
Even death.
For designing better drug delivery strategies, we should focus upon the
differences between cancer cells and normal cells at olecular level. Conventional
methods target rapidly dividing cells. The disadvantge of this approach is that,
it cannot distinguish cancer cells from the stem cells, which leads to a number
serious side effects.
The properties of cancer cells that are unique to them should be exploited for
drug targetting. A few moleculare features of cancer cells that may serve as
molecular targets in chemotherapy are listed below-
Cancer cells have been found to be much less adhesive to other cells and non
cellular substrates. It is this lack of adhesiveness that permits cancer cells to
metastasize. This happens because of the expression of new cell surface proteins
reffered to as tumor associated antigens in cancer cells that can induce
modiications at the cell surface, thereby leading to the loss of adhesiveness.
Cancer cells require large amounts of glucose for energy production and
growth. When cells become cancerous, they require more energy and the level of
proteins needed for glucose transport and metabolism increases.
These differences could be employed for transpoting the DNA binding drugs to the
cancer cells without affecting the healthy cells of the body.
The whole concept rounds upto the fact that the product (drug DNA complex)
must be more stable than the starting elemnt - unbound drug.
CONCLUSION
Thus, we see that DNA binding drugs of all categories have displayed a
promising potential in the treatment various deadly viral diseases and cancers.
For this reason they have become targets of clinical research across the globe.
DNA binding drugs such as cis-Platin have revolutionised chemotherapy so that now
it is possible to completely root out cancers. However, there several hurdles
still to be cleared before these drugs can be considered as a safe cure for
cancer. The scientific community understands this and therefore full fledged
research work is being conducted in several big research institutes and
laborataries to design better and safer drugs.
SUMMARY
• Certain molecules are able to mimic the naturally occuring DNA binding
proteins such as transcription factors and DNA polymerases.
• These molecules are used as drugs that can be bound physically to the DNA
for interrupting key cellular activities such as DNA replication and gene
expression.
• DNA drug interactions can be covalent or non covalent.
• DNA binding drugs can be grouped into 3 categories – minor groove binders,
intercalators and covalent binders.
• Important forces contributing to drug DNA interactions are- hydrophobic
force, hydration/dehydration energies, van der waals interactions and hydrogen
bonds, ion effects, etc
• Sveral DNA binding drugs have played an invaluable role in cancer
chemotherapy, such as cis-Platin, daunomycin, and so on.
• Side effects of chemotherapy can be minimised by designing strategies for
efficient drug targetting and destabilising the drug-DNA complexes in healthy
cells.
Assignment
Structural Biology
Introduction to DNA
2. Replication: DNA is responsible for its own regeneration, i.e., DNA self
replicates.
DNA is present in the body in the form of a double helix, where each strand is
composed of a combination of four nucleotides, adenine (A), thymine (T), guanine
(G) and cytosine (C). Within a strand these nucleotides are connected via
phosphodiester linkages. The two strands are held together primarily via Watson
Crick hydrogen bonds where A forms two hydrogen bonds with T and C forms three
hydrogen bonds with G (Figure2).
Upon administration, a chloride ligand undergoes slow displacement with water (an
aqua ligand) molecules, in a process termed aquation. The aqua ligand in the
resulting [PtCl(H2O)(NH3)2]+ is easily displaced, allowing cisplatin to coordinate
a basic site in DNA. Subsequently, the platinum cross-links two bases via
displacement of the other chloride ligand.[1] Cisplatin crosslinks DNA in several
different ways, interfering with cell division by mitosis. The damaged DNA elicits
DNA repair mechanisms, which in turn activate apoptosis when repair proves
impossible.
Non-covalently bound drugs :
1. Minor groove binders- Minor groove binding drugs are usually crescent
shaped, which complements the shape of the groove and facilitates binding by
promoting van der Waals interactions. Additionally, these drugs can form hydrogen
bonds to bases, typically to N3 of adenine and O2 of thymine. Most minor groove
binding drugs bind to A/T rich sequences.
Table 1. Drug, action and mode of binding for some DNA binding drugs.
1. Neidle, S., Thurston, D.E. (2005) Chemical approaches to the discovery and
development of cancer therapies Nat Rev Cancer, 5, 285-96.
2. Geierstanger, B.H., Wemmer, D.E. (1995) Complexes of the minor groove of DNA.
Annu. Rev. Biophys. Biomol. Struct., 24, 463-493.
3. Chaires, J. B. (1998) Drug--DNA interactions. Curr. Opin. Struc. Biol., 8, 314-
320.
4. Neidle, S. (2001) DNA minor-groove recognition by small molecules. Nat. Prod.
Rep., 18, 291-309.
5. Hurley, L. H. (2002) DNA and its associated processes as targets for cancer
therapy. Nature Reviews Cancer, 2, 188-200.
6. Wemmer, D. E., Dervan, P. B. (1997) Targeting the minor groove of DNA. Curr.
Opin. Struc. Biol., 7, 355-61.
7. Jones, S, van Heyningen, P, Berman, H. M., Thornton, J. M. (1999) Protein-DNA
interactions: A structural analysis. J. Mol. Biol., 287, 877-896.
8. Jen-Jacobson, L. (1997) Protein-DNA recognition complexes: conservation of
structure and binding energy in the transition state. Biopolymers, 44,153-180.
9. Janin, J. (1999) Wet and dry interfaces: the role of solvent in protein-protein
and protein-DNA recognition. Structure Fold Des., 7, R277-279.
10. Turner, P. R., Denny, W. A. (2000) The genome as a drug target: sequence
specific minor groove binding ligands Curr. Drug Targ., 1, 1-14.
11. Goodsell, D. S. (2001) Sequence recognition of DNA by lexitropsins. Curr. Med.
Chem., 8, 509-516.
12. Reddy, B. S., Sondhi, S. M., Lown, J. W. (1999) Synthetic DNA minor groove-
binding drugs. Pharmacol. Ther., 84, 1-111.
13. Dervan, P. B., Edelson, B. S. (2003) Recognition of the DNA minor groove by
pyrrole-imidazole polyamides. Curr. Opin. Struct. Biol., 13, 284-299.
14. Jayaram, B., Beveridge, D.L. (1996) Modeling DNA in aqueous solutions:
theoretical and computer simulation studies on the ion atmosphere of DNA. Annu.
Rev. Biophys. Biomol. Struct., 25, 367-394.
15. Auffinger, P., Westhof, E. (1998) Simulations of the molecular dynamics of
nucleic acids. Curr. Opin. Struct. Biol., 8, 227–236.
STRUCTURAL BIOLOGY ASSIGNMENT
DNA-DRUG INTERACTION
MADE BY:
DNA is present in the body in the form of a double helix, where each strand is
composed of a combination of four nucleotides, adenine (A), thymine (T), guanine
(G) and cytosine (C). Within a strand these nucleotides are connected via
phosphodiester linkages. The two strands are held together primarily via Watson
Crick hydrogen bonds where A forms two hydrogen bonds with T and C forms three
hydrogen bonds with G (Figure2).
Fig.2 Watson Crick Base pairing, A-T and G-C base pairing
DNA-Drug Interaction :
Transcription and replication are vital to cell survival and proliferation as well
as for smooth functioning of all body processes. DNA starts transcribing or
replicating only when it receives a signal, which is often in the form of a
regulatory protein binding to a particular region of the DNA. Thus, if the binding
specificity and strength of this regulatory protein can be mimicked by a small
molecule, then DNA function can be artificially modulated, inhibited or activated
by binding this molecule instead of the protein. Thus, this synthetic/natural
small molecule can act as a drug when activation or inhibition of DNA function is
required to cure or control a disease (Table 1).
DNA activation would produce more quantities of the required protein, or could
induce DNA replication; depending on which site the drug is targeted. DNA
inhibition would restrict protein synthesis, or replication, and could induce cell
death. Though both these actions are possible, mostly DNA is targeted in an
inhibitory mode, to destroy cells for antitumor and antibiotic action.
Non-covalently bound drugs mostly fall under the following two classes:
2. Intercalators-
These contain planar heterocyclic groups which stack between adjacent DNA base
pairs. The complex, among other factors, is thought to be stabilized by π-π
stacking interactions between the drug and DNA bases. Intercalators introduce
strong structural perturbations in DNA.
The structure of the antibiotic triostin A shows the presence of two quinoxaline
(groups to the right; double aromatic rings) units linked through a cyclic peptide
structure (center left) which is stabilized at its center by a cystein pair
(disulfhydril covalent bond).
The space filled side view indicates how the two quinoxaline rings are positioned
by the linker peptide in co-planar fashion suitable for intercalating with DNA
base pairs. As a rule, the more intercalating sidechains are linked within a
single ligand structure, the stronger the expected binding affinity.
Triostatin A belongs to a family of antibiotics which are characterized by cross-
linked octapeptide rings bearing two quinoxaline chromophores. Since the spacing
between the chromophores is 3.5A, the intercalation process sandwiches two base
pairs between the two quinoxalines. This phenomenon is called bis-intercalation
and has first been described for echinomycin by showing that bis-intercalating
drugs cause twice the DNA helix extension and unwinding seen as compared to single
intercalating molecule like ethidium. The latter is a chromophore which is
activated by UV light and is used by molecule biologists to label nucleic acids in
gel electrophoresis or ion gradient centrifugation.
The following characteristics of non covalent bond formation are associated with
the binding sites indicated above:
Hairpin minor grove binding molecules have been identified and synthesized that
bind to GC reach nucleotide sequences. Hairpin polyamides are linked systems that
exploit a set of simple recognition rules for DNA base pairs through specific
orientation of imidazole (Im) and pyrrole (Py) rings. The hairpin polyamides
originated from the discovery of the three-ring Im-Py-Py molecule that bound to
minor groove DNA as an antiparallel side by side dimer.
Fig. Structure of hairpin ligand (right) on DNA minor groove (left)
The compound was found to recognize GC base pairs. Solid phase synthesis of
polyamides of variable length has produced efficient ligands, e.g. the eight ring
hairpin polyamide ImPyPyPy-g-ImPyPyPy-b-Dp (Dp dimethylamino propylamide) shown in
the figure above. This small synthetic molecule has an binding constant in the
order of 0.03nM.
The optimal goal of polyamide ligand design has been reached with finding
structures able to recognize DNA sequences of specific genes. The structure shown
above inhibits the expression of 5S RNA in fibroblast cells (skin cancer cells) by
interfering with the transcription factor IIIA-binding site.
A new strategy of rational drug design exploits the combination of polyamides with
bis-intercalating structures. WP631 is a dimeric analog of the clinically proven
anthracycline antibiotic daunorobuicin.
Fig. Structure of WP631
This new synthetic compound shows an affinity of 10pM and also showed to be
resistant against multidrug resistance mechanisms often encountered in antitumor
therapy. Multidrug resistance is a phenomenon where small aromatic compounds are
efficiently expelled from the cell by cell membrane transport proteins commonly
referred to as ABC transporters (or ATP Binding Cassette proteins).
Structural and conformational changes in the DNA and drug on binding in solution
are associated with enthalpic and entropic contributions to the binding free
energy, which can be theoretically estimated from ensembles of structures
generated via simulations. The only drawback of this approach is the long time
taken for the simulations.
The other terms, namely, electrostatics, van der Waals, hydrophobic component,
rotational and translational entropy can be estimated from single structures.
The web tool, PreDDICTA, estimates the components of DNA-drug binding free energy
which can be calculated from a single structure, and correlates it with
experimental binding free energy and ∆Tm, thus providing a swift method for
evaluation of potential lead candidates for researchers pursuing structure based
drug design for DNA.
Chapter-21
Technique to study protein
Introduction:
Proteins are fundamental components of all living cells. They exhibit an enormous
amount of chemical and structural diversity, enabling them to carry out an
extraordinarily diverse range of biological functions. Scientists know that the
critical feature of a protein is its ability to adopt the right shape for carrying
out a particular function. But sometimes a protein twists into the wrong shape or
has a missing part, preventing it from doing its job. Many diseases, such as
Alzheimer's and "mad cow", are now known to result from proteins that have adopted
an incorrect structure.
X-ray Crystallography
. The basic building block of a crystal is called a unit cell. Each unit cell
contains exactly one unique set of the crystal's components, the smallest possible
set that is fully representative of the crystal. Crystals of a complex molecule,
like a protein, produce a complex pattern of X-ray diffraction, or scattering of
X-rays. When the crystal is placed in an X-ray beam, all of the unit cells present
the same face to the beam; therefore, many molecules are in the same orientation
with respect to the incoming X-rays. The X-ray beam enters the crystal and a
number of smaller beams emerge: each one in a different direction, each one with a
different intensity. If an X-ray detector, such as a piece of film, is placed on
the opposite side of the crystal from the X-ray source, each diffracted ray,
called a reflection, will produce a spot on the film. However, because only a few
reflections can be detected with any one orientation of the crystal, an important
component of any X-ray diffraction instrument is a device for accurately setting
and changing the orientation of the crystal. The set of diffracted, emerging beams
contains information about the underlying crystal structure.
1-D spectra contain the information about all the chemical shifts of all the H in
the protein. The frequency resolution is often not enough to distinguish
individual chemical shifts. 2-D NMR solves these problems by containing
information about the relative position of H in molecular structures. 2-D NMR
spectra contain information about interaction between H that is covalently linked
through one or two other atoms (COSY or correlation spectroscopy). Alternatively,
pairs of H that can be close in space, even if they are from residues that are not
close in sequence (NOE spectra, or Nuclear Overhauser Effect). A complete
structure can thus be calculated by sequentially assigning cross peak correlations
in 2-D spectra. Currently, the size limit for proteins amenable to NMR solution
structure analysis is about 200 amino acids. An important feature of the
identification of cross peaks is that regular patterns can be recognized that stem
from secondary structure elements such as alpha helices and parallel or anti-
parallel beta sheets because they contain typical hydrogen bonding networks.
NMR also requires the knowledge of the amino acid sequence, but the protein does
not have to be in an ordered crystal, yet high concentrations of solubilized
protein must be available (NMR structures are therefore also called solution
structures). In biopolymers, the primary structure (sequence) logically breaks up
the molecule into groups of coupled spins normally one or two groups per residue.
This is true not only for proteins, but also for nucleic acids and
polysaccharides.
The distances measured in this way for both the 6-s-cis- and 6-s-trans-retinoic
acid model compounds agreed well with crystallographically known distances. In
bacteriorhodopsin the exchange trajectory between C-8 and C-18 was in good
agreement with the internuclear distance for a 6-s-trans configuration [4.2
angstroms (A)] and inconsistent with that for a 6-s-cis configuration (3.1 A). The
results illustrate that rotational resonance can be used for structural studies in
membrane proteins and in other situations where diffraction and solution NMR
techniques yield limited information.
Structure of bacteriorhodopsin:
General:
Current strategies for determining the structures of membrane proteins in lipid
environments by NMR spectroscopy rely on the anisotropy of nuclear spin
interactions, which are experimentally accessible through experiments performed on
weakly and completely aligned samples. Importantly, the anisotropy of nuclear spin
interactions results in a mapping of structure to the resonance frequencies and
splittings observed in NMR spectra. Distinctive wheel-like patterns are observed
in two-dimensional 1H-15N heteronuclear dipolar/15N chemical shift PISEMA
(polarization inversion spin-exchange at the magic angle) spectra of helical
membrane proteins in highly aligned lipid bilayer samples. One-dimensional dipolar
waves are an extension of two-dimensional PISA (polarity index slant angle) wheels
that map protein structures in NMR spectra of both weakly and completely aligned
samples. Dipolar waves describe the periodic wave-like variations of the
magnitudes of the heteronuclear dipolar couplings as a function of residue number
in the absence of chemical shift effects. Since weakly aligned samples of proteins
display these same effects, primarily as residual dipolar couplings, in solution
NMR spectra, this represents a convergence of solid-state and solution NMR
approaches to structure determination
References:
2. Wikipedia.
3. Biochemistry by Lehninger,
Chapter no.4:
“The three dimensional structure of Proteins”, page no.116.
Chapter-22
Enzymology of DNA folding and unfolding
WHAT IS DNA???
DNA STRUCTURE
DNA is a long polymer made from repeating units called nucleotides.[1][2] The DNA
chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit
is 3.3 Ångstroms (0.33 nanometres) long.[3] Although each individual repeating
unit is very small, DNA polymers can be enormous molecules containing millions of
nucleotides. For instance, the largest human chromosome, chromosome number 1, is
220 million base pairs long.[4]
In living organisms, DNA does not usually exist as a single molecule, but instead
as a tightly-associated pair of molecules.[5][6] These two long strands entwine
like vines, in the shape of a double helix. The nucleotide repeats contain both
the segment of the backbone of the molecule, which holds the chain together, and a
base, which interacts with the other DNA strand in the helix. In general, a base
linked to a sugar is called a nucleoside and a base linked to a sugar and one or
more phosphate groups is called a nucleotide. If multiple nucleotides are linked
together, as in DNA, this polymer is referred to as a polynucleotide.[7]
The backbone of the DNA strand is made from alternating phosphate and sugar
residues.[8] The sugar in DNA is 2-deoxyribose, which is a pentose (five carbon)
sugar. The sugars are joined together by phosphate groups that form phosphodiester
bonds between the third and fifth carbon atoms of adjacent sugar rings. These
asymmetric bonds mean a strand of DNA has a direction. In a double helix the
direction of the nucleotides in one strand is opposite to their direction in the
other strand. This arrangement of DNA strands is called antiparallel. The
asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′
(three prime) ends. One of the major differences between DNA and RNA is the sugar,
with 2-deoxyribose being replaced by the alternative pentose sugar ribose in
RNA.[6]
The DNA double helix is stabilized by hydrogen bonds between the bases attached to
the two strands. The four bases found in DNA are adenine (abbreviated A), cytosine
(C), guanine (G) and thymine (T). These four bases are shown below and are
attached to the sugar/phosphate to form the complete nucleotide, as shown for
adenosine monophosphate.
These bases are classified into two types; adenine and guanine are fused five- and
six-membered heterocyclic compounds called purines, while cytosine and thymine are
six-membered rings called pyrimidines.[6] A fifth pyrimidine base, called uracil
(U), usually takes the place of thymine in RNA and differs from thymine by lacking
a methyl group on its ring. Uracil is not usually found in DNA, occurring only as
a breakdown product of cytosine, but a very rare exception to this rule is a
bacterial virus called PBS1 that contains uracil in its DNA.[9] In contrast,
following synthesis of certain RNA molecules, a significant number of the uracils
are converted to thymines by the enzymatic addition of the missing methyl group.
This occurs mostly on structural and enzymatic RNAs like transfer RNAs and
ribosomal RNA.[
0]
Animation of the structure of a section of DNA. The bases lie horizontally between
the two spiraling strands. Large version[11]
The double helix is a right-handed spiral. As the DNA strands wind around each
other, they leave gaps between each set of phosphate backbones, revealing the
sides of the bases inside (see animation). There are two of these grooves twisting
around the surface of the double helix: one groove, the major groove, is 22 Å wide
and the other, the minor groove, is 12 Å wide.[12] The narrowness of the minor
groove means that the edges of the bases are more accessible in the major groove.
As a result, proteins like transcription factors that can bind to specific
sequences in double-stranded DNA usually make contacts to the sides of the bases
exposed in the major groove.[13]
Replication
Cell division is essential for an organism to grow, but when a cell divides it
must replicate the DNA in its genome so that the two daughter cells have the same
genetic information as their parent. The double-stranded structure of DNA provides
a simple mechanism for DNA replication. Here, the two strands are separated and
then each strand's complementary DNA sequence is recreated by an enzyme called DNA
polymerase. This enzyme makes the complementary strand by finding the correct base
through complementary base pairing, and bonding it onto the original strand. As
DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different
mechanisms are used to copy the antiparallel strands of the double helix.[71] In
this way, the base on the old strand dictates which base appears on the new
strand, and the cell ends up with a perfect copy of its DNA
DNA DENATURATION :
The two DNA strands, which form the double helix, are in opposite orientations
(one runs in 5'-3'direction, the complementary in 3'-5'direction) and are
connected by hydrogen bonds (see DNA structure). The rupture of these hydrogen
bonds causes the DNA to separate or to "denature". Inside the cell, a partial
separation of the DNA strands is necessary for replication and transcription and
is caused by several proteins that use ATP. But in vitro the rupture of the
hydrogen bonds can be caused by heat, alcaline conditions or chemical compounds
Chemical compounds like urea or formamide denature the DNA by directly reacting
with the bases, thereby preventing normal base-pairing. The Tm is reduced
proportionally to the concentration of denaturating chemical agents. If we
decrease the concentration of either urea or formamide, DNA will renature again.
Urea is used in denaturing gels to sequence DNA.
DNA RENATURATION :
The temperature at which DNA is half unfolded is called the melting temperature.
Tm is a measure of the stability of DS-DNA under a given set of conditions.
Stability, and therefore Tm, is affected by....
Base Composition - higher the GC content, the higher the Tm.
Ionic Strength - as the ionic strength increases, so does Tm. Double helical DNA
is stabilised by cations.
Divalent cations (eg Mg2+) are more effective than monovalent cations (<NA+ or
K+).
Organic Solvents - formamide for instance lowers the Tm by weakening the
hydrophobic interactions.
The unwinding of DNA strands in the presence of small concentrations of Mn2+ ions
(2 × 10-4-4 × 10-4M) has been studied. The process of unwinding is nonequilibrium;
the DNA strands are gradually unwound at a constant temperature corresponding to
the beginning of the melting curve. There is no true renaturation in the partially
melted DNA. It is shown in the paper that these effects are due to the aggregation
of the unwound DNA regions. The Mn2+ ions are responsible for the binding of the
unwound strands. The aggregation precludes renaturation, shifts the equilibrium
towards the melted state, and causes slow unwinding at a constant temperature. The
binding of denaturated regions seems to occur through the guanines
ADVANTAGES OF DENATURATION…
The performance and convenience of a PCR melting profile (PCR MP) technique based
on using low denaturation temperatures during ligation mediated PCR (LM PCR) of
bacterial DNA is shown. We found that PCR MP technique is a rapid method that
offers good discriminatory power, excellent reproducibility and may be applied for
epidemiological studies. Results from strain genotyping illustrate that PCR MP is
useful for the study of intraspecific genetic relatedness of strains and is as
effective in discriminating closely related strains as the PFGE method, which is
currently considered to be the gold standard for epidemiological studies. The
usefulness of the PCR MP for molecular typing was shown for clinical strains of
Escherichia coli, Enterococcus faecium VRE and Stapylococcus aureus.
3.GENOMIC SEQUENCING
Unique DNA sequences can be determined directly from mouse genomic DNA. A
denaturing gel separates by size mixtures of unlabeled DNA fragments from complete
restriction and partial chemical cleavages of the entire genome. These lanes of
DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a
short 32P-labeled single-stranded probe produces the image of a DNA sequence
"ladder" extending from the 3' or 5' end of one restriction site in the genome.
Numerous different sequences can be obtained from a single membrane by reprobing.
Each band in these sequences represents 3 fg of DNA complementary to the probe.
Sequence data from mouse immunoglobulin heavy chain genes from several cell types
are presented. The genomic sequencing procedures are applicable to the analysis of
genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein
interactions at single nucleotide resolution
4.SUPERCOIL SEQUENCING:A FAST AND SIMPLE METHOD FOR SEQUENCING PLASMID DNA
A method, using LiAc to yield competent cells, is described that increased the
efficiency of genetic transformation of intact cells of Saccharomyces cerevisiae
to more than 1 X 10(5) transformants per microgram of vector DNA and to 1.5%
transformants per viable cell. The use of single stranded, or heat denaturated
double stranded, nucleic acids as carrier resulted in about a 100 fold higher
frequency of transformation with plasmids containing the 2 microns origin of
replication. Single stranded DNA seems to be responsible for the effect since M13
single stranded DNA, as well as RNA, was effective. Boiled carrier DNA did not
yield any increased transformation efficiency using spheroplast formation to
induce DNA uptake, indicating a difference in the mechanism of transformation with
the two methods.
The dideoxy sequencing method in which denatured plasmid DNA is used as a template
was improved. The method is simple and rapid: the recombinant plasmid DNA is
extracted and purified by rapid alkaline lysis followed by ribonuclease treatment.
The plasmid DNA is then immediately denatured with alkali and subjected to a
sequencing reaction utilizing synthetic oligonucleotide primers. It takes only
several hours from the start of the plasmid extraction to the end of the
sequencing reaction. We examined each step of the procedure, and several points
were found to be crucial for making the method reproducible and powerful: (i) the
plasmid DNA should be free from RNA and open circular (or linear) DNA; (ii) a
heptadecamer rather than a pentadecamer is recommended as a primer; and (iii) the
sequencing reaction should be done at 37 degrees C or higher rather than at room
temperature. The method enabled us to determine the sequence of more than a
thousand nucleotides from a single template DNA.
The rate of renaturation of T2 DNA has been studied as a fuction of ethidium bound
per nucleotide of denatured DNA. The Binding constants and number of binding sites
for ethidium have been determined by spectral titration for denatured DNA at 55,
65, and 75°C and for native DNA at 65°C in 0.4M Na+. The rate of renaturation of
T2 DNA was found to be independentof ethidium binding up to 0.03 moles per mole of
nucleotide. Above 0.03 moles, the rate drops off precipitously approaching zero at
0.08 and 0.06 moles bound ethidium per nucleotide at 65°C respectively. A study
was also made of the use of bound ethidium fluorescence as a probe for monitoring
DNA renaturation reactions.
Solvents which accelerate DNA renaturation rates have been investigated. Addition
of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at
45°C and then leads to a loss of second-order behavior. The greatest accelerations
are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most
effective method of accelerating DNA renaturation with concentrated DNA. Addition
of dextran sulfate beyond 10-12% in 2.4M Et4NCl fails to increase the acceleration
beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35-
40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to
be more effective, although acceleration may be achieved in solvents containing
formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of
the normal concentration and temperature dependence of DNA renaturation and is
also independent of dextran sulfate concentration if sufficient dextran sulfate is
used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
Introduction
Only very few enzymes present hazards, because of their catalytic activity, to
those handling them in normal circumstances but there are several areas of
potential hazard arising from their chemical nature and source. These are
allergenicity, activity-related toxicity, residual microbiological activity, and
chemical toxicity.
All enzymes, being proteins, are potential allergens and have especially potent
effects if inhaled as a dust. Once an individual has developed an immune response
as a result of inhalation or skin contact with the enzyme, re-exposure produces
increasingly severe responses becoming dangerous or even fatal. Because of this,
dry enzyme preparations have been replaced to a large extent by liquid
preparations, sometimes deliberately made viscous to lower the likelihood of
aerosol formation during handling. Where dry preparations must be used, as in the
formulation of many enzyme detergents, allergenic responses by factory workers are
a very significant problem particularly when fine-dusting powders are employed.
Workers in such environments are usually screened for allergies and respiratory
problems. The problem has been largely overcome by encapsulating and granulating
dry enzyme preparations, a procedure that has been applied most successfully to
the proteases and other enzymes used in detergents. Enzyme producers and users
recognise that allergenicity will always be a potential problem and provide safety
information concerning the handling of enzyme preparations. They stress that dust
in the air should be avoided so weighing and manipulation of dry powders should be
carried out in closed systems. Any spilt enzyme powder should be removed
immediately, after first moistening it with water. Any waste enzyme powder should
be dissolved in water before disposal into the sewage system. Enzyme on the skin
or inhaled should be washed with plenty of water. Liquid preparations are
inherently safer but it is important that any spilt enzyme is not allowed to dry
as dust formation can then occur. The formation of aerosols (e.g. by poor
operating procedures in centrifugation) must be avoided as these are at least as
harmful as powders.
Activity-related toxicity is much rarer but it must be remembered that proteases
are potentially dangerous, particularly in concentrated forms and especially if
inhaled. No enzyme has been found to be toxic, mutagenic or carcinogenic by itself
as might be expected from its proteinaceous structure. However, enzyme
preparations cannot be regarded as completely safe as such dangerous materials may
be present as contaminants, derived from the enzyme source or produced during its
processing or storage.
The organisms used in the production of enzymes may themselves be sources of
hazardous materials and have been the chief focus of attention by the regulatory
authorities. In the USA, enzymes must be Generally Regarded As Safe (GRAS) by the
FDA (Food and Drug Administration) in order to be used as a food ingredient. Such
enzymes include α-amylase,β-amylase, bromelain, catalase, cellulase, ficin, -
galactosidase, glucoamylase, glucose isomerase, glucose oxidase, invertase,
lactase, lipase, papain, pectinase, pepsin, rennet and trypsin.
In the UK, the Food Additives and Contaminants Committee (FACC) of the Ministry
of Agriculture, Fisheries and Food classified enzymes into five classes on the
basis of their safety for presence in the foods and use in their manufacture.
Group A. Substances that the available evidence suggests are acceptable for use
in food.
Group B. Substances that on the available evidence may be regarded as
provisionally acceptable for use in food but about which further information must
be made available within a specified time for review.
Group C. Substances for which the available evidence suggests toxicity and which
ought not to be permitted for use in food until adequate evidence of their safety
has been provided to establish their acceptability.
Group D. Substances for which the available information indicates definite or
probable toxicity and which ought not to be permitted for use in food.
Group E. Substances for which inadequate or no toxicological data are available
and for which it is not possible to express an opinion as to their acceptability
for use in food.
This classification takes into account the potential chemical toxicity from
microbial secondary metabolites such as mycotoxins and aflotoxins. The growing
body of knowledge on the long-term effects of exposure to these toxins is one of
the major reasons for the tightening of legislative controls.
The enzymes that fall into group A are exclusively plant and animal enzymes such
as papain, catalase, lipase, rennet and various other proteases. Group B contains
a very wide range of enzymes from microbial sources, many of which have been used
in food or food processing for many hundreds of years. The Association of
Microbial Food Enzyme Producers (AMFEP) has suggested subdivisions of the FACC's
group B into:
Class ain8 microorganisms that have traditionally been used in food or in food
processing, including Bacillus subtilis, Aspergillus niger, Aspergillus oryzae,
Rhizopus oryzae, Saccharomyces cerevisiae, Kluyveromyces fragilis, Kluyveromyces
lactis and Mucor javanicus.
Class bin8 microorganisms that are accepted as harmless contaminants present in
food, including Bacillus stearothermophilus, Bacillus licheniformis, Bacillus
coagulans, and Klebsiella in8aerogenes.
Class cin8 microorganisms that are not included in Classes b and c, including
Mucor miehei, Streptomyces albus, Trichoderma reesei, Actinoplanes missouriensis,
and Penicillium emersonii.
It was proposed that Class a should not be subjected to testing and that Classes b
and c should be subjected to the following tests:
acute oral toxicity in mice and rats,
subacute oral toxicity for 4 weeks in rats,
oral toxicity for 3 months in rats, and
in vitro mutagenicity.
In addition Class c should be tested for microorganism pathogenicity and, under
exceptional circumstances, in vivo mutagenicity, teratogenicity, and
carcinogenicity.
The cost of the various tests needed to satisfy the legal requirements are very
significant and must be considered during the determination of process costs.
Plainly the introduction of an enzyme from a totally new source will be a very
expensive matter. It may prove more satisfactory to clone such an enzyme into one
of AMFEP's Class a organisms but this will first require new legislation to
regulate the use of cloned microbes in foodstuffs. Some of the safety problems
associated with the use of free enzymes may be overcome by using immobilised
enzymes . This is an extremely safe technique, so long as the materials used are
acceptable and neither they, nor the immobilised enzymes, leak into the product
stream.