Two Types of Protein

Conformations: Fibrous and

Globular

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Fibrous Proteins
Fibrous proteins: contain polypeptide chains
organized approximately parallel along a single axis.
They
consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature
Examples are
keratin of hair and wool
collagen of connective tissue of animals including
cartilage, bones, teeth, skin, and blood vessels

Globular Proteins
Globular proteins: proteins which are folded
to a more or less spherical shape
they tend to be soluble in water and salt solutions
most of their polar side chains are on the outside
and interact with the aqueous environment by
hydrogen bonding and ion-dipole interactions
most of their nonpolar side chains are buried inside
nearly all have substantial sections of -helix and
-sheet

Fig. 4-12a, p. 93

3 Structure

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 The 3-dimensional arrangement of atoms in

the molecule.
In fibrous protein, backbone of protein does
not fall back on itself, it is important aspect of
3 not specified by 2 structure.
In globular protein, more information needed.
3k structure allows for the determination of the
way helical and pleated-sheet sections fold
back on each other.

Interactions between side chains also plays a

role.

Forces in 3 Structure
Noncovalent interactions, including
hydrogen bonding between polar side chains, e.g.,
Ser and Thr
hydrophobic interaction between nonpolar side
chains, e.g., Val and Ile
electrostatic attraction between side chains of
opposite charge, e.g., Lys and Glu
electrostatic repulsion between side chains of like
charge, e.g., Lys and Arg, Glu and Asp

Covalent interactions: Disulfide (-S-S-)

bonds between side chains of cysteines

Forces That Stabilize Protein

Structure

3and 4Structure
Tertiary (3) structure: the arrangement in
space of all atoms in a polypeptide chain
it is not always possible to draw a clear distinction
between 2and 3structure

Quaternary (4) structure: the association of

polypeptide chains into aggregations
Proteins are divided into two large classes
based on their three-dimensional structure
fibrous proteins
globular proteins

Determination of 3Structure
X-ray crystallography
uses a perfect crystal; that is, one in which all
individual protein molecules have the same 3D
structure and orientation
exposure to a beam of x-rays gives a series
diffraction patterns
information on molecular coordinates is extracted
by a mathematical analysis called a Fourier series

2-D Nuclear magnetic resonance

can be done on protein samples in aqueous
solution

X-Ray and NMR Data

High resolution method to determine 3

structure of proteins (from crystal)
Diffraction pattern produced by electrons
scattering X-rays
Series of patterns taken at different
angles gives structural information

Determines solution structure

Structural info. Gained from
determining distances between
nuclei that aid in structure
determination

Myoglobin

A single polypeptide chain of 153 amino acids

A single heme group in a hydrophobic pocket
8 regions of -helix; no regions of -sheet
Most polar side chains are on the surface
Nonpolar side chains are folded to the interior
Two His side chains are in the interior, involved with
interaction with the heme group
Fe(II) of heme has 6 coordinates sites; 4 interact with
N atoms of heme, 1 with N of a His side chain, and 1
with either an O2 molecule or an N of the second His
side chain

The Structure of Myoglobin

The Structure of the heme group

Fig. 4-16, p. 98

propionate

methyl

methyl

vinyl
methyl

methyl

vinyl

15

Oxygen Binding Site of Myoglobin

Fig. 4-18, p. 99

Denaturation
Denaturation: the loss of the structural order (2, 3, 4,
or a combination of these) that gives a protein its
biological activity; that is, the loss of biological activity
Denaturation can be brought about by

heat
large changes in pH, which alter charges on side
chains, e.g., -COO- to -COOH or -NH + to -NH
detergents such as sodium dodecyl sulfate (SDS)
which disrupt hydrophobic interactions
urea or guanidine, which disrupt hydrogen bonding
mercaptoethanol, which reduces disulfide bonds

Quaternary Structure

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19

 Quaternary (4) structure: the

association of polypepetide
monomers into multisubunit
proteins
dimers
trimers
tetramers

Noncovalent interactions
electrostatics, hydrogen bonds,
hydrophobic

Oxygen Binding of Hemoglobin (Hb)

A tetramer of two -chains (141 amino acids
each) and two -chains (153 amino acids
each); 2 2
Each chain has 1 heme group; hemoglobin
can bind up to 4 molecules of O2
Binding of O2 exhibited by positive
cooperativity; when one O2 is bound, it
becomes easier for the next O2 to bind

 The function of hemoglobin is to transport

oxygen
The structure of oxygenated Hb is different
from that of unoxygenated Hb
H+, CO2, Cl-, and 2,3-bisphosphoglycerate
(BPG) affect the ability of Hb to bind and
transport oxygen

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Structure of Hemoglobin

Conformation Changes That Accompany

Hb Function
Structural changes occur during binding of
small molecules
Characteristic of allosteric behavior

Hb exhibits different 4 structure in the bound

and unbound oxygenated forms
Other ligands are involved in cooperative
effect of Hb can affect proteins affinity for
O2 by altering structure

Fig. 4-22, p. 102

Iron lies 0.4Ao outside the protophorphyrin plane in

deoxyhemoglobin

26

The binding of oxygen allows iron to move into the plane

of the protoporphyrin ring.

27

On oxygenation, one pair of subunits shifts with

respect to the other by a rotation of 15o

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Oxy- and
Deoxyhemoglobin

Fig. 4-23, p. 103

H+ ions and
bisphophoglycerate
regulate oxygen binding
to hemoglobin in vivo

The general features of the Bohr Effect

Fig. 4-24, p. 103

Fig. 4-25, p. 104

This interaction locks the 1His146

to form salt bridge with 1Asp 94

33

Table 4-1, p. 104

2,3-Bisphosphoglycerate
Fig. 4-26, p. 104

Fig. 4-27, p. 105

38

Fig. 4-28, p. 105

Fig. 4-29, p. 105

Collagen Triple Helix

Consists of three polypeptide chains wrapped around
each other in a ropelike twist to form a triple helix called
tropocollagen; MW approx. 300,000
30% of amino acids in each chain are Pro and Hyp
(hydroxyproline); hydroxylysine also occurs
Every third position is Gly and repeating sequences are
X-Pro-Gly and X-Hyp-Gly
Each polypeptide chain is a helix but not an a-helix
The three strands are held together by hydrogen bonding
involving hydroxyproline and hydroxylysine
With age, collagen helices become cross linked by
covalent bonds formed between Lys and His residues

p. 91

A Triple
Helix

Fig. 4-11, p. 92

Keratin
Fibrous (structural) proteins.
Individual molecules combine to
form insoluble structures.
Keratins are the molecular basis
for hair, nails, wool, feathers,
beaks, claws and horns.
Keratin is also found in the
cytoskeleton of cells.

 alpha isomer found in cytoskeleton and

hair.
beta isomer found mostly in birds and
reptiles. It is the building block of
scales, feathers and claws.
alpha form can be stretched up to 120%
in moist heat, beta form is rigid.
Cysteine can form disulfide bridges with
other cysteine residues. These crosslinkages decrease the elasticity of alphakeratin.
45

Scanning electron micrograph of sectioned

human skin. The layers of dead epidermal
cells at the top consist mostly of keratin

Arrangement of residues in a coiled coil.

This view down the axis of two sevenresidue shows that amino acids at 1
and 4 line up on one side of each helix

Three views of a coiled coil

Each -helical chain
contains 100
residues. The
nonpolar strip along
each helix contact
each other, so that
the two helices wind
around each other in
a gentle left-handed
coil.

Model of an
intermediate
filament.

Pairs of polypeptide form coiled coil. These

dimers associate to form tetramers and so,
on, ultimately producing an intermediate
filament composed of 16 to 32 polypeptides
in cross section.

Silk fibroin
The fibrous protein present in
cocoons, webs, nests and egg stalks
Consist of antiparallel sheets whose
chains extend parallel to the fiber
axis
Contain six residue repeat
(-G-S-G-A-G-A)n

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Denaturation of a Protein

Denaturation and Refolding in Ribonuclease

Several ways to
denature proteins
Heat

pH
Detergents

Urea
Guanadine
hydrochloride