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TECHNIQUES FOR
BIOMOLECULE
PURIFICATION
Principles of chromatography
Purification of biological macromolecules (DNA, Proteine) with maintaining the biological function.
The separate steps are carried out predominantly (at low temperatures) in aqueous buffer systems.
Proteins have a very complex three-dimensional structure, which is important for the biological function and which must
remain unchanged as far as possible during purification steps.
Using correct terminology, it is an amino carbonic acid which contains an amino group (-NH2) and a carboxylic group (-
COOH).
Amino acids have a common basic structure, different amino acids vary from each other only by their side chain (R).
Most proteins are build from different combinations of only twenty different amino acids. This pool of twenty amino acids
can be classified according to:
Source:
Principles of Biochemistry
Source:
Principles of Biochemistry
The characteristics imparted to the protein by the amino acid side chains serve as bases for purification process, and
include solubility, charge, hydrophobicity and intermolecular binding.
Chromatography
Column liquid chromatography
Thin layer chromatography
Partitioning chromatography
Electrophoresis
Precipitation
Microfiltration/Dialysis
Extraction
Crystallisation
Centrifugation
Chromatography is the collective term ... for the separation of mixtures. It involves passing a mixture dissolved in a
mobile phase through a stationary phase, which separates the analyte to be measured from other molecules in the
mixture based on differential partitioning between the mobile and stationary phases.
Source:
Wikipedia
Principles of Biochemistry
chromatogram
12 Chromatography techniques for biomolecule purification | 29.07.2016
Chromatogram
data acquisition
sample
pump detector
A B load
fraction collector
+ +
+ +
++
+
+
+
+
++ +
+ ++
Adsorptive Polarity
Ion exchange chromatography Normal phase chromatography
Affinity chromatography Reversed phase chromatography
Hydrophobic interaction
chromatography
Non-adsorptive
Size exclusion chromatography
(Gel filtration)
Source:
Principles of Biochemistry
20 Chromatography techniques for biomolecule purification | 29.07.2016
Ion exchange chromatography
One important characteristic of biomolecules is the iso-electric point or pI, this is the pH at which the total number of
positive and negative charges are equal and the net charge on the molecule is zero.
NH3+ < pI
net charge: positive
COO-
NH3+ = pI
net charge : neutral
R
COO-
NH2 > pI
net charge: negative
isoelectric point
of the antibody
pH
The term „strong“ and „weak“ does not correspond to the strength of binding of proteins!
- -
- - - -
- + - - +- + +
+ - -
- -
tentacle resin
convent. resin
15
130 130 90 10 50 80
10 10 90
120 100 80
Conductivity [mS/cm]
70
Conductivity [mS/cm]
70 80 60
Conductivity [mS/cm]
120 90 80 90
130 110
9 9 70
9
90
130
80
120 50 90
8 8 80 8
130 90 60
120 140 70 80 80 90
110 70
140 90
7 130 7 7
90
80
6 140 6 6
130 140 90
120 70 80 90 80 90
110 100 100
5 5 5
4,00 4,25 4,50 4,75 5,00 5,25 4,00 4,25 4,50 4,75 5,00 5,25 4,00 4,25 4,50 4,75 5,00 5,25
pH pH pH
Fractogel® EMD COO- (M) Eshmuno® CPX Fractogel® EMD SO3- (M)
5.0
initial mAb aggregate level: 3.8% initial mAb aggregate level: 3.9% initial mAb aggregate level: 3.8%
4.0
3.0
2.0
87% mAb yield at target ≤ 1.5% aggregates 75% mAb yield at target ≤ 1.5% aggr. 68% mAb yield at target ≤ 1.5% aggr.
1.0
0.0
0 20 40 60 80 100 0 20 40 60 80 100 0 20 40 60 80 100
cumulative mAb pool yield (%) cumulative mAb pool yield (%) cumulative mAb pool yield (%)
Experimental:
Fractogel® EMD COO- (M) resin: 87% mAb yield at target ≤ 1.5% aggr. Column size: 200 mm L x 5 mm i.d. (CV = 3.9 mL)
Operating buffer: 50 mM acetate + 24 mM NaCl, pH 5.0
Eshmuno® CPX resin: 75% mAb yield at target ≤ 1.5% aggr. (ca. 6 mS/cm)
Linear gradient elution: 0 - 1 M NaCl in 40 CV
Fractogel® EMD SO3- (M) resin: 68% mAb yield at target ≤ 1.5% aggr. Flow rate: 200 cm/h
Starting level of aggregates: 3.8%
32 Chromatography techniques for biomolecule purification | 29.07.2016
Load: 40 mg/mL CV
Comparison of elution profiles
mAb monomer
Eshmuno® CPX
competitor (agarose)
Elution peak width
%B Eshmuno® CPX: 11.4 CV
Conductivity Competitor (agarose): 14.3 CV
mAb aggregates
Advantages
High protein binding capacity
Independent of sample volume
Target is concentrated
Easy scale-up
Drawbacks
High salt concentration interfers with binding
Eluate contains salt
Source:
Principles of Biochemistry
36 Chromatography techniques for biomolecule purification | 29.07.2016
Affinity chromatography
Only the protein of interest is bound to the specific ligand; other sample components are eluted from the column in the
washing buffer or during the loading.
Elution of the sample protein may either be specific (e.g. using an enzyme substrate) or non-specific using salt or a
change in pH.
Affinity chromatography is the most powerful purification technique for the isolation of proteins.
- - - - Impurities
- -
+
- - - -
Complex
Binding region
- - -
- - -
+ +
- - - -
Purified protein
Affinity molecule for elution
Dyes
Immobilised metal ions (IMAC)
Lectins
Biospecific ligands
Pre-Peak Post-Peak
Monomer in Overall mAb Total Aggregate
Resin % Aggregate % Aggregate
pool (%) Yield (%) Removed (%)
Removed Removed
Eshmuno® A Media 94.6 79.4 25.7 36.9 62.6
MabSelect SuRe® 88.9 80.3 6.1 26.1 32.2
Advantages
A powerful tool in capture step for mAb
Very specific - high purity (> 90%) in one step
Easy operation
Drawbacks
Resin cost is high
Protein A ligand leaching
Advantages
High capacity compared to other affinity techniques
Good selectivity
Flexibility due to the immobilization of different metal
ions
High stability of the ligand
Supported by molecular techniques (expression vectors!)
Identification of histidine residues on the protein's
surface
Scalability/cleanability
Drawbacks
Necessity of histidine residues on the surface
More steps for column preparation are necessary
Bleeding of metal ions
The eluent of choice is an inverse gradient with ammonium or sodium sulphate to buffer or water
Binding is the result of permanent dipoles of water molecules conferring an ordered structure on the water and thus
increasing the association of the hydrophobic patches of the target compound and the hydrophobic regions of the
stationary phase (increased entropy in the system).
- -
- - - -
+ - +
-
- -
- -
„Ordered“ „Disordered“
water molecules Hydrophobic patches water molecules
Advantages
Sample binding occurs in the presence of salt.
During elution salt concentration can be reduced.
Very good separation efficiency (isoenzyme separation)
Drawbacks
High salt load.
Denaturation of proteins.
Since the separation mechanism is independent from the buffer, the most
suitable buffer conditions for each protein can be used.
Source:
Principles of Biochemistry
Different migration
distances depending on the
molecule’s size and shape
60
Column dimensions (length: 40-100 cm)
50
40
Optimal column packing
30 BSA
Ovalbumin
20 Cytochrome c
10
0
0 50 100 150 200 250 300
[sodium chloride] (mM)
A280
Advantages
No adsorptive interaction between stationary phase and
sample.
Free choice of the buffer system (optimal conditions for
the target protein).
Predictable elution behavior.
Drawbacks
Loading volume is limited and large columns are
required.
Technique is unsuitable for sample molecules of similar
size.
RoboColumn
RoboColumn
MiniChrom Column
MiniChrom Column
Chromabolt® Chromabolt®
N Mobile phase
P NP P POLAR SORBENT NON-POLAR
P
N Mobile phase
PSample
NP NON-POLAR SORBENT P POLAR
P
Salts Hexane
Silica
Acids
Alcohols THF
Ketones
CN
Ethers
C4
Hydrocarbons: Acetonitrile
halogenated
C8
aromatic Alcohol
aliphatic
C18
fluorinated Water
-C2
Preparative Chromatography
PharmPrep® P spherical
Performance
LiChroprep®
irregular
10 12 20 25 40 63 200 500 µm
Particle size
Protein A
VI UF IEX UF VRF IEX UF
Soft gel
time reduction
Protein A -44%
IEX
VI UF UF VRF IEX UF
rigid
From: An evaluation of Protein A and Non-Protein A methods for the recovery of monoclonal
antibodies and considerations for process scale-up by Martin Smith, LONZA, Presented
at“Scaling-up of Biopharmaceutical Products”, 26/27thJanuary 2004, The Grand, Amsterdam
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