Input for Purification Protocol Development

Guidelines for Protein

Purification

Selection and combination of purification techniques

1

PURIFICATION STRATEGY

General approach: Protocol Development

Guidelines for Protein Purification. Commonly confronted decisions.

Properties of Target Protein

Sequence of Events: Cell harvesting, Cell Disruption, Extraction and

Clarification, Chromatography

Three Phase Strategy: Linking Chromatography Techniques

Characterization Criteria

Storage

2

Applications of Protein Purification In vitro Activity assays

Antibody development / production

Protein:protein interaction assays

Cell-based activity assays

Ligand-binding assays

Mass-spectrometric analysis

Structural analysis

In vivo activity assay

Don’t waste clear thinking on dirty

or not healthy proteins!!!!

Post-translational modification tests

N-terminal sequencing

Electromobility shift assay (band shift)

DNA footprinting

Protein cross-linking studies

Vaccine development/production

Probes for protein arrays/chips

Expression library screening

Other

For each application you need:

different quantities

different protein purity

start material is different, etc

different strategy

Each purification project must be

adapted to your start material and

your final needs

Protein Purification Strategy

4

FUSION PROTEIN

NON-FUSION PROTEIN

EXPRESSION

Simple Purification

ONE STEP Affinity

70 - 95% Purity

For higher purity

Capture Intermediate Purification

Polishing

Multi-Step Purification

Protein Purification - Aims

Satisfactory

expression levels

protein activity

purity

homogeneity

stability

Economical use of reagents/equipment

Goal to Success:

Selection or optimization of the best source or best expression

conditions

A good understanding of the protein needs

Selection and optimization of the most appropriate technique for

each step 6

Structural Studies: Crystallization – NMR- etc

Concentration & Storage

Fermentation

Scaling Up

Gene Cloning

Target Optimization

Target Selection

Selection of Expression Vector

Selection of Expression Host

Expression Analysis

Solubility Analysis

Purification Optimization

Characterization

Biochemical Studies Pharmaceutical Studies

Protein Production Pipeline

Purification

Commonly confronted decisions

Which is the best natural source?

How much do we need?

Active? Which assay?

Purification grade?

Which hosts: bacteria, yeast, insect cells or in human cells?

Which expression vector should be used? Which strain(s) should be chosen?

Should the protein be tagged? which affinity tag is the best?

Which is the best purification strategy?

Which buffers should I use?

Optimization of each purification step, where to stop?

How much can I concentrate my sample?

How to keep activity, solubility and homogenicity of my sample? 8

Overview: separation techniques

Technique Parameter Based on for separation Gel filtration Size/Shape MW, Shape, and oligomeric state of the molecule Ion exchange/ Hydroxyapatite/ Charge interaction Asp, Glu, Lys, Arg, His

Chromatofocusing

Hydrophobic/ Hydrophobic sites Trp, Phe, Ile, Leu, Tyr, Pro Reversed phase interaction Met, Val, Ala

Affinity Biological function eg: antibody – antigen

Metal chelate Affinity for metals poly His

Covalent Covalent interaction Uses SH groups (Cys)

Multimodal Mixture Hydrophobic + Ionic Interaction 9

Input for Purification Protocol Development

General Input Sample Specific Input

10

Three phase strategy

Purification protocol

Required purity and quantity

Physical-chemical properties of target and

main contaminants

Source material information

Separation technique knowledge

Scouting runs and optimization

Economy and resources

Yields from Multistep Protein Purifications

11

Number of steps

Yield (%)

95% / step

90% / step

85% / step 80% / step 75% / step

0

20

40

60

80

100

1 2 3 4 5 6 7 8

Protein Modifications May Require Further Purification

12

COOH

NH2

Proteolytic cleavage

Glycosylation

Phosphorylation

Acylation

Misfolding, random

disulfide bridges

N or C terminal

heterogeneity

Aggregation

Oxidation of methionine Desamidation of Asp and Glu

Analytical tools

A rapid and reliable assay for the target protein: biological assay,

enzymatic, SDS-PAGE, Western, etc

Purity determination

SDS-PAGE, Native, IEF, RPC, analytical GF or EIX, etc

Total protein determination – Interference of detergents, reducing

agents, sugars, others - ultraviolet absorption, colorimetric method, etc

13

Define Properties of Target Protein (I)

Temperature Stability Need to work rapidly at low temperature

pH Stability Selection of buffers for each step

Organic Solvents Stability Selection of Conditions for RPC

Salt Stability Selection of Conditions for all steps

Co-factors for Stability or Activity Selection of Additives, pH, Salts, Buffers

Protease Sensitivity Fast removal of proteases. Protease Inhibitors

Sensitivity to Metal Ions Need of EDTA or EGTA in Buffers

Define Properties of Target Protein (II)

Redox Sensitivity Need of reducing agents to protect reduce Cys: DTT, DTE or

on the contrary, need to protect disulfide bridges

Molecular Weight/Oligomeric State Selection of Gel Filtration Media / UF

Charge Properties Selection of Ion Exchange Conditions

Biospecific affinity Selection of ligand for Affinity Medium

Post Translational Modifications Selection of Group Specific Affinity: Lectins

Hydrophobicity Solubility prediction - Selection of medium for HIC

16

Initial Bioinformatics Investigation

Using Bioinformatic Tools to Strategically Design Expression/Purification Projects

Dr. Nurit Kleinberger-Doron

http://wolfson.huji.ac.il/expression/software.html

17

Bioinformatics Tools-I

Physical and chemical parameters http://www.expasy.org/tools/protparam.html Computation of various physical and chemical parameters for a given protein: molecular

weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY)

http://www.scripps.edu/~cdputnam/protcalc.html Generates molecular weight information (including scanning mass spectrometry results),

estimated charges (including pI estimation), uv absorption coefficients, crystallographic solvent content percentage and Vm, and counts atoms and residues based on the protein sequence

Proteolytic Cleavage http://www.expasy.org/tools/peptidecutter/ Predicts potential cleavage sites cleaved by proteases or chemicals in a given protein

sequence http://www.cf.ac.uk/biosi/staff/ehrmann/tools/proteases.index.html Protease database of E.Coli

18

Bioinformatics Tools-II Post-translational modification prediction

http://www.expasy.org/tools/#ptm

Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins

Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins

Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian protein

Prediction of N-glycosylation sites in human proteins

Prediction of N-terminal myristoylation by neural networks

Recombinant Protein Solubility Prediction : The statistical model predicts protein solubility assuming the protein is being overexpressed in Escherichia coli.

http://www.biotech.ou.edu/

S-S bonds: Predicts cysteins that are likely to be partners in cysteine bridges

http://clavius.bc.edu/~clotelab/DiANNA/

http://gpcr.biocomp.unibo.it/cgi/predictors/cyspred/pred_cyspredcgi.cgi

FoldIndex© tries to answer to the question: Will this protein fold? http://bip.weizmann.ac.il/fldbin/findex

Is the Recombinant Protein Correctly Expressed

19

Biological activity

Analytical GF Native PAGE / IEF

Aggregation Heterogeneity

Size Proteolytic cleavage

Stability at different pH Ionic strengths Protein concentrations Detergent concentrations

SDS-PAGE and immuno blotting

N-terminal sequencing Truncated forms Heterogenous N-terminus

PURIFICATION STRATEGY

General approach: Protocol Development

Guidelines for Protein Purification. Commonly confronted decisions.

Properties of Target Protein

Sequence of Events: Cell harvesting, Cell Disruption, Extraction and

Clarification, Chromatography

Three Phase Strategy: Linking Chromatography Techniques

Characterization Criteria

Storage

20

Advantages or Disadvantages of Intra or Extracellular Expression - I

Cell wall disruption / Osmotic Shock

Extracellular expression

Recover

Clarified

sample

Cell disruption

Harvest inclusion

bodies

Intracellular expression

Insoluble in Cytoplasm

Periplasmic space

Recover Supernatant

Soluble in Cytoplasm

Cell debris removal Clarification

Purification-Chromatography

Cell removal

Clarification

Recover

Clarified

sample

Culture medium

Extracellular expression

Recover pellet

Intracellular expression

Insoluble in Cytoplasm

Periplasmic space

Recover supernatant after cell lysis

Soluble in Cytoplasm

Recover Supernatant

Purification-Chromatography

Partially pure protein Relatively low protein target in small volume

Low lipid conc. Lower degradation Correct disulphide

bond formation Difficult to scale-up

Partially pure protein

Very large volume Low protein

concentration Lower degradation Correct disulphide

bond formation

Recover

Clarified

sample

Recover clarified sample after cell wall lysis and osmotic shock

Culture medium

High quantities of almost pure protein

Renaturation problem

Lower sensitivity to proteases

Problems with disulphide bond

formation

Highly impure protein and lipid concentration Sensitive to proteases

Sometimes well expressed Small extraction volume

Problems with disulphide bond formation

Advantages or Disadvantages of Intra or Extracellular Expression - II

Extraction and Clarification

Definition: Primary isolation of target protein from source material.

Removal of debris or other contaminants which are not compatible with

chromatography.

Goal: Preparation of clarified sample for further purification.

The chosen technique must be robust and suitable for all scales of

purification.

Choice of additives and buffers must be carefully considered before

scaling up

Use additives only if essential for stabilization of product or

improved extraction; select those that are easily removed. 23

Common Substances Used in Sample Preparation

24

Minimize use of additives: they must be removed in extra purification steps or may interfere with activity assays

Tris HCl 20-50mM pH 7.5-8.0 or other buffers (HEPES, Phosphate, etc)

NaCl/KCl 0.3-0.5M (to maintain ionic strength). For soluble proteins NaCl can lower to 50mM. For some insoluble

proteins it can be increase till 1M

Glycerol 5-10% to stabilize prone to aggregate proteins (can be increase till 20%). Increase viscosity and back flow

of columns

DNaseA 25-50µg/ml (or Benzonase): degrade DNA. Reduce viscosity. Eukaryotic cells could need more Dnase

Lysozyme 0.2mg/ml for wall lysis of bacterial cells

Detergents (NP40, Triton X100, Tween 20, OG, DDMetc) for solubilization of some insoluble proteins or extraction of

membrane proteins. Use only if it does not affect protein stability!!!!

Reducing agents: 1-15mM BME, up to 2mM DTT or DTE, 1-5mM TCEP. Use only for Cys containing proteins without

disulfide bridges (maintain Cys in reduce form). Not all the IMAC columns can be use with all the reducing agents

EDTA 1-10mM Reduce oxidation damage. Chelate metal ions. Metalloprotease inhibitor. Do not use with IMAC.

Sucrose or Glucose 25mM Stabilize lysosomal membranes in eukaryotic cells. Reduce protease release.

Protease or Phosphatase inhibitors if necessary

Protease Inhibitors

25

Protease Inhibitor

Specificity of inhibition Working concentration

Antipain-dihydrochloride

Papain, Trypsin, Cathepsin A and B 1-100µM

Aprotinin Trypsin, Plasmin, Chymotrypsin, Kallikrein

2µg/ml

Benzamidine HCl Serine Proteases 0.5-4µM

Bestatin Aminopeptidases

Chymostatin Chymotrypsin and Cysteine Proteases 10-100µM

E-64 Cysteine Proteases 10µM

EDTA (or EGTA) Metalloproteases (Calcium) 2-10mM

Leupeptin Serine and Cysteine Proteases such as Plasmin, Trypsin, Papain, Cathepsin B

10-100µM

PMSF and AEBSF Serine Proteases 0.1-1mM

Pepstatin Aspartic Proteases 1µg/ml

Phosphoramidon Metalloproteinases, specifically, Thermolysin

1-10µM

Serine proteases are widely

distributed in most types of cells.

Bacterial extracts typically

contain serine and

metalloproteases.

Extracts from animal tissues

contain mainly serine-, cysteine-,

and metalloproteases. (some also

contain aspartic proteases).

Plant extracts contain large

amounts of serine and cysteine

proteases

Remove proteases early in the first purification step!!: load on capture column

immediately after lysis and clarification.

Protease Inhibitor Cocktail Set III (Cat. No. 539134) MERCK – EMD

Recommended for mammalian cells/tissue 1 ml sufficient for 20 g cells (~1 L). Dilution 1:100 to1:300

EDTA-free (good for His-Tag® protein purification)

Cell Disruption considerations

Stability of the released protein

Location of target protein within the cell (membrane, nucleus, mitochondria, etc.)

Yield and kinetics of the process. Extent of disruption: possible use of marker

substances, measure protein concentration. Balance: volume & lysis efficiency.

Suggested lysis volume for bacterial cells: 10-20% of original cell culture

Scale-up

Consider if protein purification can be performed directly from the cell lysate

without a cell debris clarification step (bed absorption chromatography) 27

28

Methods to monitor lysis

Reduction of whole cells: decrease of Abs660nm before and

after treatment.

Decrease of weight cell pellet after lysis

Monitor nucleic acid release : Increase in the Abs260nm

during lysis

(This method could be difficult because of the “haze” generated, which can alter absorbance readings. )

Microscopically : Compare cells before and after treatment

29

CELL DESINTIGRATION AND EXTRACTION: METHODS THAT DO NOT NEED SPECIAL EQUIPMENT

Freezing and thawing: Repeated cycles (can denature protein). For cells without a cell wall (animal cells). Not suitable for large scale. Not reliable method

Osmotic shock: Transfering cells from a high to a low osmotic pressure. Useful to release periplasmic proteins from Gram negative bacteria. Not reliable method

Chaotropic agents (urea, GuHCl): Extremely denaturative. Not suitable for large scale. Use for extremely insoluble proteins or inclusion bodies

Detergents (Brij, NP40, DDM, etc.): Anionic and non-ionic detergents permeabilize Gram negative cells. Can interfere in downstream process. Dissolve membrane-bound proteins. Use in combination with mechanical methods. Problematic!!! Bacterial Expression Screen - DDM (Dodecyl Maltoside) lysis - Small Affinity binding http://wolfson.huji.ac.il/purification/TagProteinPurif/DDM_Bacterial_Expr_screen.html

Organic solvents: Toluene, ether, chloroform, isoamyl alcohol, etc at different

concentration can release different materials from the cell. Extremely denaturative. Use only for solvent resistent proteins. Not reliable method

Enzymatic lysis: Lysozyme hydrolyze linkages in the peptido-glycan of bacterial cell walls. Used for pretreatment of cells in combination with mechanical methods. Yeast cell walls can be hydrolyzed with snail gut enzymes and glucanases

30

CELL DESINTIGRATION AND EXTRACTION: METHODS THAT NEED SPECIAL EQUIPMENT

Combine with chemical treatment: lysozyme, detergents, Dnase, etc.

Mixers and blenders: Useful for animal and plant tissues (Warring-blender)

Coarse grinding Grinding with a pestle and mortar of frozen mycelium. Fine grinding in a

bed mill: Useful for yeast, larger cells, algae and filamentous fungi. Use of different glass

beads (Bead-beater)

Homogenization: Animal cells. Piston/plunger device. Wheaton-Dounce homogenizer

Sonication: Bacterial cells disrupted by high frequency sound and share forces. Low scale. Very vigorous process. Heat generation. Not reliable method

High pressure lysis: Pumping cell suspension through a narrow orifice at high pressure. Mainly for bacterial cells. Very reliable and efficient method. French-press, Microfluidizer, Avestin, etc: medium scale (20-100ml). Microfluidizer, Maunton-Gaulin: For larger volumes

31 One Shot Model Microfluidizer

Avestin Emulsiflex C3

Microfluidizer

low volume benchtop machine

Cell Lysis Equipment in LSI

As French-press but for medium/larger volumes

For bacterial and yeast cells

High speed

Other applications.

Sample Preparation before Chromatography: Cell Debris Removal, Protein Clarification and Concentration

Centrifugation For small sample volumes 15min 10000g .

For very turbid cell homogenates: 30min 50000g

Filtration before loading in chromatographic column

Pore size filter: 1 μm for particle size of chromatographic medium 90 μm and upward

Pore size filter: 0.45 μm for particle size of chromatographic medium 30 or 34 μm

Pore size filter: 0.22 μm for particle size of chromatographic medium 3, 10, 15 μm

Filtration large scale, Normal or Dead end: Hollow-fiber. Plates. Spiral Cartridge

TFF: Tangential Flow Filtration or Cross flow

Expanded Bed Adsorption

Fractional Precipitation

Ultrafiltration Membranes 32

Tangential or cross flow and Normal or dead end filtration

Membrane-Based Systems

Pressure-driven processes, such as ultrafiltration (UF), microfiltration, virus filtration, and

nanofiltration . Or electric field (electroultrafiltration, EUF)

They are mainly used for protein concentration and buffer exchange in preference to SEC on an

industrial scale.

There are charge membranes that can use as IEX, RPC,

Affinity, HIC (Pall, Mustang, etc)

Another emerging technology in membrane separation

processes is high-performance tangential flow filtration

(HPTFF).

34

Labscale™ Benchtop TFF System with

Pellicon XL module

ProFlux® M12 Benchtop TFF system with

spiral wound modules

Prep/Scale filter modules

Fully automated 80 m2 Pellicon system for concentration and diafiltration

Pellicon cassettes

Large-scale spiral wound UF/DF system

TFF: Tangential or cross flow filtration Merck

35

TFF: Tangential or cross flow filtration

Merck

36

ÄKTAcrossflow™

Fully automated filtration system for cross

flow membrane screening, process

development, and small scale processing.

Enable automation at very small scale, with

capacity ranging from liters down to 25 ml.

Kvick Cassette family

Membrane surface area

from 50 cm² to 2.5 m²

MW cutoffs (5k, 10k select,

10k, 30k, 50k, and 100k)

Hollow fiber ultrafiltration

cartridges

Available with ten

different molecular weight

Normal / Cross Flow Filtration / Ultrafiltration GE Healthcare

Syringe filters

Bottle-Top Filters

Filter capsules Membrane filtration capsules

Cross flow filtration products

Normal flow filtration products

Protein Concentration | 2012 37

Amicon / Millipore Ultra Centrifugal Devices - Merck

“How can I maximize recovery using Ultrafiltration?” Merck

Pick an appropriate NMWL:

Example: For a 60 kDa protein: two potential membrane choices are 10 kDa or 30 kDa NMWL

Pick devices with low non-specific binding

Check the chemical compatibility of your device

Devices can be use many times (Check before- Don’t spin to dryness)

Use an invert spin for small volumes

Use devices with vertical membrane panels

Ensure the protein is soluble at the desired final concentration

Allows simultaneous concentrating and desalting

Requires much less buffer volumes than dialysis

Allows multiple sample processing

Easy to use and relatively fast (if buffer is not viscous)

39

Expanded Bed Adsorption Chromatography Protein capture to resins without clarification (HIC, IEX and AC)

Sample Preparation: Fractional Precipitation

Ammonium Sulphate (salting-out): Stabilizes proteins. Non denaturative.

Useful before HIC or to concentrate proteins before GF

Dextran Sulphate or Polyvinylpyrrolidine: Precipitates lipoproteins

Polyethylene glycol - PEG > 4000 up to 20%w/v: Non-denaturative.

Supernatan can be used directly to IEX or AC

Acetone/Ethanol: Up to 80%. Useful for peptide or protein concentration.

Highly denaturative.

Polyethyleneimine 0.1%, Protamine Sulphate or Streptomycin Sulph. 1% :

Removal of nucleic acids. Precipitation of nucleoproteins. Can precipitate

negatively charge proteins

ReadyToProcess columns prepacked

Gravitation or centrifugation Disposable plastic columns

Thermo, BioRad, etc

HiTrap columns 1 & 5ml XK columns 1.6 & 2.6 cm

Prepacked Tricorn™ high-performance

columns AxiChrom column

HiScreen columns

HiScale

GE Healthcare Chromatography Columns

42

Magnetic separation

Traditional purification Magnetic bead purification

Centrifuge to pellet sample

Careful removal of supernatant required to avoid sample loss

Supernatant can be easily removed with

no sample loss

43

Advanced material with 3D macro

porous hydrogel structure

Contains high density of functional

groups

Rapid mass transfer

High binding capacity like resins at high

flow rates as membranes

Identical functional binding group as

resins

Natrix Technology: HD membranes

44

Free-flow electrophoresis (FFE) GmbH https://www.youtube.com/watch?v=umQpk-ryqEk

As it moves through the chamber and thus through the

applied electric field, the sample is being separated

either by its pI value (isoelectric focusing) or its net charge (zone

electrophoresis).

Modes of separation

Isoelectric focusing (IEF)

The separation buffers contain either commercial ampholytes or Prolyte

reagents to form a pH gradient within the separation chamber. Mainly use

for the separation of proteins and peptides

Zone electrophoresis (ZE)

Continuous technique for separating different molecules by their net charge

Classical approach for separating particles like cells and organelles

Interval Zone electrophoresis (iZE), a novel high resolution separation

technique for separating different molecules by their net charge.

Suitable for the high resolution separation of organelles and particles as

well as for separating membrane proteins, protein

complexes, proteins and protein isoforms

45

purity

step capture

intermediate purification

polishing

isolate product, concentrate, stabilize

remove bulk impurities

achieve final purity, remove trace impurities,

structural variants, aggregates etc.

Three Phase Strategy

46

Properties of each chromatographic techniques

Technique Capture Intermed. Polishing Start CConditions

End Conditions Considerations

GF * * * * Small sample volume

Diluted sample (buffer change)

Limited Sample volume. Limited flow range

IEX * * * * * * * * *

Low ionic strength

High ionic strength or pH change

HIC * * * * * *

High ionic strength

Low ionic strength

AC * * * * * * * * *

Specific binding conditions

Specific elution conditions

Protein ligand is sensitve to harsh cleaning conditions

RPC * * * *

Harsh conditions

Use of organic solvents. Loss of biol.activ.

Selection and combination of purification techniques

Every technique offers a balance between resolution,

capacity, speed and recovery

So, resins should be selected to meet the objectives of the

purification step

GOAL: Fastest route to get a product of required purity

47

For Efficient Purification Strategies

48

Capture

Purification

Polishing

Capacity Speed

Resolution

Recovery

Capture

49

Resolution

Speed

Recovery

Capacity

GOAL:Initial purification of the target molecule from clarified source material.

Rapid isolation, and concentration (volume reduction) of the target protein

BONUS: Concentration (smaller and faster columns). Stabilization (removal of proteases)

OPTIMIZATION: Speed and Capacity: Use Macroporus and Highly Substituted matrix

Most suitable techniques: IEX / HIC / (Industry)

or Affinity /IMAC/ IEX / HIC (Academics)

Maximize binding of the target proteins and

minimize binding of contaminants during loading

Maximize protein purity during wash & elution

Higher speed that do not affect

considerably the dynamic capacity of the column

Intermediate Purification

50

Resolution

Speed

Recovery

Capacity

Goal: Removal of major impurities

Focus mainly on resolution

Continuous gradient or multi-step elution

Most suitable techniques: IEX / HIC or expensive affinity

For good resolution use around 20% of column capacity

with HIC or IEX

Use a different technique (EIX, HIC, GF, Affinity),

Or change the selectivity (same IEX at different pH,

different ligands or salts concentr for HIC, etc.):

Selectivity optimization

Increase efficiency by using non-porous smaller beads

Polishing

51

Resolution

Recovery

Final removal of trace contaminants, or separation of closely related substances, like

structural variants of the target protein and aggregates.

End product of required high level purity and homogenicity (oligomeric conformation,

post-translational modificatons, phosphorilation, etc)

Suitable techniques: GF/IEX/HIC (RPC for suitable proteins)

Process Step

Capture Intermediate Polishing

Particle Size

~30 ~10-15 ~90

Speed Capacity

Three Phase Strategy

52

Step

Capture

Polishing

Bead size of

chromatographic

matrix

Intermediate

purification

53

Step

Capture

Polishing

Flow rate

Intermediate

purification

Three Phase Strategy

54

Step

Capture

Polishing

RESOLUTION

Intermediate

purification

Three Phase Strategy

55

Linking Chromatography Techniques

1. IEX HIC GF

2. AC GF

3. IEX (HIC) AC GF

4. (NH4)2SO4 HIC IEX GF

HIC IEX 5. GF GF (desalting) AC GF

6. Ni column TEV prot./dial. Neg.Ni GF

Ultrafiltration in large scale

Rapid concentration

Get rid of low MW molecules

Quick adjusting of conductivity

and pH before chromatography

IEX or HIC GF

Guidelines for Protein Purification

Define objectives: Purity, activity and quantity of final product. Avoid over or under developing a method

Define properties of target protein and critical impurities: to simplify technique selection and optimization

Develop analytical assays: for fast detection of protein activity/recovery and to work efficiently

Remove damaging contaminants like proteases early: work quickly, at 4ºC + Prot.Inh.

Minimize number of steps. Combine steps logically. Use a different technique at each step (EIX, HIC, GF,

Affinity), or change the selectivity (same IEX at different pH)

Steps that exploit the greatest differences in the physical properties of the product and the impurities

The step reducing the process volume significantly as an early-stage operation: big macroporus and highly

substituted matrix

Most expensive step toward the end, thus leading to a lower cost of processing: non-porous smaller beads

Minimize sample handling at every stage: to avoid lengthy procedures which reduce activity and recovery

(dialysis, dilutions, long assays, etc)

Minimize use of additives: they must be removed in extra purification steps or may interfere with activity

assays

KEEP IT SIMPLE!!!!! 56

Contaminants Found During the Protein Purification Procedure

Particulates: Include cells and cell debris. Removed using centrifugation or filtration

Contaminating Proteins: Include general host cell protein and proteins of similar properties to the target protein. Gross

contaminants removed using chromatography techniques

Modified target protein: Target protein modified through altered amino acid sequence, glycosylation, denaturation, etc.

Removed using chromatography

Aggregates: Natural aggregates or as a consequence of partial inclusion bodies solubilization. May be removed using gel

filtration chromatography

Lipids, lipoproteins: May be derived from host cells (membranes) or added to a fermentation (antifoams). Removed using

chromatography

Small molecules: Include salts, sugars and reagents added to a purification. Typically removed using gel filtration or diafiltration

Polyphenols: Coloured compounds often derived from plant sources or in the fermentation ingredients. Removed by

precipitation or chromatography

Nucleic acids: Released during cell lysis. Remove using ion exchange, precipitation techniques such as protamine sulfate, or

through hydrolysis with nucleases

Pyrogens: Usually lypopolysaccharides derived from Gram negative bacterial cell walls. Removed using anion exchange

chromatography and other methods

57

PURIFICATION STRATEGY

General approach: Protocol Development

Guidelines for Protein Purification. Commonly confronted decisions.

Properties of Target Protein

Sequence of Events: Cell harvesting, Cell Disruption, Extraction and

Clarification, Chromatography

Three Phase Strategy: Linking Chromatography Techniques

Storage

Characterization Criteria

58

59

Storage of biological samples General recommendations for purified proteins

For short term storage [up to 24 h], most proteins can be kept at 4°C.

For storage times longer than 24 h at 4°C, it may be necessary to filter sterilize the protein preparation [through a 0.22 µm filter] or to add a bacteriostatic agent [e.g. 0.02% sodium azide] to avoid bacterial growth. Note that not all proteins are stable at 4°C for longer periods.

For long term storage [more than a week]:

It becomes necessary to freeze the protein preparation.

Freeze it rapidly using liquid nitrogen to avoid denaturation.

Freeze the solution in small aliquots to avoid repeated freezing and thawing which may reduce the biological activity or affect the structure.

Several stabilizing agents can be added, such as glycerol [5-50% [w/v]], serum albumin [10 mg/ml], reducing agents [such as 1 mM DTT], and ligands [the nature and concentration depending on the nature and concentration of the target protein].

According to the website of The Protein Purification Service of The EMBL (European Molecular Biology Laboratory)

General advice Cannot be applied to every biological sample.

Consider properties of sample and its intended use before following any of these recommendations.

60

For several months storage at -20°C: At this temperature it is recommended to add 50% glycerol to the solution to avoid freezing (or dialyze vs. buffer with 50% glycerol).

For longer periods storage [months to years], freeze it at -70°C or even in liquid nitrogen. Although it is not really necessary to add glycerol at these temperatures, the addition of 5-50% glycerol could help to keep the protein stable.

Alternative methods are:

Storage of the protein at 4°C as an ammonium sulfate precipitate (4M).

Storage of the protein at 4°C or lower in a lyophilized form (the protein could be dissolved in a volatile buffer [such as trimethylamine/HCl; pH range 6.8-8.8]. Note that not all proteins are stable during the freeze-drying process.

Proteins sensitive to temperature: should not be stored at 4°C as they precipitate or lost ativity at this temperature. Keep at room temperature in the presence of a preserving agent.

Storage of biological samples General recommendations for purified proteins

According to the website of The Protein Purification Service of The EMBL (European Molecular Biology Laboratory)

Before anyone of these procedures, check stability of the protein with a little sample.

Aliquot before freezing

Protein Characterization: Sample Homogenity

PAGE-SDS over a range of concentrations

Higher concentrations: information about few amount of contaminants Lower Concentrations: reveal if there are more than one protein of similar MW

PAGE-SDS +/- BME or DTT +/- heat treatment

Western

Isoelectric focusing (IEF)

Non-denaturative native gel (basic, neutral, acid) +/- detergents

Two-dimensional IEF/PAGE

Protein Concentration

Biological activity - Specific activity

Analytical IEX & GF (FPLC) / RPC (HPLC) / capillary electrophoresis

Mass spectroscopy

Visible/UV/fluorescence spectroscopy/CD Ratio 260/280nm for proteins complexed with nucleic acids or with nucleotide coenzymes

Some other ratio with proteins that contain porphyrin or other chromophoric cofactors

Antibody reactivity

Metal-ion content or cofactor content

Pattern of protease digestion

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A Systematic Approach to Project Development Summary

Invest time in strategic design of your expression/purification project: construct, host, vector, tag, bio-informatic, critical impurities, etc.

Set the aims (purity and quantity) Establish a fast and reliable assay for the target protein Expression Optimization or found best natural target source Low Scale Purification: Check different columns. Optimization conditions First characterization of the target protein: PAGE-SDS, Western blot, Activity,

Analytical GF (oligomeric state) Medium Scale Purification: Select techniques and solutions compatible with sample

stability Capture step: Reduce volume in early step & Remove proteases quickly. Optimize. Use

high capacity columns (big and macroporus beads). Further steps: Use different separation principles or a different selectivity. Optimize.

Use more resolutive small-non-porous beads Use few steps and limit sample handling between purification steps Suggestion, use size-exclusion chromatography as final purification step: further

separation, final storage buffer, and separation of monomers from multimers Before scale up, optimize concentration and storage conditions for protein target

(physico-chemical and biological properties) Final protein characterization

SCALE-UP