Contents Introduction of protein Principle and methods for

Contents • Introduction of protein • Principle and methods for protein characterization • Principle and methods for protein purification • Principle and methods for detection of protein-mediated interactions • Principle and methods for structural determination of proteins

Methods and Principle for Protein Purification Yong Chen SIBCB

Proteins in a cell • In a cell, the protein concentration is very high (~300 mg/ml) • Other components – Membranes, DNA, RNA, sugars, structural elements • Goal: Isolating a specific protein from a cell for further study Ellis and Minton, Nature 425, 27 - 28 (04 Sep 2003) 3 Medalia, O. et al. Science 298, 1209– 1213 (2002)

Protein properties Different sizes Different solubility Different ligand binding Different charges Different surface features Purifying proteins takes advantage of these differences to isolate a population of a protein of interest

Methods for protein separation Different sizes Salting out Different solubility Different surface features Different charges Different ligand binding

Different solubility Salting out- Reversible precipitation with salt or organic molecules • Most proteins are less soluble at high salt concentrations, an effect called salting out. • The salt concentration at which a protein precipitates differs from one protein to another. Hence, salting out can be used to fractionate proteins. • Dialysis can be used to remove the salt if necessary. (NH 4)2 SO 4 is most commonly used: • highly soluble, inexpensive • In most cases does not denature protein.

Different solubility Salting out- Reversible precipitation with salt or organic molecules

Different solubility Hofmeister series Underlying mechanism is not known.

Methods for protein separation Centrifugation Dialysis Size-exclusion chromatography PAGE Different sizes Salting out Different solubilities Different surface features Different charges Different ligand binding

Different sizes Centrifugation Differential centrifugation as a first step in protein purification

Different sizes Dialysis – Separation based on size

Different sizes Size Exclusion (gel-filtration) chromatography

Size Exclusion chromatography 75 KD 29 KD 13. 7 KD 6. 5 KD

Different sizes Polyacrylamide Gel Electrophoresis (PAGE) Molecules are separated by size and charge in an electric field Smaller molecules migrate more rapidly through porous gel matrix PAGE separates proteins in their native state (I. e. , proteins are properly folded and disulfide bonds are intact)

Preparative PAGE

Methods for protein separation Centrifugation Dialysis Size-exclusion gel-filtration PAGE Different sizes Salting out Different solubilities Different surface features Different charges Different ligand binding Ion-exchange chromatography

Different charges Ion-Exchange Chromatography – Separation Based on Charge Cation Exchange Chromatography Elute positively charged protein bound to negatively charged beads using a gradient of increasing salt concentration (example Na. Cl); Na+ competes with the protein for binding to the beads Anion Exchange Chromatography Negatively charged proteins can be purified on column consisting of positively charged beads. Cl– or other anion competes with the protein This is cation exchange chromatography

Types of Ion-Exchange Chromatography Media Cation Exchange Binds to positively charged basic residues (examples: lysine and arginine) Anion Exchange Binds to negatively charged acidic residues (examples: aspartate and glutamate)

Ion Exchange Separation Example [salt] UV

Methods for protein separation Centrifugation Dialysis Size-exclusion gel-filtration PAGE Different sizes Salting out Different solubilities Different surface features Different charges Different ligand binding Ion-exchange chromatography Affinity chromatography

Different ligand bindings Affinity chromatography Small molecules are attached to beads and impure protein mixtures are applied. Protein that specifically binds the small molecule is retained on the column. Bound protein can be eluted with a small, competing molecule or with a salt gradient. Very powerful form of chromatography - can yield protein purity >95% from a complex mixture in a single step. • His tag and column interaction • Imidazole competes with His for Ni 2+ sites Ni Histidine Resin N NH -OOC NH N Ni N 3 H + Imidazole Ni

Affinity Tags for Recombinant Proteins

Methods for protein separation Centrifugation Dialysis Size-exclusion gel-filtration PAGE Different sizes Salting out Hydrophobic chromatography Different solubilities Different surface features Different charges Different ligand binding Ion-exchange chromatography Affinity chromatography

Different surface features Hydrophobic Interaction Chromatography • Separate proteins on the basis of relative hydrophobicity. • Column matrix has hydrophobic groups covalently attached. -e. g. Phenyl Sepharose- this is an agarose support matrix to which phenyl groups have been attached. • Proteins bind to an HIC column under high salt concentrations and are eluted in low salt concentrations.

Methods for protein separation Centrifugation Dialysis Size-exclusion gel-filtration PAGE Different sizes Salting out Hydrophobic chromatography Different solubilities Different surface features Different charges Different ligand binding Ion-exchange chromatography Affinity chromatography

Flowchart for protein purification cell 1. Release proteins from cells Soluble fraction Darnell, Lodish, Baltimore, Molecular Cell Biology 2. Crude purification DNA, RNA, etc. 3. Polishing purification High-purity proteins Low-purity proteins 99% of all of the proteins in the cell

Releasing proteins from the cell • Physical methods – Shearing open the cells using pressure or strong sound waves or mechanical means • Chemical methods – Osmotic shock, detergents, or enzymatic digestion

Methods to break the cells

The purification strategy KEEP IT SIMPLE! • Define objectives for purity, activity and quantity required of final product to avoid over or under developing a method

Define objectives for your purification Goal: To set minimum objectives for purity and quantity, maintenance of biological activity and economy in terms of money and time. Define purity requirements according to the final use of the product.

The purification strategy KEEP IT SIMPLE! • Define objectives for purity, activity and quantity required of final product to avoid over or under developing a method • Define properties of target protein and critical impurities to simplify technique selection and optimization

Define properties of target protein and critical impurities

The purification strategy KEEP IT SIMPLE! • Define objectives for purity, activity and quantity required of final product to 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 critical contaminants

Develop analytical assays More the specific assay, more effective the purification Easier the assay, the more rapid the purification Purity SDS-PAGE, IEF, Immunoblotting, Mass spectrometry Activity Binding assays, enzyme activity assays

The purification strategy KEEP IT SIMPLE! • Define objectives for purity, activity and quantity required of final product to avoid over or under developing a method • Define properties of target protein and critical impurities to simplify technique selection and optimisation • Develop analytical assays for fast detection of protein activity/recovery and critical contaminants • Remove damaging contaminants early, e. g. proteases • Use a different technique at each step to take advantage of sample characteristics which can be used for separation (size, charge, hydrophobicity, ligand specificity) • Minimize number of steps and sample handling at every stage to avoid lengthy procedures which risk losing activity/reducing recovery

Summary of protein purification • Proteins have different physical properties. • These properties can be used to isolate populations of specific proteins from one another. • The target protein should be purified efficiently, economically and in sufficient purity and quantity, by the combination of different purification steps. (多、快、好、省)

Contents • Introduction of protein • Principle and methods for protein characterization • Principle and methods for protein purification • Principle and methods for detection of protein-mediated interactions • Principle and methods for structural determination of proteins

Principle and methods for detection of proteinmediated interactions Yong Chen SIBCB

Functions of Protein-mediated Interaction Protein-Protein, Protein-DNA, Protein-RNA, Protein-ligands Folding Transporter Assembly Recruitment Catalyzation Movement

Methods for detecting proteinmediated interactions • Identifying the protein-interaction partners 1. Immunoprecipitation-Mass Spectrometry (IP-MS) 2. Yeast-two-hybrid (Y 2 H) 3. Phage display • Verifying protein-mediated interactions

How to detect protein-protein interaction? What will happen if protein A binds to protein B? EMSA 3 D shape change Charge change MST AUC Size change A FP MALS And more…. . Distance change B Refraction change Release or absorb heat Detecting protein-protein interaction is in fact to check the changes of protein properties!

Methods to characterize protein-mediated interactions Qualitative methods Yeast-two-hybrid, Bimolecular fluorescence complementation, Fluorescence Resonance Energy Transfer , Pull-down (or Co-IP), Size-exclusion chromatography, Light scattering, Crosslinking Quantitative methods Analytic ultracentrifugation, Electrophoretic mobility shift assay, Microscale Thermophoresis, Fluorescence Polarization, Isothermal Titration Calorimetry, Surface plasmon resonance, Bio-layer Interferometry

Introduction of Qualitative Methods

Yeast two hybrid And mammalian two hybrid

Yeast-two-hybrid Reporter: His 3, Ade Reporter: β-galactosidase

More two-hybrid system Split-ubiquitin yeast two-hybrid system Bait Prey N-Ub C-Ub TF Ub-specific protease TF Reporter

More two-hybrid system Enzymatic two-hybrid systems: Kinase substrate sensor You can design more!

Bimolecular fluorescence complementation Schematic representation of the principle of the Bi. FC assay. Two nonfluorescent fragments (YN and YC) of the yellow fluorescent protein (YFP) are fused to putative interaction partners (A and B). The association of the interaction partners allows formation of a bimolecular fluorescent complex. The image shows an example of a complex formed by nuclear proteins.

Pull down GST Pull down Co-Immunoprecipitation (Co-IP)

UV 280 (nm) Size-exclusion Chromatography (SEC) Void Elution volume (ml)

Fluorescence resonance energy transfer (FRET)

Bioluminescence resonance energy transfer (BRET)

Light scattering • Multi-angle static light scattering(MALS) • Dynamic light scattering (DLS)

Far-western blot

Crosslinking (CX) Chemical or UV

Label transfer protein interaction analysis

Introduction of Quantitative Methods

Interaction is a dynamic process KD is a value to estimate the affinity (equilibrium). kon and koff reflect the reaction rate (kinetics).

Analytical Ultracentrifugation (AUC)

AUC-Sedimentation Velocity In sedimentation velocity (SV), the movement of solutes in high centrifugal fields is interpreted using hydrodynamic theory to define the size, shape, and interactions of macromolecules. 。

AUC-Sedimentation Equilibrium Sedimentation equilibrium (SE) is a thermodynamic method where equilibrium concentration gradients at lower centrifugal fields are analyzed to define molecule mass, assembly stoichiometry, association constants, and solution nonideality.

Electrophoretic mobility shift assay (EMSA) Native gel Example for protein-DNA interaction

Microscale Thermophoresis (MST)

Microscale Thermophoresis (MST)

Microscale Thermophoresis (MST)

Fluorescence Polarization (FP)

Fluorescence Polarization (FP)

Isothermal Titration Calorimetry (ITC)

Isothermal Titration Calorimetry (ITC)

Surface Plasmon Resonance (SPR) Biacore systems

Surface Plasma Resonance (SPR) Biacore systems Can do both affinity and kinetic analyses

Bio-Layer Interferometry Fortebio Octet systems

Bio-Layer Interferometry Fortebio Octet system Can do both affinity and kinetic analyses

Summary Overview of methods for detecting proteinmediated interactions Pull down Y 2 H Bi. FC EMSA MST FRET AUC A FP B BRET MALS ITC SPR SEC Crosslinking BLI More methods are expected !