BICH 605

1. BICH 605 BICH 605; Fall 2009 October 6, 8, 20 & 22 Larry Dangott Department of Biochemistry and Biophysics Room 440 BioBio 845-2965 ljdangott@tamu.edu

2. BICH 605 OUTLINE Planning: • Method Development; Strategies • Activity Tracking; Fraction ‘pooling’ Techniques: • Electrophoresis (SDS, Isoelectric Focusing) • Chromatography (GFC, IEX, Affinity, rpHPLC) • Structural Characterization (Amino Acid Analysis; Protein Sequencing) • Proteomics (Protein ID and characterization using mass spectrometry) To present an OVERVIEW of techniques used in Protein Purification and Analysis.

3. Protein Purification It helps to know something about your protein • Source (organism; tissue; organelle; amount) • Assemblage vs. monomer • Cytosolic vs. membrane-bound • Size • Isoelectric point (pI) • Post-translational modification • Relative abundance

4. Protein Purification Source (organism; tissue; organelle; amount) • Natural vs. Recombinant (tagged?) • Tissue (bone (hard), blood (liquid), heart (soft), brain (fatty)); extraction • Organelle (nucleus, mitochondria, ER, plasma membrane); pre-fractionation • Amount (a LOT or a little; scale); cost and practicality (myoglobin = easy; EGFR = hard)

5. Protein Purification Multimer vs. Monomer Affects buffer choices (assembly vs. disassembly) Affects choice of separation media (size) Cytosol vs. Membrane Affects pre-fractionation choices (extraction) Separation methods (centrifuge, columns) Affects buffer choices (detergent) Size (sort of related to Multimer vs. Monomer) Affects choice of separation media (GFC) Affects solubility (larger proteins like to precipitate) Isoelectric point (pI) Affects choice of separation media (charge) Affects solubility (precipitate at pI) Affects buffer choices (precipitation point; charge) Post-Translational Modification Affects choice of separation media (affinity)

6. Protein Purification Important Steps You May Use: • Extraction (French press, sonication, detergent, homogenization) • Centrifugation (low speed, ultra-speeds, differential gradient) Protein estimation method (colorimetric, spectroscopy) • Protein concentrating method (salt or organic precipitation, lyophilization, membrane filtration) • Chromatography (IEX, gel filtration, chromatofocusing) • Electrophoresis (IEF, preparative native or SDS)

7. A SIMPLE STRATEGY His-tag: affinity Protein Purification A COMPLEX STRATEGY FOR PROTEIN PURIFICATION Sample Preparation • Extraction (grinding, detergent lysis, sonication) • Salt exchange (gel filtration, filters, dialysis) Capture • Ion Exchange • Affinity • Hydrophobic Interaction Intermediate Purification • Ion exchange • Hydrophobic Interaction Polishing • Gel Filtration • Reversed phase

8. Happy Boss Protein Purification Systematic method development requires..... Defining a way of quantifying, or at least identifying, the presence of your target molecule, and of assessing its purity. Don’t rely solely on literature (or coworker) statements. Verify yourself. 50% success rate. Keep a record of your purification process. Notebook, notebook, notebook………. . . .

9. Protein Purification Our Example: Enzyme Purification There are two major objectives in enzyme purification: To obtain the highest SPECIFIC ACTIVITY possible, measured as activity per unit protein To obtain the MAXIMUM YIELD of enzymatic activity. (Theoretically, this is 100%. Practically, one is usually happy to settle for something like 30%.)

10. Protein Purification When purifying a protein, one wants to keep track of how one is doing relative to the two major objectives. Therefore, at each step, one must measure: • Volume • Protein concentration (colorimetric assay, UV) • Enzyme activity (units/ml; specific to ‘your’ protein)

11. Protein Purification These measurements are combined in the calculation of: Total activity = Enzyme activity/aliquot volume X Total volume Total protein = Protein/aliquot volume X Total volume Specific activity = Enzyme activity in an aliquot/Amt ofProtein in the aliquot (THIS IS THE BIG ONE) (In measurements of total activity and protein, remember to adjust for volumes set aside for various reasons. If this is not done, the yield will be artificially low).

12. Calculate Activity Units and Total Protein Use to calculate Specific Activity Vol X Activity Units/vol = Total Activity Units Vol X mg/ml = Total Protein (mg) Divide Total Activity Units by Total Protein (mg) = Specific Activity in Units/protein (mg)

13. KNOWING WHICH FRACTIONS TO POOL IS IMPORTANT Fold purification goes UP Yield goes DOWN Divide current Specific Activity by Initial Specific Activity = Fold Purified Divide current Total Activity Units by Original Activity Units = % Yield

14. Selecting Fractions based on Specific Activity and SDS PAGE Mutant Tyrosine Hydroxylase; Ion Exchange; NaCl Gradient RNA? Pool Stable? Pure Mutant TyrOH has a Vmax of ~12 Data courtesy of Colette Daubner; Fitzpatrick Lab

15. Protein Purification The less prevalent the protein is in the cytosol, the higher the degree of purification that will be required for its purification to homogeneity. For example: A protein that is 50% of the cellular protein needs to be purified only 2-fold. In contrast: A protein that is only 0.1% of the cellular protein needs to be purified 1000-fold.

16. Protein Purification A TYPICAL STRATEGY FOR PROTEIN PURIFICATION • Sample Preparation • Extraction (grinding, detergent lysis, sonication) • Salt exchange (gel filtration, filters, dialysis) • Capture • Ion Exchange • Affinity • Hydrophobic Interaction • Intermediate Purification • Ion exchange • Hydrophobic Interaction • Polishing • Gel Filtration • Reversed phase Mode of monitoring the purification………………

17. Protein Purification Tracking your protein is critically important. How do you know where it is? Biological Assay (usually specific; extremely sensitive; slower) Binding Assay (usually specific; sensitive, semi-automate) Chemical Assay (colorimetric assays, enzyme assays) Physical Assay (mass spec, UV spectrometry) Separation Assay (electrophoresis)

18. SDS PAGE ELECTROPHORETIC ANALYSIS OF PROTEINS Electrophoresis is a electrically driven sieving process used to separate complex mixtures of proteins. Can be ANALYTICAL or PREPARATIVE. SDS PAGE is used to investigate subunit composition and to verify homogeneity of protein samples. It can also serve to purify proteins for use in further micro-analytical applications  Principle of SDS PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis) Most proteins bind the ionic detergent, SDS (sodium dodecyl sulfate), in a constant weight-to-detergent ratio, leading to identical negative charge density per mass for the denatured proteins and a uniform shape. Thus, theoretically, SDS-protein complexes migrate through a solid matrix (polyacrylamide) and are separated according to size, not charge.

19. SDS PAGE APPLICATIONS Polypeptide composition and fraction profiling: Purified protein complexes or multimeric proteins consisting of subunits of different molecular size will be resolved into constituent polypeptides. Screen fractions during protein purification. Quaternary structure profile: Comparison of the protein bands obtained under non-reducing and reducing conditions provides information about the molecular size of subunits and protein complexes. Size estimation: The relationship between the relative mobility and log molecular weight is linear over some range. With the use of plots like those shown here, the molecular weight of an unknown protein (or its' subunits) may be determined by comparison with known protein standards.  

20. SDS PAGE In SDS gel electrophoresis, negatively charged, SDS-coated proteins migrate in response to an electrical field through pores in a crosslinked polyacrylamide gel matrix Pore size decreases with higher acrylamide concentrations Smaller pores are used for smaller proteins/peptides; larger pore sizes are used for larger proteins.

21. SDS PAGE PROCEDURE Proteins to be analyzed are solubilized and denatured by boiling (or heating) in the presence of SDS and reducing reagent, an aliquot of the protein solution is applied to a gel lane, and the individual proteins are separated electrophoretically. The reducing reagent β-Mercaptoethanol (-ME) or (dithiothreitol (DTT)) is added during solubilization to reduce disulfide bonds.

22. SDS PAGE The polyacrylamide gel is cast as a separating gel (sometimes called the resolving or running gel) topped by a stacking gel and secured in an electrophoresis apparatus (see figure). The stacking gel is run at slightly acid pH (6.8). The separating gel is run at pH 8.8. The stacking gel is ~4% acrylamide and the separating gel is a higher concentration. The stacker brings the proteins to a common ‘starting line’ and the separator sieves them apart. The concentration of acrylamide in the separating gel is determined by the range of molecular weights of interest.

23. SDS PAGE Tris-Glycine in Upper Buffer Tris-HCl pH 6.8 in Stacking Gel Tris-HCl pH 8.8 in Separating Gel

24. SDS PAGE Glycine equilibria

25. SDS PAGE Formation of an ion front

26. SDS PAGE It is the voltage gradient that sharpens the ion boundary

27. SDS PAGE What happens to proteins?

28. SDS PAGE In separating gel Glycine mobility increases, becomes greater than protein mobility, but still slower than Cl-

29. SDS PAGE Protein sample, now in a narrow band, encounters both the increase in pH and decrease in pore size. Increase in pH would tend to increase electrophoretic mobility, but smaller pores decrease mobility. Relative rate of movement of ions in separating gel is chloride > glycinate > protein. Proteins separate based on charge/mass ratio and on size and shape parameters.

30. SDS PAGE PROTEIN DETECTION Detection limitFixing? Coomassie Blue G-250 or R-250 staining 50 ng fixing Silver 1 ng fixing Fluorescent stains (Sypro) 10 ng non-fixing Negative stains (zinc, copper) 1- 10 ng non-fixing Sypro Ruby Coomassie Blue Silver

31. Molecular Weight (Log Scale) Relative Mobility (Rf) SDS PAGE SIZE ESTIMATION IMPORTANT MW ESTIMATION BY SDS-PAGE IS ONLY APPROXIMATE AND IS REFERRED TO AS APPARENT MOLECULAR WEIGHT. Unusual protein compositions or physical properties can cause anomalous mobilities during SDS-PAGE. SDS gels can be used as a micro-purification step and the individual polypeptides can be isolated from the gel by electroelution or electroblotting and the amino acid sequences can be determined or peptide maps obtained.

32. ISOELECTRIC FOCUSING Isoelectric Point (pI) is specific pH at which net charge equals zero IEF is a technique to separate proteins based on Isoelectric Point (native or denatured) At pI, protein has no net charge and will not migrate in an electric field

33. Isoelectric Focusing IEF CAN BE PERFORMED WITH MOBILE pH GRADIENTS OR IMMOBILIZED pH GRADIENTS Mobile gradients are prepared with Carrier Ampholytes (CAs) (mixed polymers (300-1000 Da in size) mixed with solid support (mobile). Immobile gradients are prepared by covalently coupling Ampholytes to solid support and blending. Solid support is usually polyacrylamide but can be agarose for preparative purposes

34. Isoelectric Focusing MOBILE pH GRADIENT IEF IMMOBILIZED pH GRADIENT IEF • ADVANTAGES of IMMOBILIZED GRADIENTS • Stable pH gradients • Ease of handling • Reproducibility • Extreme pH resolution

35. 2 Dimensional Gel Electrophoresis Combine IEF & SDS PAGE High Resolution Zoom gels (pH range) Detect isoforms Post-translational modifications Expression Proteomics

36. 2 Dimensional Gel Electrophoresis • Combine IEF & SDS PAGE • High Resolution • Zoom gels (pH range) • ANALYTICAL • Detect isoforms • Post-translational modifications • PREPARATIVE • Mass spectrometry

37. END OF DAY 1