1. Chapter Five Protein Purification and Characterization Techniques

2. Isolation of Proteins from Cells
Many different proteins exists within one cell
• Many steps needed to extract protein of interest, and separate from many contaminants
• Before purification begins, protein must be released from cell by homogenization

3. How We Get Proteins Out of Cells

4. Salting Out
• After Proteins solubilized, they can be purified based on solubility (usually dependent on overall charge, ionic strength, polarity
• Ammonium sulfate (NH4SO4) commonly used to “salt out”
• Takes away water by interacting with it, makes protein less soluble because hydrophobic interactions among proteins increases
• Different aliquots taken as function of salt concentration to get closer to desired protein sample of interest (30, 40, 50, 75% increments)
• One fraction has protein of interest

5. Differential Centrifugation
• Sample is spun, after lysis, to separate unbroken cells, nuclei, other organelles and particles not soluble in buffer used
• Different speeds of spin allow for particle separation

6. Column Chromatography
• Basis of Chromatography
Different compounds distribute themselves to a varying extent between different phases
• Interact/distribute themselves
• In different phases
• 2 phases:
• Stationary: samples interacts with this phase
• Mobile: Flows over the stationary phase and carries along with it the sample to be separated

7. Column Chromatography

8. Size-Exclusion/Gel-Filtration
• Separates molecules based on size.
• Stationary phase composed of cross-linked gel particles.
• Extent of cross-linking can be controlled to determine pore size
• Smaller molecules enter the pores and are delayed in elution time. Larger molecules do not enter and elute from column before smaller ones.

9. Size Exclusion/Gel-filtration (Cont’d)

10. Affinity Chromatography
• Uses specific binding properties of molecules/proteins
• Stationary phase has a polymer that can be covalently linked to a compound called a ligand that specifically binds to protein

11. Ion Exchange
• Interaction based on overall charge (less specific than affinity)
• Cation exchange
• Anion exchange

12. Electrophoresis
• Electrophoresis- charged particles migrate in electric field toward opposite charge
• Proteins have different mobility:
Charge
Size
Shape
• Agarose used as matrix for nucleic acids
• Polyacrylamide used mostly for proteins

13. Electrophoresis (Cont’d)
• Polyacrylamide has more resistance towards larger molecules than smaller
• Protein is treated with detergent (SDS) sodium dodecyl sulfate
• Smaller proteins move through faster (charge and shape usually similar)

14. Isoelectric Focusing
• Isolectric focusing- based on differing isoelectric pts. (pI) of proteins
• Gel is prepared with pH gradient that parallels electric-field. What does this do?
• Charge on the protein changes as it migrates.
• When it gets to pI, has no charge and stops

15. Primary Structure Determination
How is 1˚ structure determined?
Determine which amino acids are present (amino acid analysis)
Determine the N- and C- termini of the sequence (a.a sequencing)
Determine the sequence of smaller peptide fragments (most proteins > 100 a.a)
4) Some type of cleavage into smaller units necessary

16. Primary Structure Determination

17. Protein Cleavage Protein cleaved at specific sites by:
Enzymes- Trypsin, Chymotrypsin
Chemical reagents- Cyanogen bromide
Enzymes:
Trypsin- C-terminal of (+) charged side chains
Chymotrypsin- C-terminal of aromatics

18. Peptide Digestion

19. Cleavage by CnBr
C-terminal of INTERNAL methionines

20. Determining Protein Sequence
After cleavage, mixture of peptide fragments produced.
• Can be separated by HPLC or other chromatographic techniques
• Use different cleavage reagents to help in 1˚ determination

21. Peptide Sequencing • Can be accomplished by Edman Degradation
• Relatively short sequences (30-40 amino acids) can be determined quickly
• So efficient, today N-/C-terminal residues usually not done by enzymatic/chemical cleavage

22. Peptide Sequencing