Paul D. Adams • University of Arkansas

Mary K. CampbellShawn O. Farrellhttp://academic.cengage.com/chemistry/campbell

Chapter FiveProtein Purification and

Characterization Techniques

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

How We Get Proteins Out of Cells

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

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

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

Column Chromatography

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.

Size Exclusion/Gel-filtration (Cont’d)

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

Ion Exchange

• Interaction based on overall charge (less specific than affinity)

• Cation exchange

• Anion exchange

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

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)

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

Primary Structure Determination

How is 1˚ structure determined?

1) Determine which amino acids are present (amino acid analysis)

2) Determine the N- and C- termini of the sequence (a.a sequencing), and the Internal Residues

3) Determine the sequence of smaller peptide fragments (most proteins > 100 a.a)

4) Some type of cleavage into smaller units necessary

Primary Structure Determination

Protein Cleavage

Protein cleaved at specific sites by:

1) Enzymes- Trypsin, Chymotrypsin, Carboxypeptidases (C-terminus)

2) Chemical reagents

- Cyanogen bromide, cleaves at Methionine;

- PITC, cleaves from N-terminus (Edman Degradation)

- Hydrazine, cleaves from C-terminus

Enzymes which cleaves Internal Residues:

Trypsin- Cleaves @ C-terminal of (+) charged side chains (basic amino acid)

Chymotrypsin- Cleaves @ C-terminal of aromatics

Peptide Digestion

Cleavage by CnBr

Cleaves @ C-terminal of INTERNAL methionines

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

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

Peptide Sequencing