Why would you need to purify protein?

Why would you need to purify protein?

Methods for Working with Protein 1. Protein Isolation A. Selection of a protein source i. tissue and cell cultures (bacteria, yeast, mammalian, etc.) ii. genetically engineered - tagged proteins, over-expression B. Solubilization i. osmotic lysis - hypotonic solution swelling and bursting ii. French press - high pressure & small orifice iii. sonicator iv. homogenizer -tissue grinder, v. glass beads versus mortar & pestle vi. dounce -.

What properties of proteins can be used to separate and purify them from each other?

Methods for Working with Protein 2. Separation methods A. Properties that are used to separate proteins: i. charge ii. hydrophobicity iii. affinity iv. solubility & stability v. molecular weight B. differential centrifugation - S-100 versus S-30 C. precipitation/solubility i. salting in versus salting out solubility of a protein close to its pi versus the effect of salt interacting w/ solvent & not the protein ii. examples of a. ammonium sulfate precipitation b. PEI - poly(ethyleneimine)precipitation

S solubility of protein in salt solution S` - solubility of protein in pure water

Protein Solubility Salt-in At lower ionic strength, increased salt increase solubility Salt-Out At higher ionic strengths Increased salt concentrations causes the protein to precipitate out of solution Competition between the added salt with other dissolved solutes for solvation

Solute-solute interactions > solute-solvent interactions

Solubility of lactoglobulin depends on ph

Methods for Working with Protein 2. Separation methods D. chromatography - overall example i. ion exchange - cation vs. anion a. strong versus weak (effect of ph) b. counterion present is important c. types of gradients and their application linear, nonlinear, step

Methods for Working with Protein 2. Separation methods D. chromatography - overall example ii. affinity chromatography a. ligand based: glutathione covalent linked to resin GST fusion protein b. speciality dyes - Cibracon blue and others c. Immunoaffinity: epitope tags such as FLAG, V5, etc. d. DNA - general and specific DNAs e. others (example: heparin, hydroxyapatite)

Methods for Working with Protein 2. Separation methods D. chromatography iii. gel exclusion or gel filtration a. separation based on size b. exclusion volume c. different size limit materials iv. HIC or hydrophobic interaction chromatography compare to reverse phase chromatography v. types of resin cellulose, dextran, agarose, polyacrylamide, perfusion beads

Sequence Databases Some specifically for proteins and others for DNA

PubMed access to multiple databases http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&itool=toolbar BLAST search http://blast.ncbi.nlm.nih.gov/blast.cgi

Gel filtration or size exclusion chromatography What is the size of the protein of interest and the contaminating protein? How best to separate them?

Precautions or concerns might you have about maintaining your protein s activity What can you do to avoid these problems?

Methods for Working with Protein 3. Stabilization of protein A. Changing buffer i. dialysis ii. ultracentrifugation B. Concentrating protein helps to maintain active protein sometimes addition of a carrier protein may help addition of glycerol C. Inhibitors i. proteases ii. phosphatase inhibitors

Methods for Working with Protein 4. Protein Analysis A. Gel electrophoresis i. Discontinous gel a. polyacrylamide: ratio bisacrylamide/ acrylamide b. TEMED - free radical stablizer c. ammonium persulfate d. stacking gel ph 6.8, contains glycine pk2=9.78 e. running gel is ph 8.8, sample contains bromophenol blue

Methods for Working with Protein 4. Protein Analysis A. Gel electrophoresis ii. SDS-PAGE a. SDS forms a micelle around the polypeptide the size and charge of the micelle is approximately proportional to the size of the polypeptide b. denatures proteins c. protein stains: Coomassie blue, silver stains, fluorescent stains d. gradient gels

SDS-PAGE principle Glycine is an amino acid, and its charge property changes depend on the ph. In stacking gel (ph6.8), only a little amount of glycine is negatively charged, thus, glycine moves very slowly. SDS-bound proteins move much faster in low-density gel. Thus, proteins are stacked on the running front of glycine. In separation gel (ph8.8), glycine is charged and moves very fast. Proteins can move dependent on their size. Stacking gel 5%, ph6.8 Separation gel 6-20%, ph8.8-+

Methods for Working with Protein 4. Protein Analysis B. 2-Dimensional gels 1st dimension: isoelectric focusing tube gel format ampholytes to create an immobilized ph gradient 2nd dimension is usually SDS-PAGE

General Formula of Ampholytes Each ampholyte has a different pk and isoelectric point. Each ampholyte has a particular buffering capacity

Methods for Working with Protein 4. Protein Analysis C. Immunoblotting D. Gel-shift or EMSA (electrophoretic mobility gel shift assay) assays

Western blotting