Protein Gel Electrophoresis 1.Native PAGE 2.Native Gradient PAGE 3.Urea PAGE 4.SDS PAGE 5.SDS Gradient PAGE 6.IEF 7.2D PAGE 8.Western Blot

Principle Proteins move in the electric field. Their relative speed depends on the charge, size, and shape of the protein

From large to small and simple

Protein visualization on gels Immediately after electrophoresis proteins in the gels are precipitated by either adding alcohol containing solutions or strong acids (e.g. TCA). Protein are often stained by Coomassie Blue dye or by photography-like treatment with AgNO3 (silver staining) There are many other stains available (e.g. Stains-all, fluorescence probes etc.)

Example of silver stained gel Silver staining is usually times more sensitive than Coomassie Blue staining, but it is more complicated. Faint but still visible bands on this gel contain less than 0.5 ng of protein!

Native PAGE Useful for: 1.Examining protein-protein protein-ligand interactions 2.Detecting protein isoforms/conformers Separates folded proteins and protein- protein or protein-ligand complexes by charge, size, and shape

Native PAGE examples In the absence of phospholipids, both twinfilins run as a single sharp band on this gel. PI(4,5)P2 causes twinfilin-1 and twinfilin-2 to move more rapidly toward the anode, indicating a net increase in the negative charge and thus a binding interaction. Dimerization of KIR2DL1 in the presence of Co2 Vartiainen et al. JBC 2003 Qing R. Fan et al. JBC 2000

Native gradient PAGE Separate native proteins by size – proteins stop moving when they reach a sertain gel density (but this may take a very long time...) A great technique to study protien oligomerization!

Native gradient PAGE example Zavialov et al. Mol. Microbiol Native 4-15% gradient PAGE

Urea PAGE Separates denatured proteins by size/charge Typically 6-8 M urea is added into the gel A great technique to study protein modifications!

Example of Urea PAGE Urea PAGE of samples of heat shock protein 25 Zavialov et al. BBA 1998

SDS PAGE Due to high density of binding of SDS to proteins, the ratio size/charge is nearly the same for many SDS denatured proteins. Hence proteins are separated only by length of their polypeptide chains (but not by differences in charge). Great separation. Allows estimation of the size of polypeptide chains

SDS gradient PAGE Bands in SDS gradient gel are usually sharper than in homogeneous SDS PAGE 5-20% SDS PAGE 12.5% SDS PAGE

SDS-PAGE Sodium Dodecyl Sulfate - Polyacrylamid Gel Electrophoresis

Sodium Dodecyl Sulfate SDS is a common ingredient in detergents Other names for SDS include laurel sulfate and sodium laurel sulfate As a detergent SDS destroys protein secondary, tertiary and quaternary structure This makes proteins rod shaped SDS also sticks to proteins in a ratio of approximately 1.4 g of SDS for each gram of protein Negative charge on the sulfate groups of SDS mask any charge on the protein

Polar Hydrophilic head Non-polar Hydrophobic tail SDS Sodium Dodecyl Sulfate Because it is amphipathic, SDS is a potent detergent H - C - C - C - C - C - C - C - C - C - C - C - C - O - S - O - Na + H H H H H H H H H H H H H H H H H H H H H H H H O O C 12 H 25 NaO 4 S

SDS and Proteins SDS Protein

SDS and Proteins In aqueous solutions, SDS polarizes releasing Na+ and retaining a negative charge on the sulfate head So much SDS binds to proteins that the negative charge on the SDS drowns out any net charge on protein side chains In the presence of SDS all proteins have uniform shape and charge per unit length SDS nonpolar chains arrange themselves on proteins and destroy secondary tertiary and quarternary structrure Thus shape is no longer an issue as the protein SDS complex becomes rod shaped

Acrylamide Polyacrylamide Gels Polyacrilamide is a polymer made of acrylamide (C 3 H 5 NO) and bis-acrilamide (N,N’-methylene-bis-acrylamide C 7 H 10 N 2 O 2 ) O CH CH 2 NH 2 C O CHCH 2 NH 2 C CH 2 bis-Acrylamide O CHCH 2 NH 2 C Acrylamide

Polyacrylamide Gels O CHCH 2 NH 2 C O CHCH 2 NH 2 C SO 4 -. Acrylamide polymerizes in the presence of free radicals typically supplied by ammonium persulfate

Polyacrylamide Gels 1. Acrylamide polymerizes in the presence of free radicals typically supplied by ammonium persulfate SO 4 -. O CHCH 2 NH 2 C O CHCH 2 NH 2 C O CHCH 2 C O CHCH 2 NH 2 C 2.TMED (N,N,N’,N’- tetramethylethylenediamine) serves as a catalyst in the reaction

Polyacrylamide Gels bis-Acrylamide polymerizes along with acrylamide forming cross-links between acrylamide chains O CHCH 2 NH 2 C O CHCH 2 NH 2 C O CHCH 2 NH 2 C O CHCH 2 C O CHCH 2 NH 2 C O CHCH 2 NH 2 C bis-Acrylamide O CH CH 2 NH 2 C O CHCH 2 NH 2 C CH 2

Polyacrylamide Gels bis-Acrylamide polymerizes along with acrylamide forming cross-links between acrylamide chains

Polyacrylamide Gels Pore size in gels can be varied by varying the ratio of acrylamide to bis-acrylamide Lots of bis-acrylamide Little bis- acrylamide Protein separations typically use a 29:1 or 37.5:1 acrylamide to bis ratio

1 2 3 SDS-PAGE Addition of SDS Protein becomes rod-shaped with uniform charge distribution

IEF Separates proteins by their isoelectric points (pI) Each protein has own pI = pH at which the protein has equal amount of positive and negative charges (the net charge is zero)

IEF Mixtures of ampholytes, small amphoteric molecules with high buffering capacity near their pI, are used to generate the pH gradient. Positively and negatively charged proteins move to – and +, respectively, until they reach pI. PI of proteins can be theoretically predicted. Therefore, IEF can also be used for protein identification.

IEF example Zavialov A. IEF pH gradient

2D PAGE

Lung V79 cells from chinese hamster Guillermo Senisterra Guillermo Senisterra Dept. of Physics- University of Waterloo- Waterloo-Ontario N2L 3G1-Canada

Proteomics Pathway

Western Blotting (WB) WB is a protein detection technique that combines the separation power of SDS PAGE together with high recognition specificity of antibodies An antibody against the target protein could be purified from serum of animals (mice, rabbits, goats) immunized with this protein Alternatively, if protein contains a commonly used tag or epitope, an antibody against the tag/epitope could be purchase from a commercial source (e.g. anti-6 His antibody)

WB: 4 steps 1.Separation of proteins using SDS PAGE 2. Transfer of the proteins onto e.g. a nitrocellulose membrane (blotting) 3. Immune reactions 4. Visualization

WB, Step 2: Blotting

WB, Steps 3-4: Detection