Electrophoresis

Because proteins are typically much smaller than DNA, they are run in gels containing polymers of much smaller pore size. The most common technique for protein separation is known as SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) (Figure 1). In this approach the proteins are treated with a detergent (sodium dodecyl sulfate) which unfolds them and gives them similar shape and ratio of charge to mass. Thus, proteins, treated with SDS separate on the basis of mass, with the smaller proteins migrating more rapidly through the gel. The gel matrix is polyacrylamide, a synthetic copolymer which has excellent molecular sieving properties. Polyacrylamide gels are cast between glass plates to form what is called a "sandwich." Protein gels are generally run in a vertical fashion. The electrophoresis apparatus has an upper and lower buffer tank. The top and bottom of the sandwich is in contact with either buffer. Protein is loaded into the wells in the upper buffer tank and current is applied. The proteins thus migrate down through the gel in bands, according to their sizes. After electrophoresis, the polyacrylamide gel is removed from between the Figure 3. Illustration by Hans & Cassidy. Courtesy of Gale Group. glass plates and chemically stained to show protein bands which can then be studied. The SDS-PAGE technique allows researchers to study parts of proteins and protein-protein interactions. If a protein has different subunits they will be separated by SDS treatment and will form separate bands.