SDS-PAGE

SDS is a detergent that adheres somewhat nospecifically to proteins. When at a concentration of at least 8*10^-4 moles/liter, it can unfold the protein and bind to it in a ratio of 1.4 grams SDS to 1 gram protein. This is an average of one molecule of SDS for every two amino acids in the protein. The negative charge of the detergent swamps the internal charges of the protein, giving the overall complex a negative charge that is proportional to the length of the protein. As a result, the electromotive force during electrophoresis is related to the length, allowing size based separations. Although electrophoresis separates on the basis of charge, SDS directly links size to charge, making it a size selection where the mobility is inversely proportional to the logarithm of the length of the polypeptide chain.

In order to determine the size of a new, unknown protein, one can run it on a polyacrylamide gel next to a mixture of standard proteins whose sizes are known. This usually allows determination of molecular size to with 10% of its actual value. Some proteins do bind SDS anomolously and therefore have mobilities which do not reflect their true size.

SDS: CH₃-(CH₂)₁₁-SO₄^- Na⁺

See also: Gel Filtration, Analytical Ultracentrifugation and Mass Spectrometry.