SDS is a detergent that is present in the SDS-PAGE sample buffer where, along with a bit of boiling. It’s a reducing agent to break down protein-protein disulphide bonds that disrupt the tertiary structure of proteins, and brings the folded proteins down to linear molecules. SDS coats the protein with a uniform negative charge, which masks the intrinsic charges on the R-groups. SDS binds fairly uniformly to the linear proteins (around 1.4g SDS/ 1g protein), meaning that the charge of the protein is now approximately proportional to its molecular weight. SDS is also present in the gel to make sure that once the proteins are linearized and their charges masked, they stay that way throughout the run.
The dominant factor in determining an SDS-coated protein is its molecular radius. SDS-coated proteins have been shown to be linear molecules, 18 Angstroms wide and with length proportional to their molecular weight, so the molecular radius (and hence their mobility in the gel) is determined by the molecular weight of the protein. Since the SDS-coated proteins have the same charge to mass ratio, there will be no differential migration based on charge.
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