What determines how fast a protein migrates through an SDS-PAGE gel?

The rate at which a protein migrates through an SDS-PAGE gel is primarily determined by its molecular weight. In SDS-PAGE, sodium dodecyl sulfate (SDS) binds to proteins, imparting a negative charge to them and ensuring they are denatured and linearized. This means that the protein's shape, which could affect migration, is not a factor; rather, it is the size that plays a crucial role.

Larger proteins encounter more resistance as they try to move through the pores of the gel matrix, thereby migrating more slowly in comparison to smaller proteins, which can navigate through the gel's matrix more easily. While proteins do carry a charge when coated with SDS, this charge is effectively neutralized in terms of migration direction since all proteins will migrate toward the positive electrode due to the SDS treatment.

Factors like the buffer system may influence the ionic strength and pH of the gel, but they do not directly dictate the speed of migration in the same manner that molecular weight does. Similarly, post-translational modifications might alter a protein's mass or charge characteristics, but the fundamental mechanism of migration during SDS-PAGE is predominantly determined by the molecular weight of the protein. Thus, the molecular weight is the key determinant