What kind of "size" does SDS-PAGE separate by?

Question

What is the exact property of the protein that affects migration of bands in SDS-PAGE; is it length, volume, or mass?For example, will `GGGGGGGGGG` (glycine 10-mer; mw <600) migrate more or less than `WWWWW` (tryptophan 5-mer; mw >900)?

Answer 1

SDS-PAGE separates proteins based on molecular weight, given in daltons (Da) or kilodaltons (kDa). Because SDS denatures proteins and gives the protein an overall negative charge, molecular weight is the only property that will separate proteins using this lab technique. If you are running native proteins (not using SDS) then things like amino acid charges and protein folding my affect run speed.

For your example, because the tryptophan protein has the higher mw, it will move more slowly through the gel matrix than the glycine protein. The glycine protein, although longer, has a lower mw and its band will appear farther down the gel. Hope this helps!