Proteins which run high on SDS-PAGE

[sam simons]

Prolines introduce natural "kinks" in the protein which aren't 
straightened out by denaturing. Since denaturing in SDS creates linear 
polypeptides, this bending will give a larger stokes radius to the 
protein which will cause it to run slower through SDS-PAGE. This is 
especially true if the prolines are concentrated in one stretch as it 
will tend to bend the polypeptide farther out of line. There may also be 
a charge effect if the SDS can't coat the extra surfaces as efficiently, 
but I'm not sure about that. We had the same situation with a protein in 
my last lab. Once you've ruled out post-translational modification, you 
just have to live with the difference. 

Sam

In case any of you are lawyers, here's the disclaimer,
My opinion, not Pfizer's