Apparent MW of protein on SDS-PAGE > real MW?

Warren Gallin wgallin at
Mon Mar 7 21:39:39 EST 1994

In Article <2lg72q$9sr at>,
bhuang at (Baohua Huang) wrote:
>Hi, everyone.
>A fusion protein I expressed in E. coli has a apparent MW on SDS-PAGE gel ~5 kd
>lager than it's calculated MW. This protein is 303 aa residues with a 
>calculated MW of 35 kd but it runs at 40 kd position on SDS-PAGE. The protein 
>has very high content of basic amino acids (32 lysines,  20 arginine and 16 
>histidines). My question is : does high content of basic residues make a 
>protein run slower?
>I would apreciate very much any hints to my question.
>Baohua Huang
>Ohio state Univ.

This phenomenon is not at all unusual.  Many proteins do not run on SDS-PAGE
at a position that isconsistent with their predicted molecular weights. 
Although the basic amino acid composition may be a factor, the cadherins
don't have an unusually high basic amino acid composition and they all run
about 20 kD heavier than they really are.  It also is not due to
glycosylation.  The mechanism, as far as I know is a mystery, although there
is some suggestion that changing the buffer system in the gel may give a
more realistic estimation of molecular weight relative to standards.

Warren Gallin,
Department of Zoology, University of Alberta
wgallin at

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