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

Eric Carstens carstens at
Tue Mar 15 12:45:01 EST 1994

In article <wgallin.1113482019B at NEWS.SRV.UALBERTA.CA>
wgallin at (Warren Gallin) writes:

> >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

This does happen often. We have published a report where the simple
substitution of leucine for proline altered the mobility of the
baculovirus polyehdrin polypeptide on SDS gels (J.Virol. 58:684-688,
1986 and references therein).

Eric Carstens

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