Proteins which run high on SDS-PAGE

Achim Treumann a.treumann at dundee.ac.uk
Mon May 13 12:29:57 EST 1996


Enrique, 

I am not sure, whether I agree with you. Evans et al. have shown a while 
ago (in the mid-eighties, I do not have the reference at hand just now, 
email me if you really want to know) by NMR that (-Pro-Lys-) or 
(-Pro-Glu-) repeat domains which occur naturally in many proteins have an 
almost completely extended structure. Yet these proteins do migrate 
significantly slower. Could this be because often many prolines go 
together with very hydrophilic domains which bind less SDS?

Best wishes, 
Achim

Enrique Jose Labadan Frio - SCBC - 3421101 wrote:

>         Proline structurally constrains the main chain into a rigid
> conformation (non-"linearizable" in the stretches where it occurs, if > you
> will) since it is strictly not an amino acid (imino acid for the > purists)
> and has a cyclic "side chain" (pyrrolidine, which is very constrained).
> With the  principle of SDS denaturing the protein (how much is it > really?
> 2-3 aa's perSDS moiety?) at sites where the psi/chi angles can rotate > well
> (all of the aa's at that, except proline), an > insufficiently-"linearized"
> polypeptide chain migrates slower (and thus higher on the gel) than one
> with the same size but with fewer prolines. Look up any biochem > textbook
> for the structure.
> 
>         I'm still not clear though, on why proteins with some prolines
> still migrate quite well... a lot of Pro's can make them significantly
> slower, but for fewer ones, well...
> 
>         All the best!
> 
> Querix
> g3421101 at mucc.mahidol.ac.th
> 
> ==========
> "I love you three times a day!" - Jimmy Santos (can you guess who he is?)
> :)

-- 
Achim Treumann
Dept. Biochemistry			Tel. +44-1382-344301
University of Dundee			fax  +44-1382-322583
Dundee DD1 4HN				
Scotland, UK			email a.treumann at dundee.ac.uk



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