SDS debate

Malay curiouser at ccmb.ap.nic.in
Thu Aug 9 10:33:26 EST 2001


> Proteins vary, of course, but the tendency will be for SDS to "stretch out" 
> the protein chain, so your colleague is closer to being correct. Consider 
> that SDS is highly charged at neutral pH, so that when a protein is 
> slathered in it the charges tend to want to repel each other so the chain 
> unfolds. 

I don't really think so. SDS and protein interaction is not on the basis
of charge but hydrophobicity. SDS actually partially unfolds a proteins it
acts more like a solvent to keep the protein in unfolded state and
preventing aggregation, rather than acting as denaturant per se. And even
heating doesn't unfold a protein completely ( of course not true for all
the protein ). You need to use a proper denaturant like urea/GDCL to
unfold a protein.

The last line of your mail is contradictory. Unless the protein unfolds
SDS won't get the access to hydrophobic pockets and can't sheild the
charge. And a globular protein in water will have very minimum hydrohobic
surface exposed. Logic says SDS will be a good denaturant for proteins
where there are more hydrophobic surface exposed and will be a bad one for
a highly charged protein. But I am talking out of the hat here. There are
still controversies regarding the mechanism of unfolding a protein. We
don't even know for sure how urea denatures a protein.

Regards,

Malay
 

Malay Kumar Basu 
Centre for Cellular and Molecular Biology 
Hyderabad 500007 
I N D I A

Fax: (00-91)40-7171195  Phone: (00-91)40-7172241 
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curiouser at ccmb.ap.nic.in




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