SDS debate

Malay curiouser at ccmb.ap.nic.in
Sun Aug 12 05:59:13 EST 2001


Creighton says SDS is a denaturant acting by the charge. But I am still
not convinced that SDS by itself can denature a protein. Surprisingly, all
the books have somehow missed the boiling part. They take boiling for
granted. Regarding the shape, there is no doubt that proteins + SDS
complex takes a rod like shape. There was even paper that most of the
proteins takes a helical conformation in SDS. I can dig out the reference
if anyone wants. 

What I really want to know is ( a very vital point):

"Can SDS per se (without boiling) can denature a soluble protein?"

Anyone there who can answer?

- Malay


On Sat, 11 Aug 2001, Emir Khatipov wrote:

> As far as I remember, most textbooks say that SDS denatures proteins by
> "stretching" them out, which means that the whatever native conformation is
> destroyed completely (I am talking about boiling in SDS). However, remember,
> that residual disulfide bonds may determine the shape of the denatured
> molecule. S=S bonds may not be destroyed completely by BME or DTE (the
> latter being more effective), or if destroyed, may reform under oxidizing
> conditions later on, unless you do not block SH with thiol reagents like
> maleimides, etc.
> 
> In approximation, there is one SDS molecule per 2 aa. I believe the
> detergent denatures (stretches out) the protein not because of its charge,
> but due to hydrophobic-hydrophilic interactions. An important feature is
> that coating of the protein chain with SDS gives the proteins a similar net
> negative charge that is (ideally) uniform, and constant charge-to mass
> ratio. The letter allows separation of the denatured proteins during
> SDS-PAGE exclusively by their size(mass) due to sieving effect of the gel,
> because intrinsic mobility of proteins is (due to similar charge-to-mass
> ratio) the same for most proteins. The exceptions of the latter are proteins
> with extreme pI, non-uniformly charged molecules, and short peptides.
> 
> Thus, it seems likely that SDS-denatured proteins are not exactly like a
> "ball of wool unrolled", but rather loose and changing in form bundle or
> lump. There is certainly a chance that this thread will be completely
> unwound and become a linear stretched rod, but most of the long-chain
> proteins will have a irregular bundle-like shape. Shorter peptides will
> stretch completely though.
> 
> Does this make sense?
> Emir
> 
> 
> "Michael Witty" <mw132 at mole.bio.cam.ac.uk> wrote in message
> news:Pine.SGI.4.33.0108091040010.4361379-100000 at mole.bio.cam.ac.uk...
> > Dear All,
> >         there is a debate in my lab about the extent to which SDS
> > denatures protein.  I think that SDS sticks, but the gross shape of the
> > protein is not altered very much (the protein still looks like a ball of
> > wool).  My collegue thinks that the protein is dramatically unfolded and
> > looks like a linear object, or a ball of wool unrolled.  What do we think?
> > Regards, Mike.
> >
> 
> 

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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