Protein Folding

Frank Fuerst fant.1 at gmx.net
Tue Apr 11 03:37:47 EST 2000

Edward Green wrote:

> >perhaps quantum effects are involved in protein folding - it is
> >impossible for a protein to try every possible conformation sequentially so
> >perhaps several different conformations are attempted in paralell.
> >
> >Is this at all possible?
> It sounds way cool, but why fish for the obscure before there is a
> reason to doubt that protein folding may be understood as a result of
> classical kinetics operating on a ball and stick molecule, the way we
> often understand chemical reactions.
> I think you may err in supposing that a folding protein molecule
> "tries out every conformation".  It's not solving a traveling salesman
> problem; it's simply choosing a locally best route.
> [I see you have added some heavy duty special purpose bio group, where
> there may be people who really know about protein folding... 

You're quite right. When one tries to visualize the multi-dimensional
conformational space of a protein using a two dimensional model, the
third dimension beeing the potential energy [1], on gets potential
energy surfaces with the form of a "funnel". This means that the
folding process means in general just going downhill (or diffusing in
flat valleys and terraces)[2].
Thus, the protein doesn't have to try every possible conformation.
Once that, by a statistical search, a small subset of favourable,
near-in-sequence interactions is established, these interactions are
stable and are kept throughout the rest of the folding process. The
rest of the polypeptide chain finds its native conformation either by
stepwise addition of further stable interactions to that nucleus, or
(in the case of long chains) by forming of several independent nuclei.


[1] to be exactly: the internal free energy, i.e. the Gibbs free
energy with all contributions except chain entropy
[2] things get a little more difficult when we also look at chain
PhD student, department of physical biochemistry, Potsdam university

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