is there a theory of protein folding?

Matt mp6sf at hotmail.com
Thu Dec 5 17:55:15 EST 2002


fec1375d.0212051446.528bb0f4 at posting.google.com>

     I'd like to throw some thoughts to stimulate a discussion.

     Protein folding has long attracted the interests of theoretical
and
     computational physicists, as well as other types of
theoretically-minded         people.
     There has been attempts to say something about folding based on
     concepts inspired from spin glass theory, ``energy landscapes'',
and
     a plethora of statistical mechanical and other models. What did 
     this accomplish?
     Not much, it seems to me. The spin glass analogy has proven
pretty
     much useless to understand what proteins really do. The ``new
view'',
     namely that folding is driven by a ``funnel''energy
     landscape, is quite obvious from a physical point of view and
     doesn't add anything really useful (to make predictions, that
is).
     Indeed, the basic physics (i.e. the physics which is common to
all
     proteins) is quite simple.

     Despite this, the hype around protein folding physics continues
     unabated. I would predict that at some points the funding
agencies and
     the public will realize that there isn't much beef here, and at
that
     point the whole field of energy landscape-ology etc. will be
quickly
     forgotten.

     The real, important scientific issues in protein folding have to
do to
     the SPECIFIC behavior of a given protein and its interactions
with
     other molecules. The devil really is in the details here. But
this is more
     an experimental problem than anything else. One can hope that at
     some points people will be able to do detailed, realistic
simulations.
     Whether these can provide insight that is not obtainable from 
     experiments remains to be seen, in my view.



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