QUESTIONS: alpha-helix "signals" in proteins

Simon Brocklehurst Bioc smb18 at mole.bio.cam.ac.uk
Sat Jul 9 05:21:45 EST 1994

Ken Prehoda <kenp at nmrfam.wisc.edu> writes:

I didn't deal specifically with this point in my "long" post, but
I will do so now!

>  What I am saying is that if there is some
>state that has a free energy lower than our observed state, it is
>irrelevant, if it cannot be reached.  In other words, although
>having a lower free energy state implies that the system is not
>at equilibrium, for all practical purposes, the system is at
>equilibrium if it takes the age of the universe to reach that 
>global minimum.

     I disagree that this is irrelenvant!!!!  If you could design
a potential energy function that was accurate, then you have
the possibility of predicting the 3-D structure of a protein
from it's sequence.

     If the native state is the global minimum, then the pathway
by which you searched for the native state in the computer is
unimportant.  But if the native state is not the global minimum,
you will have deal with the possibility that it might be important
to be able to simulate Nature's folding algorithm in order to
predict the structure.  Thus being able to predict the structures
of partly folded states, including intermediates and transition
states might be of central importance etc etc.

|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Oxford Centre for Molecular Sciences,
|   \>> |   Department of Biochemistry, University of Oxford,
|    \\,    Oxford, UK.
|           E-mail: smb at bioch.ox.ac.uk

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