protein folding

Dr. Peter Gegenheimer PGegen at UKans.nolospamare.edu
Sun May 20 17:49:02 EST 2001

On Thu, 17 May 2001 00:24:48, "Katerina Dimitrakopoulou"
<katerina67 at hotmail.com> wrote:

ð  I am
ð looking for the equations of the potential in protein folding problem in
ð order to find the global minimum!

Hi -- not meaning to be picky, but this is an ever-elusive grail!

Your question assumes that (1) a potential energy function can be described
and that (2) the "normal" or functional conformation of a protein is one in
which the potential energy is at a global minimum. But neither of these is a
valid assumption.

In particular, (2) is biologically meaningless, because a protein in its
global minimum would not be capable of assuming different conformations
without an external input of energy. The proper functioning of most or all
enzymes, for example, requires that they alternate between different
3-dimensional conformations. In other words, enzymes must exist in metastable
local energy minima. There may, of course, exist some "structural" proteins
which need to assume only one conformation; I very much doubt whether any real
proteins truly fit this description.

The old saying applies to enzymes, I think, just as much as to living
organisms: "A system at its global energy minimum is dead."

| Dr. Peter Gegenheimer       | Vox: 785-864-3939  FAX: 785-864-5321   |
| Department of               |   PGegen at KU.nospam.edu                 |
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| University of Kansas        |"When you have excluded the impossible, |
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