Hi Everyone,
I've got a question about the SASA term with GBIS simulations.
So I understand that in a GBIS simulation without SASA, the lack of
potential VDW interactions between water and say a hydrophobic sidechain,
means that the sidechain will tend to favour interacting with the protein,
thereby giving a partial hydrophobic effect. Moreover, when one adds in
the SASA term, the energy gradients tend to favour burial of exposed
surfaces, ideally, recapitulating in full the hydrophobic effect.
What I don't understand is, in my reading of the articles presenting these
methods, I don't see anything about the polarity of the atoms being taken
into account for this SASA term. To me, this would suggest that a solvent
accessible polar group is just as unfavourable as a similarly exposed
hydrophobic group as far as SASA is concerned. Furthermore, because
enthalpic interactions between polar groups are stronger than between
hydrophobic groups, this suggests that if one ran a GBIS + SASA simulation
of a protein for long enough, you'd end up with a "native state" in which
the polar groups were all buried in the core. This might take quite some
time, and I know that there are some studies published where the structures
are stable after 50ns, which is also what I see, but as one goes beyond
100ns, I'm seeing signs that things might break down.
There must be something critical I'm missing here?
Thanks,
~Aron
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Jul 19 2012 - 15:30:03 PDT
