From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Jul 30 2012 - 17:06:54 CDT
Just as an FYI to anyone who has this same question and discovers this
thread, Dr. David Case informs me that once the Generalized Born
calculations have taken place, all of the atoms are effectively chargeless,
since the electrostatic portion of the calculations are done, and
therefore, it is safe to treat SASA equally for all of them.
On Thu, Jul 19, 2012 at 2:34 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> Hi Everyone,
> I've asked before about the SASA term with GBIS simulations, but I'm still
> slightly confused and have what I think is a rather quick question:
> 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 that 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 would imply 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.
> There must be something critical I'm missing here?
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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