Thanks so much for the reply! I had not thought of the GB as essentially
dealing with all the charges. While I still don't completely comprehend,
it makes substantially more sense now.
~Aron
On Thu, Jul 19, 2012 at 9:43 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Jul 19, 2012, Aron Broom wrote:
>
> > 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.
>
> The idea is this: once you have removed the charges all the atoms (which
> is what the GB part estimates), you have left a completely non-polar
> "blob", where there are no longer any polar groups, and everything is
> non-polar. Then an SASA term that works the same for all atoms would be
> appropriate.
>
> For small systems, early papers often estimated the non-electrostatic
> contribution by the experimental solvation free energy of an alkane that
> had
> the same shape and size as the molecule of interest. This is based on the
> same idea, and works pretty well.
>
> [Of course, nothing above guarantees that this argument is accurate enough
> for
> anything other than government work.]
>
> > accessible polar group is just as unfavourable as a similarly exposed
> > hydrophobic group as far as SASA is concerned.
>
> Replace "polar group" with "group that was originally polar before all the
> charges were removed".
>
> > 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.
>
> Don't forget that burial of polar groups is disfavored by the GB part of
> the
> energy.
>
> ....dac
>
>
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Jul 19 2012 - 22:00:03 PDT
