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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Received on Thu Jul 19 2012 - 19:00:02 PDT
