Re: Hydrophobicity of residues
Peter Slickers (slickers@imb-jena.de)
Fri, 2 Feb 1996 17:57:25 +0100 (MET)
Simon wrote:
>
> (snip...)
> >Thus tryptophan being both non-polar and having the largest
> >accessible surface area would be the most hydrophobic.
> (snip...)
>
> >On the same scale the least hydrophobic was arginine. This is
> >essentially for the same reasons : the molecule is small, with a
> >small accessible surface area...
>
> (snip...)
>
> I have a problem with one aspect of your surface area arguments,
> as they're written. In fact, W and R have pretty similar SA
> surface areas (in extended conformations) - they're the two largest
> of the 20 amino acids.
>
> So... anyone wanting to argue for R being be regarded as the least
> hydrophobic of the 20 residues needs to use a different argument I
> think... any thoughts...?
>
>
Correlating the surface area with hydrophobicity should be
done to compare nonpolar molecules, only. In a rough approximation
it can be stated that the electrostatic potential of nonpolar molecules
is the same at each point of the surface. Therefore, for nonpolar
molecules the electrostatic aspect can be neglected and just
the surface area size remains to be different.
On the other hand it appears to me, that a better quantity to be
correlated with the hydrophobicity is the integral of the electrostatic
potential along the molecule's surface. This quantity should hold
for both, polar and nonpolar molecules, maybe should also allow to
discriminate between dissociated and nondissociated species.
Peter
---
Peter Slickers slickers@imb-jena.de
Institut fuer Molekulare Biotechnologie
Beutenbergstrasse 11, Jena Tel.: +49-3641-65-6202
Postfach 10 08 13, D-07708 Jena, Germany Fax: +49-3641-65-6210