Biochem student question.

Saco saco at moon.yerphi.am
Fri Oct 11 13:46:52 EST 2002


"Alex Becket" <abecket at cinci.rr.com> wrote in message news:<hgsp9.63746$Cz.8026438 at twister.neo.rr.com>...
> I am a biochemistry student at the University of Cincinnati. I am doing a
> study of the relative hydrophobicities of amino acid side chains. My
> question is:  does a larger surface area available to water increase or
> decrease an amino acid's hydrophobicity? For example, tryptophan has a
> larger surface area available to water than phenylalanine, yet phenylalanine
> is more hydrophobic (unless using long chain alcohols as the nonpolar
> phase).
> 
> any response would be greatly appreciated.

My guess its because Nitrogen is more electronegative than Carbon, so
the additional N in Trp makes it less hydrophobic. It makes me think
now whether ab initio protein folding programs where salvation effect
depend only though the surface area are correct? Does anyone know ab
initio protein folding program where this is not the case (i.e.
salvation effect depend not only on the surface area but also on
detailed molecular composition).



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