On 8 Mar 1996, James R. Miller wrote:
> In article <4hiihk$31d at vixen.cso.uiuc.edu>, dalke at ks.uiuc.edu (Andrew
> Dalke) wrote:
>> > It is a simple question, does glycine have a sidechain? If you say an amino
> > acid base has an group "R" off the CA which is called a sidechain, then the
> > answer is, "yes, and the sidechain is a hydrogen".
> > I can accept that. However, as I think I've mentioned here before, I'm
> > working on a visualization and analysis program (ObPlug:
> > http://www.ks.uiuc.edu/Research/vmd). I want to add an atom selection term
> > called "sidechain" which picks the sidechain atoms. It works for every case
> > except glycine, where I have to determine which of the two hydrogens (in
> an all
> > atom model, such as charmm-22) is the sidechain.
> > Currently I choose the one with the alphabetically smallest name, so for a
> > charmm-22 model, HC1 is the sidechain and HC2 is not. One of the researchers
> > pointed out that I could find the hydrogen which is closest in position
> to where
> > a C-beta would be. The problem is when we compute the molecular
> dynamics of the
> > protein I don't know if the closest hydrogen will always be the same one. I
> > consider it bad if the sidechain alternates between two atoms.
> > Of course, in a reduced atom model, glycine doesn't even have hydrogen
> off the
> > CA.
> > So, does glycine really have a side chain? If so, what is the "right"
> > (IUPAC?) way of finding it?
>> Probably the biggest problem (and a trick question when taking my exams
> for doctoral degree) is that glycine is not optically active. That is,
> without the "sidechain", glycine is an amino acid, but not L- or R-. When
> translated into protein the Hydrogens at the alpha carbon have no
> identity, except by an NMR signal based on what those hydrogens are
> nearest to. Even then the glycine may rotate freely if in the proper
> environment and that signal may be obscured.
>> The amino acids in protein are L-amino acids except for glycine.
>> Now, have I mudded the waters even more?! :-)
> > Andrew
> > dalke at ks.uiuc.edu>> Jim Miller
> Lilly Research Labs
> Indianapolis, IN
>jrm at lilly.com>> ---------------------------------------------------------------------
But, the _program_ should be able to distinguish the hydrogens, and call
one the "side chain" and one the "just a hydrogen," because one is pro-R
and one is pro-S. They are distinct, though not chemically distinct.
skrishna at opal.tufts.eduskrishna at diamond.tufts.edu