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What is the glycine sidechain?

James R. Miller jrm at lilly.com
Fri Mar 8 16:39:10 EST 1996

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


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