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What is the glycine sidechain?

Sanjay Krishnaswamy skrishna at diamond.tufts.edu
Wed Mar 13 12:54:33 EST 1996


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.
-S.



> 
> 

_______________________________________________________________________________
Sanjay Krishnaswamy                                
skrishna at opal.tufts.edu
skrishna at diamond.tufts.edu
_______________________________________________________________________________




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