Subject: Poly Ala vs Poly Gly

From: Shaun Black <[email-masked]>
Date: Fri, 14 Jun 91 14:12:14 EST

Scott-
    I'm not absolutely certain of the answer, but perhaps my thoughts will
help you get closer.  Poly-L-Ala is a model polymer (as is Poly-L-Glu) of
peptides that readily assume an alpha helical conformation.  The methyl side
chain ("R" group) of Ala is both hydrophobic enough and bulky enough to exclude
water, yet not so bulky as to cause unfavorable van der Waal's contacts between
adjacent residues;  thus, a helical structure is favored.  Gly is commonly
assumed to be a "helix breaker" because it has an "R" group of Hydrogen which
lacks the hydrophobicity and steric bulk needed to exclude water from the
helix.  If water has access to the helix, the carbonyl...HN- hydrogen bonds
can be broken by exchange and the helix would "fall apart" (revert to another
conformation).  This should be the case for poly-Gly.  Thus, if you do energy
minimization/dynamics for poly-Gly in vacuuo, I would assume that helical
structure would result (left of right handed pitch), because the hydrogen bonds
could form and the side chain (hydrogen) would offer no steric repulsion.
However, it would be essentially impossible for helical structure to exist in
the presence of water.  So, my answere is *both* helical and non-helical,
depending on the experimental or computational conditions (vacuum/organic
solvent vs water).  Hope this helps!

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Shaun D. Black          | Bitnet: [email-masked]
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From: [email-masked] (Peter S. Shenkin)
Date: Fri, 14 Jun 91 16:11:46 EDT

Excuse me...  It is my recolletion that Poly-Ala is almost completely
insoluble in water, though it does form helix in the non-polar solvents
that it dissolves in.  Can someone verify or correct me?  I'm not sure
about poly-gly in this regard, but the reason it's felt to be a helix-
breaker in proteins is, I think, because so much more of the
Ramachandran map is accessible to it, since it has no C-beta;  thus
there is more of an entropy loss in being frozen into a helix.  Now that
I think about it, though, this makes little sense, since I know of no
data that says that gly is in fact less ordered (eg, higher T factor)
than other residues in proteins, though this would be interesteing to
look at.  But in any case, it has more intrinsic flexibility than the other
amino acids, and any interactions present which stress the helix would
be likely to break it at its "weak link."

	-P.
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Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027
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