Poly Ala vs Poly Gly

[Shaun Black <BLACK (+ at +) OHSTPHRM.PHARMACY.OHIO-STATE.EDU>]

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: black (+ at +) ohstphrm.bitnet
 Ohio State University   | Internet: black (+ at +)
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