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Molecular dynamics simulations of polypeptide conformations in water: A comparison of α, β, and poly(pro)II conformations

✍ Scribed by Narasimha Sreerama; Robert W. Woody

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
224 KB
Volume
36
Category
Article
ISSN
0887-3585

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✦ Synopsis

A significant fraction of the socalled ''random coil'' residues in globular proteins exists in the left-handed poly(Pro)II conformation. In order to compare the behavior of this secondary structure with that of the other regular secondary structures, molecular dynamics simulations, with the GROMOS suite of programs, of an alanine octapeptide in water, in ␣-helix, ␤-strand, and lefthanded poly(Pro)II conformations, have been performed. Our results indicate a limited flexibility for the ␣-helix conformation and a relatively larger flexibility for the ␤-strand and poly(Pro)II conformations. The behavior of oligopeptides with a starting configuration of ␤-strand and poly(Pro)II conformations, both lacking interchain hydrogen bonds, were similar. The (, ) angles reflect a continuum of structures including both ␤ and P II conformations, but with a preference for local P II regions. Differences in the network of water molecules involved in hydrogen bonding with the backbone of the polypeptide were observed in local regions of ␤ and P II conformations. Such water bridges help stabilize the P II conformation relative to the ␤ conformation.

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