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• W2155364056 abstract "A significant fraction of the so-called “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 α-helix, β-strand, and left-handed poly(Pro)II conformations, have been performed. Our results indicate a limited flexibility for the α-helix conformation and a relatively larger flexibility for the β-strand and poly(Pro)II conformations. The behavior of oligopeptides with a starting configuration of β-strand and poly(Pro)II conformations, both lacking interchain hydrogen bonds, were similar. The (ϕ, ψ) angles reflect a continuum of structures including both β and PII conformations, but with a preference for local PII regions. Differences in the network of water molecules involved in hydrogen bonding with the backbone of the polypeptide were observed in local regions of β and PII conformations. Such water bridges help stabilize the PII conformation relative to the β conformation. Proteins 1999;36:400–406. © 1999 Wiley-Liss, Inc." @default.
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• W2155364056 date "1999-09-01" @default.
• W2155364056 modified "2023-10-16" @default.
• W2155364056 title "Molecular dynamics simulations of polypeptide conformations in water: A comparison of ?, ?, and poly(pro)II conformations" @default.
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• W2155364056 doi "https://doi.org/10.1002/(sici)1097-0134(19990901)36:4<400::aid-prot3>3.0.co;2-b" @default.
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