β‐Hairpins, α‐helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β‐hairpin of SH3 domain

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Abstract
Energy landscape of a peptide, extracted from a distal β-hairpin of src SH3 domain, in explicit water was obtained with the multicanonical molecular dynamics. A variety of β-hairpins with various strand–strand hydrogen bonds were found in the energy landscape at 300 K. There was no energy barrier between random-coil and hairpins. Thus, the peptide conformation can easily change from the random-coil to the hairpins in the thermal fluctuations at 300 K. The landscape also included two clusters of α-helices, among which an energy barrier existed, and besides, these helix clusters were separated from the other conformations. Thus, the free-energy barrier exists among the helices and the other conformations. Intermediate clusters were found between the helix and the hairpin clusters. The current study showed that the isolated state of this peptide in water fluctuates among random-coil, β-hairpin, and α-helix. In SH3 domain, which has a topology of mainly β-protein, the whole-protein folding may proceed when the segment is folded in the β-hairpin and the other parts of the protein are coupled with the β-hairpin in an energetically or kinetically favorite way. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 310–318, 2003