Premium
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
Author(s) -
Ikeda Kazuyoshi,
Galzitskaya Oxana V.,
Nakamura Haruki,
Higo Junichi
Publication year - 2003
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10160
Subject(s) - random coil , energy landscape , folding (dsp implementation) , molecular dynamics , helix (gastropod) , crystallography , peptide , chemistry , alpha helix , hydrogen bond , chemical physics , sh3 domain , molecule , computational chemistry , circular dichroism , biology , biochemistry , proto oncogene tyrosine protein kinase src , ecology , organic chemistry , kinase , snail , electrical engineering , engineering
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