Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations

Citation
J. Higo et al., Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations, PROTEIN SCI, 10(6), 2001, pp. 1160-1171
Citations number
91
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEIN SCIENCE
ISSN journal
0961-8368 → ACNP
Volume
10
Issue
6
Year of publication
2001
Pages
1160 - 1171
Database
ISI
SICI code
0961-8368(200106)10:6<1160:ELOAPC>2.0.ZU;2-1
Abstract
The energy landscape of a peptide [Ace-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in explicit water was studied with a multicanonical molecular dynamics simulat ion, and the AMBER parm96 force field was used for the energy calculation. The peptide was taken from the recognition helix of the DNA-binding protein , c-Myb. A rugged energy landscape was obtained, in which the random-coil c onformations were dominant at room temperature. The CD spectra of the synth esized peptide revealed that it is in the random state at room temperature. However, the 300 K canonical ensemble, Q(300K), contained alpha -helix, 3( 10)-helix, beta -turn, and beta -hairpin structures with small but notable probabilities of existence. The complete alpha -helix, imperfect alpha -hel ix, and random-coil conformations were separated from one another in the co nformational space. This means that the peptide must overcome energy barrie rs to form the alpha -helix. The overcoming process may correspond to the h ydrogen-bond rearrangements from peptide-water to peptide-peptide interacti ons. The beta -turn, imperfect 3(10)-helix, and beta -hairpin structures, a mong which there are no energy barriers at 300 K, were embedded in the ense mble of the random-coil conformations. Two types of P-hairpin with differen t beta -turn regions were observed in Q(300K). The two beta -hairpin struct ures may have different mechanisms for the beta -hairpin formation. The cur rent study proposes a scheme that the random state of this peptide consists of both ordered and disordered conformations. In contrast, the energy land scape obtained from the parm94 force field was funnel Like, in which the pe ptide formed the helical conformation at room temperature and random coil a t high temperature.