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Titolo:
Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations
Autore:
Higo, J; Ito, N; Kuroda, M; Ono, S; Nakajima, N; Nakamura, H;
Indirizzi:
Biomol Engn Res Inst, Suita, Osaka 5650874, Japan Biomol Engn Res Inst Suita Osaka Japan 5650874 uita, Osaka 5650874, Japan Tanabe Seiyaku Co Ltd, Osaka 5328205, Japan Tanabe Seiyaku Co Ltd Osaka Japan 5328205 u Co Ltd, Osaka 5328205, Japan Osaka Univ, Inst Prot Res, Suita, Osaka 5650871, Japan Osaka Univ Suita Osaka Japan 5650871 rot Res, Suita, Osaka 5650871, Japan
Titolo Testata:
PROTEIN SCIENCE
fascicolo: 6, volume: 10, anno: 2001,
pagine: 1160 - 1171
SICI:
0961-8368(200106)10:6<1160:ELOAPC>2.0.ZU;2-1
Fonte:
ISI
Lingua:
ENG
Soggetto:
MOLECULAR-DYNAMICS SIMULATIONS; MONTE-CARLO METHOD; SELF-OVERLAP ENSEMBLE; LONG-RANGE STRUCTURE; DENATURED STATE; STAPHYLOCOCCAL NUCLEASE; PROTEIN-G; MULTICANONICAL ENSEMBLE; RESIDUAL STRUCTURE; PARAMAGNETIC RELAXATION;
Keywords:
folding; rugged surface; funnel; beta-hairpin; alpha-helix; random state; multicanonical; force field;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
91
Recensione:
Indirizzi per estratti:
Indirizzo: Higo, J Tokyo Univ Pharm & Life Sci, Sch Life Sci, Lab Bioinformat, 1432-1Horinouchi, Tokyo 1920392, Japan Tokyo Univ Pharm & Life Sci 1432-1 Horinouchi Tokyo Japan 1920392
Citazione:
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

Abstract

The energy landscape of a peptide [Ace-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] inexplicit water was studied with a multicanonical molecular dynamics simulation, 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 conformations were dominant at room temperature. The CD spectra of the synthesized 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 notableprobabilities of existence. The complete alpha -helix, imperfect alpha -helix, and random-coil conformations were separated from one another in the conformational space. This means that the peptide must overcome energy barriers to form the alpha -helix. The overcoming process may correspond to the hydrogen-bond rearrangements from peptide-water to peptide-peptide interactions. The beta -turn, imperfect 3(10)-helix, and beta -hairpin structures, among which there are no energy barriers at 300 K, were embedded in the ensemble of the random-coil conformations. Two types of P-hairpin with different beta -turn regions were observed in Q(300K). The two beta -hairpin structures may have different mechanisms for the beta -hairpin formation. The current study proposes a scheme that the random state of this peptide consists of both ordered and disordered conformations. In contrast, the energy landscape obtained from the parm94 force field was funnel Like, in which the peptide formed the helical conformation at room temperature and random coil at high temperature.

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Documento generato il 15/07/20 alle ore 14:45:32