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Titolo:
Explicit and implicit water simulations of a beta-hairpin peptide
Autore:
Ma, BY; Nussinov, R;
Indirizzi:
NCI, FCRF, FCRDC, Lab Expt & Computat Biol, Frederick, MD 21702 USA NCI Frederick MD USA 21702 Expt & Computat Biol, Frederick, MD 21702 USA SAIC, Intramural Res Support Program, Lab Expt & Computat Biol, Frederick,MD USA SAIC Frederick MD USA rogram, Lab Expt & Computat Biol, Frederick,MD USA Tel Aviv Univ, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel Tel Aviv Univ Tel Aviv Israel IL-69978 ol Med, IL-69978 Tel Aviv, Israel
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 1, volume: 37, anno: 1999,
pagine: 73 - 87
SICI:
0887-3585(19991001)37:1<73:EAIWSO>2.0.ZU;2-T
Fonte:
ISI
Lingua:
ENG
Soggetto:
SOLVATION FREE-ENERGIES; FORMING LINEAR PEPTIDE; DYNAMIC PROPERTIES; FORCE-FIELDS; MODEL; THERMODYNAMICS; CONFORMATIONS; METHODOLOGY; RELAXATION; MOLECULES;
Keywords:
beta-hairpin peptide; conformational energy; peptide conformation; continuum solvation model; explicit water model; free-energy simulation; hydrophobic interaction; vibrational entropy;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
33
Recensione:
Indirizzi per estratti:
Indirizzo: Nussinov, R NCI, FCRF, FCRDC, Lab Expt & Computat Biol, Bldg 469,Room 151,Frederick, MD 21702 USA NCI Bldg 469,Room 151 Frederick MD USA 21702 ick, MD 21702 USA
Citazione:
B.Y. Ma e R. Nussinov, "Explicit and implicit water simulations of a beta-hairpin peptide", PROTEINS, 37(1), 1999, pp. 73-87

Abstract

The conformational properties of a beta-hairpin peptide (YITNSDGTWT) were studied by using both explicit and implicit water simulations, The conformational space of the peptide was scanned by using a restricted hydrogen-bonding search method. The search method used generated the conformational space with enough diversity and good representation of beta-hairpin structures. By using a total surface area-based treatment of hydrophobic interactions,implicit water simulations failed to discriminate between experimental beta-hairpin structures from the rest of the conformers present in the authors' conformation library. However, with inclusion of vibrational free energy and accounting separately for polar and nonpolar surface areas, the nuclearmagnetic resonance structure was ranked successfully as the most stable conformation. There is a loose correlation between the conformational energies by the continuum model and the conformational energies by explicit water simulation for conformers with similar structures. However, in terms of solvation energy, both approaches have a much better correlation. By using proper treatment of surface effect (partition of the surface area into polar and nonpolar areas) and including vibrational free-energy contribution, the continuum models should be reliable. Furthermore, the authors found that, for this peptide, beta-hairpin structures have large vibrational entropy that contributes decisively to the stability of folded beta-hairpin structures. (C) 1999 Wiley-Liss, Inc.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 12/07/20 alle ore 09:46:33