Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field influence on the folding properties of two beta-peptides in methanol

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field : influence on the folding properties of two beta-peptides in methanol

Copyright © 2012 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 33(2012), 24 vom: 15. Sept., Seite 1907-17
1. Verfasser: Horta, Bruno A C (VerfasserIn)
Weitere Verfasser: Lin, Zhixiong, Huang, Wei, Riniker, Sereina, van Gunsteren, Wilfred F, Hünenberger, Philippe H
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2012
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article Research Support, Non-U.S. Gov't Acetamides Peptides Water 059QF0KO0R N-methylacetamide V0T777481M Methanol Y4S76JWI15
Beschreibung
Zusammenfassung:Copyright © 2012 Wiley Periodicals, Inc.
Considering N-methylacetamide (NMA) as a model compound, new interaction parameters are developed for the amide function in the GROMOS force field that are compatible with the recently derived 53A6(OXY) parameter set for oxygen-containing chemical functions. The resulting set, referred to as 53A6(OXY+A) , represents an improvement over earlier GROMOS force-field versions in the context of the pure-liquid properties of NMA, including the density, heat of vaporization, dielectric permittivity, self-diffusion constant and viscosity, as well as in terms of the Gibbs hydration free energy of this molecule. Assuming that NMA represents an adequate model compound for the backbone of peptides, 53A6(OXY+A) may be expected to also provide an improved description of polypeptide chains. As an initial test, simulations are reported for two β-peptides characterized by very different folding properties in methanol. For these systems, earlier force-field versions provided good agreement with experimental NMR data, and the test shows that the improved description achieved in the context of NMA is not accompanied by any deterioration in the representation of the conformational properties of these peptides
Beschreibung:Date Completed 03.12.2012
Date Revised 21.11.2013
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.23021