Premium
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
Author(s) -
Horta Bruno A. C.,
Lin Zhixiong,
Huang Wei,
Riniker Sereina,
van Gunsteren Wilfred F.,
Hünenberger Philippe H.
Publication year - 2012
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.23021
Subject(s) - force field (fiction) , chemistry , context (archaeology) , solvation , folding (dsp implementation) , molecule , thermodynamics , amide , computational chemistry , physics , organic chemistry , paleontology , quantum mechanics , electrical engineering , biology , engineering
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. © 2012 Wiley Periodicals, Inc.