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Development and validation of force‐field parameters for molecular simulations of peptides and proteins containing open‐shell residues
Author(s) -
Barone Vincenzo,
Capecchi Gabriella,
Brunel Yvon,
Dheu Andriés MarieLouise,
Subra Robert
Publication year - 1997
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/(sici)1096-987x(19971115)18:14<1720::aid-jcc2>3.0.co;2-m
Subject(s) - force field (fiction) , chemistry , alanine , dodecameric protein , conformational isomerism , molecular dynamics , glycine , crystallography , computational chemistry , residue (chemistry) , nucleic acid , amino acid , molecule , stereochemistry , physics , quantum mechanics , organic chemistry , biochemistry
Parameters suitable for extending the AMBER force field for nucleic acids and proteins to open‐shell derivatives of amino acid residues are proposed and tested. Two new atom types (radical carbon [CE] and hydrogen directly bonded to it [HE]) are introduced, whose parameters have been determined by a best fitting of quantum‐mechanical computations of the simplest analogue of glycine radical (GlyR) in a peptide. The new force field is able to fit the reference results concerning both the structural parameters and the relative stabilities of the different conformers. It has been next applied to a conformational study of the distortions induced by extraction of the glycine H α atom in an initially helical structure of a dodecamer of alanine including a central glycine residue. Our results show that the helical structure corresponds to a local energy minimum, but deeper minima are found which correspond to a fully planar GlyR residue included in a distorted helical sequence. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1720–1728, 1997