DEVELOPMENT AND VALIDATION OF FORCE-FIELD PARAMETERS FOR MOLECULAR SIMULATIONS OF PEPTIDES AND PROTEINS CONTAINING OPEN-SHELL RESIDUES

Parameters suitable for extending the AMBER force field for nucleic ac ids and proteins to open-shell derivatives of amino add residues are p roposed and tested. Two new atom types (radical carbon [CE] and hydrog en directly bonded to it [HE]) are introduced, whose parameters have b een 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 co nformers. it has been next applied to a conformational study of the di stortions induced by extraction of the glycine H-alpha atom in an init ially helical structure of a dodecamer of alanine including a central glycine residue. Our results show that the helical structure correspon ds to a local energy minimum, but deeper minima are found which corres pond to a fully planar GlyR residue included in a distorted helical se quence. (C) 1997 John Wiley & Sons, Inc.