MOLECULAR MECHANICAL AND MOLECULAR DYNAMICAL SIMULATIONS OF GLYCOPROTEINS AND OLIGOSACCHARIDES .1. GLYCAM-93 PARAMETER DEVELOPMENT

A new parameter set (GLYCAM_93) that is consistent with the all-atom AMBER force field has been developed for molecular dynamics simulations of glycoproteins and oligosaccharides. Torsional energy terms were derived from ab initio molecular orbital calculations performed at the restricted Hartree-Fock (RHF) level with the split valence 6-31G* basis set on a series of moderately large representative ''fragments'', each a derivative of tetrahydropyran. High-level ab initio calculations have been performed that indicate that a gauche preference in 1,2-dimethoxyethane, of particular relevance to 1-->6 linked sugars, does not exist in the gas phase. Net atomic charges that reproduce molecular electrostatic potentials (ESPs) at the HF/6-31G* level were employed and have been determined for each relevant monosaccharide. These ESP-charges are consistent with the TTP3P water model. Two approaches that minimize the problem of the conformational dependence of partial atomic charges are discussed. The new parameters correctly predicted the subtle effects on the rotational properties of the glycosidic linkages in models for methyl alpha-D-gluco- and alpha-D-mannopyranoside.