Conformational free energy maps for globobiose (alpha-D-Galp-(1 -> 4)-beta-D-Galp) in implicit and explict aqueous solution

摘要

Four Ramachandran maps of the conformational potential of mean force (PMF) for the galactose disaccharide globobiose (alpha-D-Galp-(1 -> 4)-beta-D-Galp) were calculated in vacuum, explicit water, with a simple high dielectric constant and a distancedependent dielectric coefficient, respectively. This simple model of the galactan alpha-(1 -> 4)-linkage is shown to be conformationally restricted, with only a small range of syn-phi/syn-Psi conformations predominating at standard temperature and pressure. This has implications for the preferred conformation and chain dynamics of alpha-galactosides. In addition, comparison of the relevant PMF surfaces reveals the substitution of a high dielectric constant for explicit water solution to be a valid approximation for reproducing the minimum energy conformation of this glycosidic linkage. (c) 2008 Elsevier Ltd. All rights reserved.