UCT CS Research Document Archive

Conformational free energy maps for globobiose
(a-D-Galp-(1-4)-b-D-Galp) in implicit and explict aqueous solution

Kuttel, Michelle M. (2008) Conformational free energy maps for globobiose
(a-D-Galp-(1-4)-b-D-Galp) in implicit and explict aqueous solution. Carbohydrate Research 343(6):1091-1098.

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Abstract

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 distance dependent dielectric coefficient, respectively. This simple model of the galactanalpha-(1-4)-linkage is shown to be conformationallyrestricted, 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.

EPrint Type:Journal (Paginated)
Keywords:Globobiose
Digalactoside
Disaccharide
Distance-dependent dielectric
Subjects:I Computing Methodologies: I.6 SIMULATION AND MODELING
ID Code:486
Deposited By:Kuttel, Michelle
Deposited On:22 October 2008