Conformational free energy maps for globobiose (alpha-D-Galp-(1-->4)-beta-D-Galp) in implicit and explicit aqueous solution.
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 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.
Kuttel
Michelle M
MM
Department of Computer Science, University of Cape Town, Cape Town, South Africa. mkuttel@cs.uct.ac.za
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry*; D019277:Entropy; D005690:Galactose / Q000737:chemistry*; D008962:Models, Theoretical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D013816:Thermodynamics
D004187:Disaccharides; D005690:Galactose