Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridine diphosphate-glucose in the presence of monovalent cations

The nucleotide-sugars are metabolites of primary importance in the biosynth esis of polysaccharides and glycoconjugates since they serve as sugar donor s in the reactions of glycosyltransferases, enzymes that displays a high sp ecificity Sor both donors and acceptors. In order to determine the conforma tional behavior of uridinediphosphoglucose in dilute aqueous solution that includes a physiologically relevant concentration of salt, parallel NMR and molecular modeling investigations have been conducted Nine molecular dynam ics trajectories of 3 ns each were calculated in presence of explicit water and monovalent cations with the use of the AMBER force field with recently developed energy parameters for nucleotide-sugars (P. Petrova, J. Koca, an d A. Imberty: Journal of American Chemical Society, 1999, vol. 121, pp. 553 5-5547). Theoretical nuclear Overhauser effect data were calculated from th ese simulations using a model-free approach that rakes into account interna l motions. Comparison of theoretical and experimental data gives excellent agreement for the region surrounding the glucose-phosphate linkage includin g the pyrophosphate linkage itself: Less satisfactory agreement is obtained for the ribose ring and the base orientations, On the whole, both NMR and molecular dynamics simulations predict the molecule to be flexible, and to visit a large number of conformations while maintaining an extended overall shape. (C) 2001 John Wiley & Sons, Inc.