The conformational study of β-d-GlcA-(1,4)-l-Rha in solution by NMR and molecular dynamics simulations Original Research Article

The conformation and the dynamics of a disaccharide, β-d-GlcA-(1,4)-l-Rha (GR) in aqueous solution are studied using nuclear magentic resonance (NMR) and unrestrained molecular dynamics (MD). NMR experiments reveal that the solution conformation of GR is insensitive to the orientation of the anomeric proton at the reducing residue. Distance ratios of proton pairs and J coupling constants obtained from the MD simulation in solution are found to be in good accordance with the corresponding experimental data. Comparison between the results from MD simulation in vacuo and those in solution shows that the solvent has little influence on the conformation of either sugar ring, but it has strong influence on the conformation of the glycosidic bond as well as that of the carboxyl group in the glucuronic acid (GlcA). The dynamic behaviors of the GR molecule in solution are also found quite different from those in vacuo. The influence of the solvent is mainly ascribed to formation of intermolecular hydrogen bonds between water and the solute molecule, instead of those intramolecular hydrogen bonds formed in vacuo.