Conformational studies of a trisaccharide epitope in solution by using NMR spectroscopy and molecular mechanics and dynamics calculations with the MM3* program

Abstract

The solution conformations of methyl β-D-galactopyranosyl-(1 → 2)-xylopyranoside (1) and methyl α-L-fucopyranosyl-(1 → 2)-β-D-galactopyranosyl-(1 → 2)-xylopyranoside (2) have been analysed by NMR spectroscopy and molecular mechanics and dynamics calculations. The comparison between NMR experimental results (NOES based on NOESY, ROESY, T-ROESY and steady-state experiments) and expected data [from ensemble average distributions of conformers and molecular dynamics (MD) simulations] indicates that both compounds present a moderate flexibility around their glycosidic linkages. A van der Waals interaction between the remote fucopyranosyl and xylopyranosyl moieties of 2 can be deduced from the theoretical and experimental data.