Conformational analysis of disaccharides using molecular dynamics and NMR methods

The internal dynamics of four disaccharides, a galacturonic acid dimer, β-ethyl-lactoside, sucralose and arabinobiose, have been studied using molecular dynamics and nuclear magnetic resonance methods. Theoretical motional models, which include order parameters and correlation times for internal motions, were extracted from dynamics trajectories in vacuo. In parallel, theoretical NOESY volumes were calculated from averaged distance matrices using ‘model-free’ spectral densities. These data were least-squares fitted to the normalized experimental NOESY volumes using the order parameters and internal motion correlation times as adjustable parameters. The resulting ‘experimental’ motional models were in good agreement with the theoretical ones with the exception of the galacturonic acid dimer which was best described by the rigid molecule approximation.