CONFORMATIONAL-ANALYSIS OF THE DISACCHARIDE ALPHA-L-RHAP-(1-]2)-ALPHA-L-RHAP-OME - COMPARISON OF DYNAMICS SIMULATIONS WITH NMR EXPERIMENTS

The conformational behaviour of the disaccharide alpha-L-Rhap-(1 --> 2 )-alpha-L-Rhap-(1 --> OMe) has been examined using molecular dynamics (MD) and Langevin dynamics simulations and nuclear magnetic resonance (NMR) spectroscopy; an 800 ps MD trajectory with the explicit inclusio n of water was also determined. The results of the MD simulations were found to be sensitive to the choice of dielectric constant and force- field parameters. NOE build-up curves were constructed from the water and vacuum dynamics trajectories and compared with experimental values . Calculation of NOE data sets from the simulations was problematic fo r several resons, including the similarity in time scales for the inte rnal and overall motions.