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Conformational analysis of the disaccharide alpha-L-Rhap-(1-->2)-alpha-L-Rhap-OMe: comparison of dynamics simulations
1Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20852-1448, USA.
Abstract:
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 inclusion 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 for several reasons, including the similarity in time scales for the internal and overall motions.