The program characterizes the structure and dynamics of biomolecules, including oligosaccharides and polypeptides. NMR and molecular dynamics (MD) and Langevin dynamics (LD) simulations were used to investigate the solution conformation of two trisaccharides of D-Glcp, alpha-D-Glcp-(1->2)-beta-D-Glcp-(1->3)-alpha-D-Glcp-OMe (I) and alpha-D-Glcp-(1->3)-beta-D-Glcp(1->4)-alpha-D-Glcp-OMe (II). The NOE data and simulations at 298 K all indicate that trisaccharide I is a single all-syn conformer in solution. Given that previous studies showed evidence of anti-conformers in beta-D-Glcp-(1->2)-beta-D-Glcp-(1->3)-alpha-D-Glcp-OMe, this result provides an example of how changing the anomeric configuration of one residue from beta to alpha can make an oligosaccharide more rigid. Discrepancies in the inter-ring distances obtained by experiment and by simulation of the all-syn conformer of II suggests the presence of an anti-psi conformation at the beta-(1->4) linkage. A combined analysis of measured and calculated translational diffusion constants and 13C T1 relaxation times yield order parameters of 0.9 for each trisaccharide. This implies that any interconversion among conformations is significantly slower than tumbling. Anisotropies of approximately 1.6 and 1.3 calculated for I and II, respectively, are consistent with the observed relatively flat T1 profiles because the tumbling is not in the motional narrowing regime. Currently we are working to characterize the structure and dynamics of a polypeptide, partly in support of the development of force fields for simulations.
