Molecular dynamics simulation and NMR study of aqueous neocarrabiose 4(1)-sulfate, a building block of kappa-carrageenan

The solution conformation of neocarrabiose 4(1)-sulfate, which is a buildin g block Of K-carrageenan, was investigated by a combination of molecular dy namics simulations and H-1 NMR experiments. The calculated Ramachandran-typ e potential energy map for the glycosidic torsion angles phi and psi of thi s dimer showed that there are two principal minimum-energy conformations, d esignated here as "a" and "b". Comparison of the depths of these minima and the MID trajectories started from each minimum indicated that in a vacuum the molecular conformation in the "a" well is more stable than that in the "b" well. On the other hand, MID simulations in water showed that trajector ies started from each minimum position stayed within their respective wells throughout the time courses of the simulations. However, analysis of the h ydration water around the , molecule indicated that the stability of the mo lecular conformation in the "a" well would be favored by solvation compared to the "b" well. Analysis of the experimental NOE-NMR data using the above computational results strongly indicated that the conformation in the "a" well is the only stable one in water for neocarrabiose 41-sulfate. This con formation is very similar to that reported by X-ray diffraction experiment for iota -carrageenan fiber, although the molecular size and the experiment al conditions are different between the two cases.