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Journal of Physical Chemistry B, Vol.105, No.36, 8629-8638, 2001
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 building block Of K-carrageenan, was investigated by a combination of molecular dynamics simulations and H-1 NMR experiments. The calculated Ramachandran-type potential energy map for the glycosidic torsion angles phi and psi of this dimer showed that there are two principal minimum-energy conformations, designated 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 trajectories started from each minimum position stayed within their respective wells throughout the time courses of the simulations. However, analysis of the hydration water around the , molecule indicated that the stability of the molecular 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 conformation is very similar to that reported by X-ray diffraction experiment for iota -carrageenan fiber, although the molecular size and the experimental conditions are different between the two cases.