Molecular dynamics simulations of carrabiose

Molecular mechanics calculations have been performed for the disaccharide carrabiose, one of the repeat units of beta-carrageenan, as a general model for the (1-->4)-linkage in the carrageenans. An adiabatic conformational energy map for this unsulfated molecule was prepared by constrained energy minimization and compared to a previously reported rigid-residue energy map for the sulfated molecule and to a similar adiabatic map for neocarrabiose, the related (1-->3)-linked dimer repeat unit of beta-carrageenan. Molecular dynamics simulations of this molecule in vacuo and in an aqueous (TIP3P) solution were calculated, and the observed motions were found to be generally consistent with the vacuum adiabatic energy map. Unlike the case observed in previous simulations of neocarrabiose, little solvation shift in the molecular conformation was observed for carrabiose. From the dynamics, the linkage was observed to be relatively flexible, as has been inferred from experiment on sulfated carrageenan polymers. (C) 1997 John Wiley & Sons, Inc.