MOLECULAR MECHANICS AND DYNAMICS SIMULATI ON ON THE CONFORMATION OF DIMER UNITS OF CARRAGEENAN IN WATER

Molecular conformation of the repeating units of kappa-carrageenan was investigated as the first step to clarify the solution conformation o f carrageenan and the related polysaccharides by using the simulation methods of the molecular mechanics and molecular dynamics. The repeati ng units of kappa-carrageenan consist of the 4,1 linked and 1,3 linked dimers of the 3,6-anhydro alpha-D-galactose and beta-D-galactose-4-su lphate. Potential energy maps for both 4,1 and 1,3 linked dimers were obtained as a function of the dihedral angles for their glycosil linka ges. The energy map for the 1,3 linked dimer was found to have large m inimum area, where the dihedral angles of the glycosil linkage can flu ctuate easily at room temperature. When the sulphate group was removed from the 1,3 linked dimer, the above area was limited to around the ( phi = 171, phi = 188). This area corresponds to the one for the double helical conformation of carrageenan obtained from X-ray diffraction e xperiment. From the analysis of the molecular dynamics simulation of t he dimer units with surrounding water molecules, a bridge of the hydro gen bonds which include a water molecule between pyranose rings of the 1,3 linked dimer was found. This may play an important role in the st ability of a conformation in water.