MOLECULAR-DYNAMICS SIMULATION OF A DOUBLE-HELICAL BETA-CARRAGEENAN HEXAMER FRAGMENT IN WATER

Molecular dynamics simulations were conducted of two hexasaccharide st rands of beta-carrageenan in aqueous (TIP3P) solution in the double-he lical conformation proposed for iota-carrageenan from fiber diffractio n experiments. A similar simulation was performed for the complex in v acuum as a theoretical control. In the vacuum simulation the individua l chains made conformational transitions, but the complex remained a d ouble helix overall, apparently owing to the persistence of the stabil izing interchain hydrogen bonds. In the solution simulations, however, these interchain hydrogen bonds did not persist, but rather exchanged for hydrogen bonds to solvent, and possibly as a result, the double h elix was observed to begin to unravel. However, the individual glycosi dic linkages in the separate strands appear to be more stable in the f iber diffraction conformation in solution than in the vacuum simulatio n, suggesting that the polysaccharide exists in solution as a single h elix with approximately the same conformation as previously proposed f or these chains in the double helix.