Molecular Dynamics Simulation of a Double-Helical β-Carrageenan Hexamer Fragment in Water

Abstract

Molecular dynamics simulations were conducted of two hexasaccharide strands of β-carrageenan in aqueous (TIP3P) solution in the double-helical conformation proposed for ι-carrageenan from fiber diffraction experiments. A similar simulation was performed for the complex in vacuum as a theoretical control. In the vacuum simulation the individual chains made conformational transitions, but the complex remained a double helix overall, apparently owing to the persistence of the stabilizing 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 helix was observed to begin to unravel. However, the individual glycosidic linkages in the separate strands appear to be more stable in the fiber diffraction conformation in solution than in the vacuum simulation, suggesting that the polysaccharide exists in solution as a single helix with approximately the same conformation ...