title: The effect of hydration upon the conformation and dynamics of neocarrabiose, a repeat unit of beta-carrageenan.
abstract: Molecular mechanics calculations have been performed for the disaccharide neocarrabiose, one of the repeat units of beta-carrageenan, as a general model for the (1-->3)-linkage in the carrageenans. An adiabatic conformational energy map for this molecule has been prepared by constrained energy minimization and compared to previously reported relaxed maps. Neither the experimentally determined crystal structure of neocarrabiose nor the fiber diffraction conformation of iota-carrageenan is a low energy conformation on the relaxed Ramachandran map. Molecular dynamics simulations in vacuum produced trajectories consistent with this relaxed vacuum surface. However, a simulation with explicitly included solvent water molecules produced a trajectory that remained in the region of the two experimental structures. This dramatic solvation effect is apparently the result of the breaking of an interring hydrogen bond between the O2 hydroxyl groups of neocarrabiose as both groups hydrogen bond to solvent.
authors.affiliation: Department of Chemistry, Hiroshima University, Higashi-Hiroshima, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Ueda
authors.forename: J W
authors.initials: JW
authors.lastname: Brady
mesh_terms: D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D002351:Carrageenan / Q000737:chemistry*; D006878:Hydroxides / Q000378:metabolism; D008969:Molecular Sequence Data
chemical_list: D006878:Hydroxides; C068279:neocarrabiose; D002351:Carrageenan