Structural fluctuation of methyl N,N'-diacetyl-beta-D-chitobioside in vacuo and in aqueous solution: molecular dynamics simulations and proton NMR spectroscopy.
Molecular dynamics (MD) simulations of methyl N,N'-diacetyl-beta-D-chitobioside (GlcNAc beta-(1-->4)GlcNAc beta-OMe) have been performed both in vacuo and in aqueous solution with the explicit inclusion of the solvent water molecules. The beta-(1-->4) glycosidic linkage fluctuates considerably, over a range of +/- 10 degrees, in each of the MD simulations in vacuo and in aqueous solution. The intra- and inter-residue hydrogen bonds in vacuo are replaced by intermolecular hydrogen bonds with the solvent water molecules in aqueous solution. Multiple conformations (gg and gt) exist for the exocyclic hydroxymethyl groups. The results of the MD simulations are compared with those of 1H-1H nuclear Overhauser effect measurements.
Aida
M
M
Biophysics Division, National Cancer Center Research Institute, Tokyo, Japan.
Sugawara
Y
Y
Oikawa
S
S
Umemoto
K
K
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012984:Software; D012996:Solutions; D012997:Solvents; D013997:Time Factors
D004187:Disaccharides; D012996:Solutions; D012997:Solvents; C016570:O-methyl-di-N-acetyl beta-chitobioside