Three-dimensional structure of oligosaccharides from molecular dynamics simulations

Detta är en avhandling från Stockholm : Stockholm University

Sammanfattning: This thesis focuses on the conformation and flexibility of oligosaccharides around the glycosidic linkage. The methods employed for the elucidation of the three-dimensional structures of biomolecules are briefly described. The main techniques used here are computer simulations and molecular dynamics simulations in aqueous solution in particular. The experimental data derived from these simulations have been compared with nuclear magnetic resonance measurements. The results obtained demonstrate the occurrence of more than one conformation, even though at the same time the high value of the generalised order parameter indicates rigidity. Of special interest are the folded conformers discovered at the same linkage in a vicinally substituted trisaccharide dissolved in water. Such, folded conformers have been detected in carbohydrates earlier, but never at the same linkage.The free energy simulation methods thermodynamic perturbation and thermodynamic integration are described briefly and have been used to calculate the anomeric ratio of the monosaccharides D-xylose in water and methyl D-xyloside in methanol. Solvent effect of the a/b ratios were found to be small. The solvent structures surrounding these four monosaccharides were investigated utilising radial and spatial distribution functions.

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