Abstract
The hydration behaviour of two Lewis carbohydrate determinants, Lewis X (Lex) (1a) and Lewis Y (Ley) (1b), have been investigated by a comparative 20 ns molecular dynamics (MD) study. The detailed hydration of the two oligosaccharides was described using the AMBER-based GLYCAM04 force field which is developed specifically for modelling carbohydrates. In comparison with previous in vacuo MD simulations and high resolution NMR studies, the solvated structures have shown to be dynamically stable and equally rigid with regards to glycosidic linkage torsion angles. Comparisons have also been made between the solvated structures and crystal structures currently available, namely the Lex dimer crystal, the crystal structure of Lex complex with the 291-2G3-A-Fab antibody; and the crystal structures of Ley complexed with the hu3S193 and CBR96 antibodies. When the solvated structures and respective crystal structures were overlaid for comparison the only significant difference was the Galp(3)-O5-C5-C6-O6 and the GlcpNAc(2)-O5-C5-O6-C6 orientations. The hydration sphere was investigated using a radial pair distribution function. Several solute heteroatoms were identified for the occurrence of bridging events where a solute heteroatom is linked to (at least) one other via a solvent molecule.
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