Computer simulation studies of the solvation of oligosaccharides

Abstract

Computer simulations of the hydration of the tetrasaccharide αLFuc(1 → 2)βDGal(1 → 3) αLFuc(1 → 4) βDGlcNAc-OMe and one of its deoxy derivatives were carried out as a first step toward an understanding of the role of water in the recognition of oligosaccharides by proteins. The model consisted of one solute molecule in one of its low-energy conformations, surrounded by 250 water molecules. The solute–water and water–water interaction energies were evaluated with Clementi's potentials. Ensemble states for the derivation of average properties were generated by Monte Carlo methods. As expected, the strength of interaction between water and the amphiphilic solute was found to be considerably greater at hydrophilic than at hydrophobic sites. Furthermore, the average distance between the solvation shell and the solute surface was about 1 Å greater near hydrophobic than around hydrophilic groups. There is also a definitive alignment of the water dipole around the hydroxyl groups of the saccharide, which is not evident over the hydrophobic regions. Finally, in a parallel investigation the tetrasaccharides were solvated by adding water to the solute at sites of minimum energy of association, in order to explore less-CPU-time-consuming alternatives to Monte Carlo simulations. While the patterns of interaction energies, distances, and dipole orientations were found to be similar to Monte Carlo results, the time savings were not as significant as hoped. Keywords: Monte Carlo simulations, numerical solvation studies, solvation simulations of oligosaccharides, molecular recognition, carbohydrate solvation.