Extended binding site of ricin B lectin for oligosaccharide recognition

The plant lectin ricin B chain binds oligosaccharide with more affinity than the mono‐ or disaccharide ligands. The experiments indicated that a biantennary oligosaccharide could bind itself to any of the crystallographically established 1st or 2nd binding sites. After manual docking of either terminal galactose residues of the oligosaccharide in the 1st and 2nd binding sites of Ricin B and simulating the systems over nanosecond trajectories in implicit solvent, it was observed that the protein bound the oligosaccharide strongly through both its 1st and 2nd binding sites. Not only were the terminal galactose residues, several other residues of the oligosaccharide were involved in the binding scheme. Average gas phase energies were calculated molecular mechanically, solvation energies were calculated by Generalized Born model and the normal mode analysis was used to calculate the entropic contribution of binding. The entropy/enthalpy compensation has been observed for the protein–oligosaccharide interactions. The binding was found to be enthalpically favorable and compensating for the unfavorable entropic contribution. Comparison of the calculated free energy with the experimental data clearly suggests that binding is mono‐dentate rather than bi‐dentate through a single Gal‐containing antenna. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 311–320, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com