Relative Energies of Binding for Antibody−Carbohydrate-Antigen Complexes Computed from Free-Energy Simulations

Abstract

Free-energy perturbation (FEP) simulations have been applied to a series of analogues of the natural trisaccharide epitope of Salmonella serotype B bound to a fragment of the monoclonal antiSalmonella antibody Se155-4. This system was selected in order to assess the ability of free-energy perturbation (FEP) simulations to predict carbohydrate-protein interaction energies. The ultimate goal is to use FEP simulations to aid in the design of synthetic high affinity ligands for carbohydratebinding proteins. The molecular dynamics (MD) simulations were performed in the explicit presence of water molecules, at room temperature. The AMBER force field, with the GLYCAM parameter set for oligosaccharides, was employed. In contrast to many modeling protocols, FEP simulations are capable of including the effects of entropy, arising from differential ligand flexibilities and solvation properties. The experimental binding affinities are all close in value, resulting in small relative free energies of binding. Many of the ΔΔG values are on the order of 0-1 kcal mol −1 , making their accurate calculation particularly challenging. The simulations were shown to reasonably reproduce the known geometries of the ligands and the ligand-protein complexes. A model for the conformational behavior of the unbound antigen is proposed that is consistent with the reported NMR data. The best agreement with experiment was obtained when histidine 97H was treated as fully protonated, for which the relative binding energies were predicted to well within 1 kcal mol −1 . To our knowledge this is the first report of FEP simulations applied to an oligosaccharide-protein complex.

Binding diversity of the two binding sites of ricin B lectin

“…Like the monosaccharide, the Gal terminal disaccharide Gal(1,4)Glc binds well in binding site 1. The average interaction energy of Gal(1,4)Glc is À97.71 kcal mol À1 and that of Glc (1,4)Gal is also À25.69 kcal mol À1 for binding site 1. The interaction energy of Glc (1,4)Gal is comparable with that of the monosaccharide glucose (À24.26 kcal mol À1 ), indicating that addition of a galactose residue at the second position does not improve the binding; however, addition of a glucose moiety at the second position after the terminal galactose [i.e., Gal(1,4)Glc] improves the binding affinity substantially, with the average interaction energy going up from *À69 to *À98 kcal mol À1 for galactose to lactose, respectively.…”

“…The other two replicas retained their ring conformation and showed favorable interaction energy. When Glc (1,4) Gal was placed in the first binding site, the disaccharide slowly drifted away from the binding site as the simulation progressed. The RMSD of the sugars as a function of time in both the binding sites are given in Figure 3(a,b).…”

“…The O3 of Gal residue of Gal(1,4)Glc is hydrogen bonded with the amide hydrogen of Lys40, and the HO4 of Gal residue of Gal (1,4)Glc is hydrogen bonded with Asp22. Similarly, the Glc residue of Glc (1,4) Gal forms H-bonds with Lys40 only through the O3 atom. However, neither of the second residues of these two disaccharides formed any direct H-bonds with the protein.…”

“…To compare the ligand potency and diversity toward the two binding sites, we have studied the binding of ricin with three different monosaccharides and two disaccharides. Solvated molecular dynamics simulation of RTB with galactose, fucose, and glucose in the two different binding sites as monosaccharides and Gal(1,4)Glc and Glc (1,4)Gal as the disaccharides have been performed. Thermodynamic integration (TI) 17 data for the relative binding affinities of galactose, fucose, and glucose towards the protein have been calculated.…”

Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity

“…Explicitly solvated MD simulations have been shown to reproduce the experimental structures of lectin-carbohydrate 26,27 and antibodycarbohydrate 28,29 complexes. Nevertheless, to establish the accuracy of the theoretical methods in the case of galectin-1, preliminary simulations were performed on the X-ray structure of the galectin-1-LacNAc complex.…”