Relative energies of binding for antibody-carbohydrate-antigen complexes computed from free-energy simulations

Free-energy perturbation (FEP) simulations have been applied to a series of analogues of the natural trisaccharide epitope of Salmonella serotype B bo und to a fragment of the monoclonal anti-Salmonella antibody Se155-4. This system was selected in order to assess the ability of free-energy perturbat ion (FEP) simulations to predict carbohydrate-protein interaction energies. The ultimate goal is to use FEP simulations to aid in the design of synthe tic high affinity ligands for carbohydrate-binding 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 para meter 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. T he experimental binding affinities are all close in value, resulting in sma ll relative free energies of binding. Many of the Delta Delta G values are on the order of 0-1 kcal mol(-1), making their accurate calculation particu larly challenging. The simulations were shown to reasonably reproduce the k nown geometries of the ligands and the Ligand-protein complexes. A model fo r the conformational behavior of the unbound antigen is proposed that is co nsistent 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 ol igosaccharide-protein complex.