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 anti-Salmonella 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 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 parameter set for oligosaccharides, was employed. In contrast to many modeling protocols, FEP simulations are capable of includin

SUBMITTER: Pathiaseril A 

PROVIDER: S-EPMC1764640 | biostudies-literature | 2000 Jan

REPOSITORIES: biostudies-literature