Quantum mechanical model assembly study on the energetics of binding of arabinose, fucose, and galactose to L-arabinose-binding protein.

Binding energies of L-arabinose, D-fucose, and D-galactose to L-arabinose-binding protein was investigated theoretically. The calculated binding energies were composed of three contributions: 1) direct ligand-active site interaction energies calculated using static ab initio model assemblies; 2) solvation energies of the ligands; and 3) long-range electrostatic interaction energies between the ligands and the protein matrix. The calculated binding energies and the contributions of the energy components were used to analyze the experimental affinities of the ligands.