Voronoi binding site model of a polycyclic aromatic hydrocarbon binding protein

Abstract

A three-dimensional Voronoi binding site model has been formulated from a series of competitors for the binding site on a recently isolated polycyclic aromatic hydrocarbon binding protein (PBP) from mouse liver. The PBP binds polycyclic aromatic hydrocarbons, such as benzo[a]pyrene (B[a]P), with high affinity and shows other characteristics associated with receptor-ligand complexes. Altogether, the in vitro binding constant of seven molecules were used to deduce the geometry and the energetics of a possible site model consisting of five regions: one tetrahedron-shaped finite central hydrophobic pocket, one infinite region representing access to the solvent, and three strongly repulsive regions representing the sterically forbidden walls of the pocket. The model then predicted the binding energies correctly for nine additional competitors and suggests that competition of monoaromatic (benzene) derivatives with B[a]P would be weak.