Two Rules on the Protein-Ligand Interaction

Abstract

So far, we still lack a clear molecular mechanism to explain the protein-ligand interaction on the basis of electronic structure of a protein. By combining the calculation of the full electronic structure of a protein along with its hydrophobic pocket and the perturbation theory, we found out two rules on the protein-ligand interaction. One rule is the interaction only occurs between the lowest unoccupied molecular orbitals (LUMOs) of a protein and the highest occupied molecular orbital (HOMO) of its ligand, not between the HOMOs of a protein and the LUMO of its ligand. The other rule is only those residues or atoms located both on the LUMOs of a protein and in a surface pocket of a protein are activity residues or activity atoms of the protein and the corresponding pocket is the ligand binding site. These two rules are derived from the characteristics of energy levels of a protein and might be an important criterion of drug design.