Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs)

Li, H.*; Sakuraba, Shun; Chandrasekaran, A.*; Yang, L.-W.*

We provide evidence supporting that protein-protein and protein-ligand docking poses are functions of protein shape and intrinsic dynamics. Over sets of 68 protein-protein complexes and 240 non-homologous enzymes, we recognize common predispositions for binding sites to have minimal vibrations and angular momenta while two interacting proteins orient so as to maximize the angle between their rotation/bending axes (). The findings are then used to define quantitative criteria to filter out docking decoys less likely to be the near-native poses, hence the chances to find near-native hits can be doubled. With the novel approach to partition a protein into `domains' of robust but disparate intrinsic dynamics, 90% of catalytic residues in enzymes can be found within the first 50% of the residues closest to the interface of these dynamics domains. The results suggest an anisotropic rather than isotropic distribution of catalytic residues near the mass centers of enzymes.