Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces

Protein-DNA interactions play an essential role in the genetic activities of life. Many structures of protein-DNA complexes are already known, but the common rules on how and where proteins bind to DNA have not emerged. Many attempts have been made to predict protein-DNA interactions using structural information, but the success rate is still about 80%. We analyzed 63 protein-DNA complexes by focusing our attention on the shape of the molecular surface of the protein and DNA, along with the electrostatic potential on the surface, and constructed a new statistical evaluation function to make predictions of DNA interaction sites on protein molecular surfaces. The shape of the molecular surface was described by a combination of local and global average curvature, which are intended to describe the small convex and concave and the large-scale concave curvatures of the protein surface preferentially appearing at DNA-binding sites. Using these structural features, along with the electrostatic potential obtained by solving the Poisson-Boltzmann equation numerically, we have developed prediction schemes with 86% and 96% accuracy for DNA-binding and non-DNA-binding proteins, respectively.