title: Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces.
abstract: 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.
authors.affiliation: Institute for Protein Research, Osaka University, Osaka, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Tsuchiya
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D036262:Empirical Research; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D015203:Reproducibility of Results; D055672:Static Electricity
chemical_list: D004268:DNA-Binding Proteins