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

Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura

Research output: Contribution to journalArticlepeer-review

82 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)885-894
Number of pages10
JournalProteins: Structure, Function and Genetics
Volume55
Issue number4
DOIs
Publication statusPublished - 2004 Apr 1
Externally publishedYes

Keywords

  • Computational method
  • Connolly surface
  • Poisson-Boltzmann equation
  • Protein function prediction
  • Protein informatics
  • Statistical potential
  • Three-dimensional structure

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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