Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

Kengo Kinoshita, Haruki Nakamura

Research output: Contribution to journalArticlepeer-review

134 Citations (Scopus)

Abstract

The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.

Original languageEnglish
Pages (from-to)1589-1595
Number of pages7
JournalProtein Science
Volume12
Issue number8
DOIs
Publication statusPublished - 2003 Aug 1
Externally publishedYes

Keywords

  • Clique search algorithm
  • Electrostatic potential
  • Molecular surface
  • Protein function prediction
  • Three-dimensional structure

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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