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

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.