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.Keywords: Protein function prediction; three-dimensional structure; molecular surface; electrostatic potential; clique search algorithm With the progress of genome projects, more than 60 genomic sequences have already been provided. However, large fractions of the gene products have not been annotated, and even when annotations were assumed, not all of them might be reliable due to the inherent ambiguity in functional inference using conventional methods based mainly on sequence homology ( The protein function is considered to have two different aspects: a biological function and a biochemical function.From the viewpoint of molecular biology, the former function could be described in terms of protein-protein interactions, whereas the latter should be directly related to each protein structure. Our goal in the present study was to develop a reliable method to predict the biochemical functions of proteins from their three-dimensional (3D) structures.Our approach is to search for similar substructures of known proteins against hypothetical proteins. Currently, it is well known that fold-level similarity can give us only a limited amount of information regarding the hypothetical proteins' function (Thornton et al. 2000;Todd et al. 2002). Thus, our method should be able to detect the similarities among proteins that have different folds. For that purpose, we focused our attention on the local structures of the functional sites in proteins.In particular, we describe the protein structure based on the molecular surfaces of the proteins and the electrostatic potential on the surface, in order to discriminate the physicochemical differences in the local surface.

Comparison of protein active site structures for functional annotation of proteins and drug design

“…[14][15][16][17][18][19]58 Like CPASS, these approaches are using information about the protein's active site to make a correlation with a known protein and assign a function to the unknown protein. Nevertheless, the application and details of the CPASS approach are fundamentally distinct from these other methods.…”

“…This is typically accomplished by developing structural descriptors of active sites for defi ned protein functional classes and then fi tting these structural templates to novel folds to identify putative active sites and annotate the hypothetical proteins. A variety of approaches are being applied that include aligning structures to match a few consensus or enzymatic catalytic residues, [14][15][16][17][18][19][20][21][22][23] identifi cation of cavities consistent with shapes of known ligands, 24 a sequence independent force fi eld to extract common active site features, 25 theoretical prediction of titration curves, 26 using chemical properties and electrostatic potentials of amino acid residues consistent with active site characteristics, 27,28 neural network analysis of spatial clustering of residues, 29 and conserved residues from multiple sequence alignments (phylogenetic motifs). 20,30 Nevertheless, direct experimental observation of protein-ligand interactions are a more reliable mechanism for the proper and accurate identifi cation of protein active sites.…”

Protein structure prediction on the Web: a case study using the Phyre server

“…We use the eF Site database 22 as a source of such information and highlight identities and conservative mutations between query and template residues that form known binding sites. In addition, it has been known for some time that the active site of a protein is frequently found within large clefts or pockets in the protein 23 .…”

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

“…Much of this work includes identification of functionally-relevant residues in biomolecules by looking at electrostatic destabilization of conserved residues [18], highly shifted pK a values [44], clusters of charged residues [59], protein-membrane interactions [40], and other structural characteristics [55]. Other research has focused on comparisons of electrostatic potentials including global analyses of the biomolecular structure [38,9,40,51,37,30,36,47,43,8,53,34,46,35,52] both in threedimensional space over the entire biomolecular structure and at localized regions such as active sites [52,6,22]. While the past characterization of electrostatic properties of biomolecules has provided insight into a variety of biomolecular properties, previous applications focused only on a few quantitative measures of electrostatic properties and, with a few exceptions [8,57], limited their studies to relatively small numbers of biomolecules.…”