Computational Tools and A Database for the Analysis of Binding Sites in Enzymes

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A major challenge in structural genomics is the elucidation of enzyme active sites from molecular structure. The characterization of the ligand/substrate binding site provides the basis for a number of applications, including the design of inhibitors for the analysis of biochemical and signal transduction pathways, drug design, and protein engineering aimed at altered specificity or catalytic activity. The primary sources of information on specific molecular interactions are the structures of the enzyme (or its homologues) co-crystallized with various ligands (substrates, cofactors, inhibitors, products, and transition state analogs). Although such structures are available for over 70% of the enzymes currently in the Protein Data Bank, collecting all binding site information for a particular protein requires substantial efforts. The goal of this proposal is to develop a computational resource and database, called Predicted and Consensus Interaction Sites in Enzymes (PRECISE), which will provide query and visualization tools for the comparative analyses of the interactions extracted from all relevant structures. For each enzyme, the web-based analysis tool will determine the consensus binding site, obtained by aligning all homologous sequences, identifying the residue positions that are important for the binding of any ligand, and assessing the roles of amino acids at these positions. A dynamic retrieval system will help to examine individual interactions, and to generate various statistics. In addition to the interaction extracted from enzyme structures, the database will also store putative interactions, based on mutation studies or theoretical predictions. Such interactions can be submitted to the website and checked for consistency with all the interactions extracted from structural data. The submissions will be stored in a separate table, adding a predicted interaction component to the database. The database will also house the results of applying computational solvent mapping, a novel binding site prediction method, to a large set of well-characterized enzymes. The method moves molecular probes - small organic molecules or functional groups - on the protein surface in order to identify the positions that bind the highest number of different probes. It was shown that such consensus binding occurs at major subsites of the enzyme binding site, and the amino acid residues that interact with the probes also bind the specific ligands of the enzyme. Thus, computational solvent mapping can be used for the identification and characterization of enzyme binding sites. In addition to providing solvent mapping results for a set of well-characterized enzymes, an e-mail server will be set up, so that solvent mapping calculations can be requested for any enzyme. It is expected that the PRECISE website will become a central depository of enzyme binding site information, will have a major impact on enzymology research due to the solvent mapping web-server, as well as provide an important educational resource for studies in biochemistry and molecular biology.