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

结构基因组学的一个主要挑战是从分子结构中阐明酶的活性部位。配体/底物结合位点的表征为许多应用提供了基础，包括用于分析生化和信号转导途径的抑制剂的设计、药物设计和旨在改变特异性或催化活性的蛋白质工程。关于特定分子相互作用的主要信息来源是酶(或其同系物)与各种配体(底物、辅因子、抑制剂、产物和过渡态类似物)共结晶的结构。虽然目前蛋白质数据库中70%以上的酶都有这样的结构，但收集特定蛋白质的所有结合位点信息需要付出大量的努力。这项提议的目标是开发一个计算资源和数据库，称为酶的预测和共识相互作用位点(PRECISE)，它将为从所有相关结构提取的相互作用的比较分析提供查询和可视化工具。对于每种酶，基于网络的分析工具将确定共识结合位点，通过比对所有同源序列，识别对任何配体的结合重要的残基位置，并评估这些位置上的氨基酸的作用。动态检索系统将有助于检查个人互动，并生成各种统计数据。除了从酶结构中提取的相互作用外，数据库还将存储基于突变研究或理论预测的假定相互作用。这样的交互可以提交到网站，并检查与从结构数据中提取的所有交互的一致性。提交将存储在单独的表中，将预测的交互组件添加到数据库中。该数据库还将存储将计算溶剂映射(一种新的结合位点预测方法)应用于一大组特征良好的酶的结果。该方法在蛋白质表面移动分子探针--小的有机分子或官能团--以识别与最多不同探针结合的位置。结果表明，这种共识结合发生在酶结合位点的主要亚基上，与探针相互作用的氨基酸残基也与酶的特定配体结合。因此，计算溶剂映射可用于鉴定和表征酶结合位点。除了提供一组具有良好特性的酶的溶剂映射结果外，还将建立一个电子邮件服务器，以便可以请求对任何酶进行溶剂映射计算。预计Precision网站将成为酶结合位点信息的中央储存库，并将因溶剂图谱网络服务器而对酶学研究产生重大影响，并为生物化学和分子生物学的研究提供重要的教育资源。

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.