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

用于分析酶结合位点的计算工具和数据库

• 批准号: 0213832
• 负责人: Sandor Vajda
• 金额: --
• 依托单位: Trustees of Boston University
• 依托单位国家: 美国
• 项目类别: Continuing grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-08-15 至 2006-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0213832&HistoricalAwards=false
• 关键词: Computational; Tools; Database; Analysis; Binding

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.

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位点。配体/底物结合位点的表征为许多应用提供了基础，包括用于生化和信号转导途径分析的抑制剂的设计、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信息的主要来源是与各种配体（底物、辅因子、抑制剂、产物和过渡态类似物）共结晶的酶（或其同系物）的结构。虽然目前在蛋白质数据库中有超过70%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大量的努力。该提案的目标是开发一个计算资源和数据库，称为酶中的预测和共识相互作用位点（PRECISE），它将为从所有相关结构中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有结合位点，该位点是通过比对所有同源序列、识别对任何配体结合重要的残基位置并评估这些位置上氨基酸的作用而获得的。一个动态的检索系统将有助于检查个人的相互作用，并产生各种统计数据。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。此类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。提交的数据将存储在一个单独的表中，并向数据库中添加一个预测的交互组件。该数据库还将包含将计算溶剂映射（一种新的结合位点预测方法）应用于大量表征良好的酶的结果。该方法移动分子探针-小有机分子或功能基团-在蛋白质表面上，以确定结合最高数量的不同探针的位置。结果表明，这种共识结合发生在酶结合位点的主要亚位点，与探针相互作用的氨基酸残基也结合酶的特异性配体。因此，计算溶剂映射可用于酶结合位点的鉴定和表征。除了提供一组充分表征的酶的溶剂图谱结果外，还将建立一个电子邮件服务器，以便可以请求任何酶的溶剂图谱计算。预计PRECISE网站将成为酶结合位点信息的中央储存库，由于溶剂绘图网络服务器，将对酶学研究产生重大影响，并为生物化学和分子生物学研究提供重要的教育资源。