ENZYME ACTIVE SITE TEMPLATES

酶活性位点模板

• 批准号: 8170507
• 负责人: PATRICIA CLEMENT BABBITT
• 金额: $ 1.79万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8170507
• 关键词: Active Sites; Architecture; Bioinformatics; Chimera organism; Computer Retrieval of Information on Scientific Projects Database; Computer software; Development; Diagnostic; Enzymes; Family; Funding; Goals; Grant; Institution; Methods; Proteins; Publishing; Research; Research Personnel; Resources; Source; Structure; United States National Institutes of Health; Work; base; enolase; haloacid dehalogenase; tool; web site

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Babbitt group has been a pioneer in identifying enzyme superfamilies, that is, groups of proteins that are distantly evolutionarily related and share nearly undetectable sequence similarity, but that share an architecture and certain aspects of their function. We are comparing structures and observables based on structure among and between families and superfamilies of proteins, with the goal of better understanding how sequence and structure are constrained. We are identifying 3D motifs or active site templates, spatial arrangements of small sets of residues that can be diagnostic of membership in a family or superfamily of proteins. Besides studying known superfamilies, we also wish to characterize sets of related proteins that have not already been well described. Chimera and other sequence and structure analysis tools available locally and on the RBVI web site are employed in this work. We collaborate with the Chimera development team as needed to further the research and facilitate the creation of useful research software. Our initial work on active site templates for the enolase and haloacid dehalogenase superfamilies has been published in Proteins (see below). More recently, our method to automatically discover 3D motifs shared among any group of related proteins has been published in Bioinformatics.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 中心，不一定是研究者的机构。 巴比特小组是鉴定酶超家族的先驱， 也就是说，在进化上有很远的相关性的蛋白质组 具有几乎无法检测到的序列相似性，但共享架构和功能的某些方面。 我们正在根据蛋白质家族和超家族之间的结构来比较结构和可观测值，目的是更好地了解序列和结构是如何受到限制的。 我们正在识别 3D 基序或活性位点模板、一小组残基的空间排列，这些残基可以诊断蛋白质家族或超家族的成员资格。 除了研究已知的超家族之外，我们还希望表征尚未得到充分描述的相关蛋白质组。 这项工作采用了 Chimera 以及本地和 RBVI 网站上提供的其他序列和结构分析工具。 我们根据需要与 Chimera 开发团队合作，以进一步研究并促进有用的研究软件的创建。 我们对烯醇酶和卤酸活性位点模板的初步工作 脱卤酶超家族已发表在《蛋白质》杂志上（见下文）。最近，我们自动发现任何相关蛋白质组之间共享的 3D 基序的方法已在《生物信息学》上发表。