COMPUTATIONAL DESIGN AND EVALUATION OF NOVEL ENZYME CATALYSTS

新型酶催化剂的计算设计和评估

• 批准号: 8364203
• 负责人: KENDALL N HOUK
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364203
• 关键词: 3-hydroxybutanal; Active Sites; Biological Models; Biomedical Research; Catalytic Domain; Elasticity; Enzymes; Evaluation; Funding; Grant; High Performance Computing; Methods; National Center for Research Resources; Natural regeneration; Passive Immunization; Penetration; Principal Investigator; Procedures; Process; Production; Proteins; Protocols documentation; Quantum Mechanics; Reaction; Reporting; Research; Research Infrastructure; Resources; Solvents; Source; Structure; Time; United States National Institutes of Health; Water; catalyst; computing resources; cost; design; gene therapy; human tissue; molecular dynamics; next generation; novel

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination and the retro-aldol reaction. We studied these proteins together with a set of previously unpublished inactive designs in order to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechanics (QM) on truncated model systems to the treatment of the full protein with ONIOM QM/MM and AMBER molecular dynamics (MD) were explored. The most effective procedure involved explicit-solvent, periodic-boundary molecular dynamics, and a general MD protocol was established (see supporting information "Evaluation and Ranking of Enzyme Designs with Molecular Dynamics"). Substantial deviations from the ideal catalytic geometries were observed for a number of designs. Penetration of water into the catalytic site and insufficient residue-packing around the active site are the main factors that can cause enzyme designs to be inactive. Where in the past, computational evaluations of designed enzymes were too time-extensive for practical consideration, it has now become feasible to rank candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process. Employing computational resources from the DESRES Anton machine will be instrumental to further develop and refine our MD-assisted enzyme design protocol and to facilitate the production of next-generation catalysts for a plethora of useful applications that range from alternative fuels to regenerating human tissue elasticity to novel passive immunizations and gene therapy.

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的主要研究者可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 2008 年，据报道，一种成功的计算设计程序产生了用于 Kemp 消除和逆羟醛反应的活性酶催化剂。我们将这些蛋白质与一组先前未发表的非活性设计一起研究，以确定活性或缺乏活性的来源，并预测哪些设计的结构最有可能具有催化作用。探索了从截断模型系统上的量子力学 (QM) 到使用 ONIOM QM/MM 和 AMBER 分子动力学 (MD) 处理完整蛋白质的方法。最有效的程序涉及显式溶剂、周期边界分子动力学，并建立了通​​用MD方案（参见支持信息“分子动力学酶设计的评估和排名”）。在许多设计中观察到与理想催化几何形状的显着偏差。水渗透到催化位点和活性位点周围残留物填充不足是导致酶设计失活的主要因素。过去，设计酶的计算评估对于实际考虑而言过于耗时，现在可以在实验之前并结合实验对候选物进行计算排名，从而显着提高酶设计过程的效率。利用 DESRES Anton 机器的计算资源将有助于进一步开发和完善我们的 MD 辅助酶设计方案，并促进下一代催化剂的生产，这些催化剂适用于从替代燃料到再生人体组织弹性到新型被动免疫和基因治疗等众多有用应用。