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 We studied these proteins together with a set of previously unpublished inactive designs in order to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be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.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 在2008年，据报道，成功的计算设计程序产生了活跃的酶催化剂，以消除kemp和恢复反应。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，以确定活动的来源或缺乏活性，并预测哪种设计结构最有可能是催化性的。探索了从截短模型系统上的量子力学（QM）到使用ONIOM QM/mm和琥珀分子动力学（MD）处理完整蛋白质的方法。建立了最有效的程序，涉及明确溶剂，周期性的分子动力学和一般MD方案（请参阅支持信息“使用分子动力学的酶设计评估和排名”）。对于许多设计，观察到与理想催化几何形状的实质性偏差。将水渗透到催化位点，而在活性部位周围的残留物包装不足是可能导致酶设计不活跃的主要因素。在过去的情况下，对设计酶的计算评估对于实际考虑而言太时了，现在可以在候选人进行计算之前和与实验结合进行计算，从而显着提高了酶设计过程的效率。从Desres Anton机器中使用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，以实现多种有用的应用，范围从替代燃料到重生的人类组织弹性到新的被动免疫免疫和基因治疗。