Protein Dynamics in Enzymatic Catalysis

描述（由申请人提供）：该项目名为“酶催化中的蛋白质动力学”，其​​目标是研究酶中的原子运动。我们建议研究蛋白质的动态性质如何影响酶的功能以及从酶底物到酶上过渡态形成的酶的能量景观的概念。我们汇集了一支具有不同背景的熟练研究小组，旨在了解酶的功能。重要的是，我们采用独特、先进、有效的实验和理论方法，对从皮秒到分钟的多个时间尺度上蛋白质结构的演化敏感。有四个项目和两个核心。项目 1：“在广泛的时间尺度上研究 LDH 中的能量景观编码功能”将 (1) 探究从皮秒到毫秒的构象运动如何促进乳酸脱氢酶中过渡态的形成，以及不同时间尺度上的运动如何相互关联；(2) 探究促进振动对酶催化的贡献。项目 2：“嘌呤核苷磷酸化酶的动力学和过渡态”研究 (1) 导致 PNP 中过渡态形成的运动，以及 (2) 通过定位和表征动态促进振动以及生成振动改变的酶（其局部和集体键动力学改变达到过渡态的概率），PNP 中过渡态的性质。项目 3：“绘制 DHFR 催化的能量图谱”旨在 (1) 确定二氢叶酸还原酶中底物结合和米氏复合物形成的动力学以及耦合蛋白质运动； (2)确定DHFR中质子转移的动力学； (3)确定振动在DHFR催化反应中的促进作用。项目4：“酶催化中的能量景观和运动时间尺度”研究多个时间尺度上酶的动力学，并通过以下方式为其他项目提供理论支持：（1）研究较长时间的构象运动如何对酶功能做出贡献，以及在原子细节上，不同时间尺度的运动如何相互关联； (2) 确定蛋白质结构如何导致酶中的振动能量“通道”，并研究突变如何影响这种结构； (3)阐明过渡态紧束缚的概念，并展示在特定反应中如何接近和过渡过渡态。设备核心（核心 A）支持该计划的专用综合仪器套件。行政核心（核心 B）管理计划项目。 公众健康相关性：酶是多种药物的靶标。人们对蛋白质中的原子运动如何引起酶催化作用知之甚少。酶过渡态的详细结构是药物设计的强大目标，增加对酶如何形成这种状态的了解对于所有催化剂，特别是设计新类别的药物来说是基础。

DESCRIPTION (provided by applicant): The goal of this Program Project, entitled Protein Dynamics in Enzymatic Catalysis, is to study atomic motion in enzymes. We propose to study concepts of how the dynamical nature of proteins affects enzymic function and the energy landscape of enzymes from enzyme-substrate to on-enzyme transition state transition state formation. We bring together a skilled research group of diverse backgrounds all aimed at understanding enzyme function. Importantly, we bring to bear unique, advanced, and effective experimental and theoretical approaches sensitive to the evolution of protein structure on multiple time scales, from ps to minutes. There are four projects and two cores. Project 1: 'Energy Landscapes Encoding Function in LDH Investigated Over Broad Time Scales' will (1) probe how conformational motion from picoseconds to milliseconds contributes transition state formation in lactate dehydrogenase and how motions on different timescales are related to each other and (2) probe the contribution of promoting vibrations to enzymic catalysis. Project 2: 'Dynamics and the Transition State of Purine Nucleoside Phosphorylase' studies (1) the motions leading to transition state formation in PNP and (2) the nature of the transition state in PNP by locating and characterizing dynamic promoting vibrations and by generating a vibrationally altered enzyme whose local and collective bond dynamics alter the probability of reaching the transition state. Project 3: 'Mapping the Energy Landscape of Catalysis in DHFR' aims to (1) determine the dynamics of substrate binding and Michaelis complex formation and coupled protein motions in dihydrofolate reductase; (2) determine the dynamics of proton transfer in DHFR; and (3) determine the role of promoting vibrations in the catalytic reaction of DHFR. Project 4: 'Energy Landscapes and Motional Timescales in Enzyme Catalysis' investigates dynamics in enzymes on multiple time scales and provides theoretical support to the other projects by (1) investigating how longer time conformational motion contributes to enzyme function, and in atomic detail, how motions at different timescales are related to each other; (2) determining how protein architecture results in vibrational energy "channeling" in enzymes and study how mutation effects this architecture; and (3) elucidating the concept of the tight binding of the transition state and show how, in a specific reaction, the transition state is approached and transited. The Equipment Core (Core A) supports the specialized comprehensive suite of instrumentation for the Program. The Administrative Core (Core B) administers the Program Project. PUBLIC HEALTH RELEVANCE: Enzymes are targets for a broad array of Pharmaceuticals. How atomic motion in proteins brings about enzymatic catalysis is very poorly understood. The detailed structure of the enzymatic transition state is a powerful target for drug design, and increased knowledge of how enzymes form this state is fundamental for all catalysts and specifically for designing new classes of drugs.