Coupling between conformation and chemistry in enzymes

酶的构象与化学之间的耦合

基本信息

批准号：
7579119
负责人：
Qiang Cui
金额：
$ 18.93万
依托单位：
UNIVERSITY OF WISCONSIN-MADISON
依托单位国家：
美国
项目类别：
财政年份：
2005
资助国家：
美国
起止时间：
2005-03-01 至 2010-08-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7579119
关键词：
ATPase Domain Actins Active Sites Adenosine Triphosphate Amino Acids Arts Binding Biochemical Biological Process Biophysics Cardiomyopathies Chemicals Chemistry Collaborations Complement Computing Methodologies Coupled Coupling Data Dependence Discipline Disease Electrostatics Enzymatic Biochemistry Enzymes Free Energy Functional disorder Future Goals Hand Hybrids Hydrolysis Kinetics Letters Methods Microscopic Molecular Molecular Conformation Molecular Motors Motor Muscle Contraction Mutagenesis Myosin ATPase Myosin Type II Nucleotides Play Positioning Attribute Process Property Proteins Research Research Personnel Resolution Role Signal Transduction Site Structure System Techniques Testing Theoretical Studies Theoretical model Universities Vesicle Water Work cell motility conformational conversion design insight molecular dynamics mutant nucleotide analog research study simulation trafficking

项目摘要

DESCRIPTION (provided by applicant): Myosin is a superfamily of prototypical molecular motors that play important roles in diverse biological processes ranging from vesicle trafficking, cell motility to muscle contractions and signal transductions. Although the functional cycle of myosins is understood in an out-line form, many detailed questions remain concerning the coupling between conformational properties of the motor domain and the ATPase activity. We hypothesize that conformational transitions in myosin gate ATP hydrolysis through regulating not only positions of specific amino acids in the active site but also the orientation and dynamics of water molecules surrounding the hydrolysis site. To verify and consolidate such a hypothesis, state-of-the-art molecular simulations are proposed to analyze the mechanism of ATP hydrolysis in different conformational states of the myosin II motor domain and relevant mutants; the simulations include classical molecular dynamics and combined QM/MM methods. The specific aims are: (1) Determine the catalytic mechanism of ATP hydrolysis in the closed state of the motor domain. (2) Determine if ATP hydrolysis is prohibited in the open state of the motor domain, and if so, identify key differences between the open and closed conformations that dictate the hydrolysis energetics. (3) Explain, in energetical and mechanistic terms, the roles of active site residues, which have been shown by mutagenesis studies to have various effects on ATP hydrolysis and motility. Myosin-ll was chosen because it is the only motor system that has high-resolution structures for multiple conformational states, and computational results can be compared with a large body of biochemical and biophysical data. The proposed simulation study will provide a framework for bridging experimental data from different disciplines to establish sensible theoretical models for mechanochemical coupling in myosin and other molecular motors; the microscopic insights will have a profound impact on our ability to design strategies to treating serious diseases caused by myosin dysfunction such as cardiomyopathy. The simulation work will be closely coupled to experimental studies through collaborations; the combination of structural, kinetic and motility data will provide the experimental tests necessary to verify and refine simulation techniques, which is of tremendous value to the field of computational enzymology.

描述（由申请人提供）：肌球蛋白是典型分子马达的超家族，在从囊泡运输、细胞运动到肌肉收缩和信号转导的多种生物过程中发挥重要作用。尽管肌球蛋白的功能循环已被大致了解，但关于运动结构域的构象特性与 ATP 酶活性之间的耦合仍然存在许多详细问题。我们假设肌球蛋白中的构象转变不仅通过调节活性位点中特定氨基酸的位置，而且还通过调节水解位点周围水分子的方向和动力学来控制 ATP 水解。为了验证和巩固这一假设，提出了最先进的分子模拟来分析肌球蛋白 II 运动结构域和相关突变体不同构象状态下 ATP 水解的机制；模拟包括经典分子动力学和组合的 QM/MM 方法。具体目标是：（1）确定运动域关闭状态下ATP水解的催化机制。 (2) 确定在运动域的开放状态下 ATP 水解是否被禁止，如果是，则确定决定水解能量的开放构象和闭合构象之间的关键差异。 (3) 从能量和机制方面解释活性位点残基的作用，诱变研究表明活性位点残基对 ATP 水解和运动具有多种影响。选择肌球蛋白-II 是因为它是唯一具有多种构象状态高分辨率结构的运动系统，并且计算结果可以与大量生化和生物物理数据进行比较。拟议的模拟研究将为桥接不同学科的实验数据提供一个框架，为肌球蛋白和其他分子马达的机械化学耦合建立合理的理论模型；微观见解将对我们设计治疗由肌球蛋白功能障碍引起的严重疾病（例如心肌病）的策略的能力产生深远影响。模拟工作将通过合作与实验研究紧密结合；结构、动力学和运动性数据的结合将为验证和完善模拟技术提供必要的实验测试，这对计算酶学领域具有巨大的价值。