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）：肌球蛋白是原型分子电动机的超家族，在从囊泡运输，细胞运动到肌肉收缩到信号转导的各种生物学过程中起着重要作用。尽管以外线形式理解了肌球蛋白的功能周期，但许多详细的问题仍然涉及运动域的构象性能与ATPase活性之间的耦合。我们假设肌球蛋白栅极ATP水解中的构象过渡不仅通过调节活性位点中特定氨基酸的位置，还可以调节特定氨基酸的位置，还可以调节水解位点周围的水分子的方向和动力学。为了验证和巩固这种假设，提出了最先进的分子模拟来分析在肌球蛋白II运动结构域和相关突变体的不同构象状态下ATP水解的机制；模拟包括经典的分子动力学和QM/mm方法。具体目的是：（1）确定运动结构域封闭状态下ATP水解的催化机理。（2）确定在运动结构域的开放状态下是否禁止ATP水解，并确定决定水解能量学的开放构和闭合构象之间的关键差异。（3）用能量和机械术语解释活性位点残基的作用，诱变研究表明，这对ATP水解和运动性具有各种影响。之所以选择肌球蛋白-LL，是因为它是唯一具有多种构象状态的高分辨率结构的运动系统，并且可以将计算结果与大量的生化和生物物理数据进行比较。拟议的仿真研究将为桥接不同学科的实验数据提供一个框架，以建立明智的理论模型，以用于肌球蛋白和其他分子电动机中的机械化学耦合。微观见解将对我们设计策略来治疗肌球蛋白功能障碍（例如心肌病）引起的严重疾病的能力产生深远的影响。模拟工作将通过协作密切与实验研究结合；结构，动力学和运动数据的组合将提供验证和完善模拟技术所需的实验测试，这对计算酶学领域具有巨大的价值。