Molecular dynamics studies of muscle proteins

肌肉蛋白的分子动力学研究

• 批准号: 7666918
• 负责人: EDWARD F PATE
• 金额: $ 25.2万
• 依托单位: WASHINGTON STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7666918
• 关键词: ATP Hydrolysis; Actins; Active Sites; Binding; Biochemical; Cardiomyopathies; Chemicals; Coiled-Coil Domain; Coupled; Data; Databases; Dimerization; Elements; Enzymes; Familial Hypertrophic Cardiomyopathy; Free Energy; Generations; Goals; Guanosine Triphosphate; Head; Human; Hydrolysis; Hypertrophic Cardiomyopathy; Investigation; Lead; Link; Microfilaments; Modeling; Modification; Molecular Conformation; Molecular Models; Motion; Motor; Muscle; Muscle Proteins; Mutation; Myopathy; Myosin ATPase; Myosin Rod; Myosin Type II; Myosin Type V; Neck; Nucleotides; Operative Surgical Procedures; Pattern; Peripheral; Physiological; Physiology; Play; Positioning Attribute; Property; Protein Isoforms; Proteins; Protocols documentation; Purines; Pyrimidine; Pyrimidines; Regulation; Relative (related person); Research Personnel; Roentgen Rays; Role; Sensorineural Hearing Loss; Site; Smooth Muscle Myosins; Solutions; Structure; Study models; Substrate Interaction; Substrate Specificity; Sudden Death; Syndrome; Techniques; Testing; Thermodynamics; Thick Filament; Translating; Tropomyosin; Upper arm; Water; Work; analog; base; cell motility; flexibility; forging; genetic regulatory protein; improved; in vivo; inorganic phosphate; insight; melting; molecular dynamics; molecular modeling; muscle disorder therapy; myosin VI; nucleotide analog; numb protein; programs; protein function; purine; research study; simulation; tripolyphosphate

DESCRIPTION (provided by applicant): Determining the atomic level mechanism by which muscle proteins generate force and motion remains one of the fundamental questions in physiology. The recent determinations of the x-ray structures of different conformations of the motor protein, myosin, have provided new hypotheses as to its mechanism of function. However, a unifying framework defining the interaction of the nucleotide, ATP, with myosin to generate force and motion remains undetermined. Nucleotide (ATP) analogs allow one to perturb the interaction of the substrate with the protein, and correlate the perturbations with modulation of contractile activity. This can serve as a probe of the mechanism by which nucleotide hydrolysis drives the conformational changes in myosin that result in motility. We will use molecular dynamics (MD) simulations to investigate the interaction of ATP and nucleotide analogs with myosin x-ray structures as a probe of the mechanism by which nucleotide hydrolysis drives the conformational changes in myosin that generate force and motion. Our fundamental working hypothesis is that quantitative analyses of the x-ray structures can yield insights into function that other approaches have failed to discern. The simulation of nucleotide analogs at the active site will perturb the nucleotide-protein patterns normally associated with ATP binding, and allow further structure- function correlations to be drawn regarding the interaction of protein and substrate. A major goal will be to relate the simulation analyses to existing experimental data, and to identify further experimental challenges to the hypotheses generated by our modeling studies. Additional MD simulations will investigate the thermodynamic stability of the myosin dimerization domain and other alpha-helical coiled coil structures. The stability of the dimerization domain and the implications for myosin head-head interactions and the regulation of function remain unresolved, with some models suggesting a melting of the coiled coil as crucial to function. Quantitative MD simulations will be employed to analyze the relative stabilities of the coiled-coil domains of different myosin isoforms and their relationship to function. In addition to myosin II, we will investigate myosin V and myosin VI. In the latter isoform, the presence of an unstable coiled-coli domain has been hypothesized to be crucial for function. The protocols will be extended to study mutations in the coiled-coil regulatory protein, tropomyosin, which are associated with familial hypertrophic cardiomyopathy (FHC). An atomic level understanding of muscle protein function can be expected to lead to more rational therapies for FHC and other muscle diseases. Improved understanding of the function of myosin V and myosin VI can be anticipated to improve therapies for Griscelli syndrome and myosin Vl-based sensorineural hearing loss in humans.

描述（由申请人提供）：确定肌肉蛋白产生力和运动的原子水平机制仍然是生理学中的基本问题之一。最近对运动蛋白肌球蛋白不同构象的X射线结构的测定为其功能机制提供了新的假设。然而，一个统一的框架定义的相互作用的核苷酸，ATP，与肌球蛋白产生的力量和运动仍然没有确定。核苷酸（ATP）类似物允许干扰底物与蛋白质的相互作用，并将干扰与收缩活性的调节相关联。这可以作为一个探针的机制，核苷酸水解驱动肌球蛋白的构象变化，导致运动。我们将使用分子动力学（MD）模拟来研究ATP和核苷酸类似物与肌球蛋白X射线结构的相互作用，作为核苷酸水解驱动肌球蛋白构象变化产生力和运动的机制的探针。我们的基本工作假设是，X射线结构的定量分析可以产生其他方法无法识别的功能。在活性位点处的核苷酸类似物的模拟将扰乱通常与ATP结合相关的核苷酸-蛋白质模式，并且允许关于蛋白质和底物的相互作用绘制进一步的结构-功能相关性。一个主要的目标将是相关的模拟分析，现有的实验数据，并确定进一步的实验挑战，我们的建模研究所产生的假设。额外的MD模拟将研究肌球蛋白二聚化结构域和其他α-螺旋卷曲螺旋结构的热力学稳定性。二聚化结构域的稳定性和肌球蛋白头-头相互作用和功能调节的影响仍然没有得到解决，一些模型表明卷曲螺旋的熔化对功能至关重要。定量MD模拟将被用来分析不同肌球蛋白亚型的卷曲螺旋结构域的相对稳定性及其与功能的关系。除了肌球蛋白II，我们将研究肌球蛋白V和肌球蛋白VI。在后一种亚型中，不稳定的卷曲大肠杆菌结构域的存在被假设为对功能至关重要。该方案将扩展到研究卷曲螺旋调节蛋白原肌球蛋白的突变，这与家族性肥厚型心肌病（FHC）有关。对肌肉蛋白功能的原子水平理解有望为FHC和其他肌肉疾病带来更合理的治疗方法。对肌球蛋白V和肌球蛋白VI的功能的更好理解可以预期改善对人类Griscelli综合征和基于肌球蛋白VI的感音神经性听力损失的治疗。