MYOSIN VI STEPS BACKWARDS: A COMPUTATIONAL STUDY TO ELUCIDATE THE MECHANISM

肌球蛋白 VI 倒退：一项阐明其机制的计算研究

• 批准号: 7399685
• 负责人: Victor Ovchinnikov
• 金额: $ 4.96万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-01 至 2011-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7399685
• 关键词: ATP Hydrolysis; Actins; Affinity; Binding; Cell Adhesion; Cell physiology; Cells; Cereals; Class; Complex; Coupling; Cryoelectron Microscopy; Data; Disease; Elasticity; Endocytosis; Eukaryota; Eukaryotic Cell; Exhibits; Free Energy; Hand; Head; Inherited; Kinetics; Laboratories; Lead; Ligands; Literature; Maintenance; Malignant neoplasm of ovary; Measurement; Mechanics; Methods; Microfilaments; Mitosis; Modeling; Molecular; Molecular Conformation; Molecular Machines; Molecular Motors; Motion; Motor; Motor Activity; Movement; Muscle; Muscle Contraction; Myosin ATPase; Myosin Type II; Myosin Type V; Normal Cell; Organelles; Pathway interactions; Pliability; Proteins; Purpose; Research; Resolution; Roentgen Rays; Role; Series; Signal Transduction; Speed; Stereocilium; Structure; Takeda brand of pioglitazone hydrochloride; Temperature; Testing; Thermodynamics; Vesicle; Walking; cancer cell; computer studies; conformer; design; dimer; hearing impairment; human disease; inorganic phosphate; interest; molecular dynamics; myosin VI; programs; research study; simulation; single molecule; theories

DESCRIPTION (provided by applicant): Myosins are ubiquitous intracellular motors that use the energy of ATP hydrolysis to move on actin filaments. After myosin II was first characterized in vertebrate muscle, various other classes have been found. Class VI myosin has been shown recently to walk "backwards" on actin, i.e. in the direction opposite to that of other myosins. Subsequent studies revealed important transport and anchoring roles for this backward motor in a variety of cells. Several crystal structures of the motor in various conformations have been obtained recently. In this proposal, we intend to utilize these structures and other experimental data to elucidate the complete cycle and energetics of the myosin VI motor at the atomic level by means of numerical simulations. We will determine transition paths between the available crystal structures using Minimum Energy Path (MEP), Block Normal Mode (BNM) analysis, and steered/biased/targeted Molecular Dynamics. The potential of mean force associated with the transitions will be computed, which will give the free energy change associated with the transitions. We will determine the affinities of the crystal structures for the various ligands by free energy simulation methods to determine how different conformations are stabilized by the different ligands. To understand the differences between myosin VI and other (forward-stepping) myosins, we will compare the mechanisms of myosin VI and myosin V (research on the myosin V is currently being done in the Karplus laboratory). Many of the methods mentioned above have been implemented in the program CHARMM, which we will use for simulation and analysis. Combining our analysis of the motor head with available cryo-electron microscopy structures of the acto-myosin complex, single-molecule studies in the literature, and elasticity theory, we will develop a coarse-grained model for this unusual myosin. Myosin VI malfunction is associated with hereditary hearing loss, and myosin VI concentration is much higher in ovarian cancer cells than in normal cells. Results of our research could lead to the design of new therapies for these diseases. For example, an understanding of the mechanism of myosin VI can identify ways to regulate the activity of this motor.

描述（由申请人提供）：肌球蛋白是普遍存在的细胞内马达，它利用 ATP 水解的能量在肌动蛋白丝上移动。肌球蛋白 II 首次在脊椎动物肌肉中得到表征后，又发现了各种其他类型的肌球蛋白。最近表明，VI 类肌球蛋白在肌动蛋白上“向后”行走，即与其他肌球蛋白相反的方向。随后的研究揭示了这种向后运动在多种细胞中的重要运输和锚定作用。最近获得了多种不同构象的电机晶体结构。在本提案中，我们打算利用这些结构和其他实验数据，通过数值模拟的方式在原子水平上阐明肌球蛋白 VI 马达的完整循环和能量学。我们将使用最小能量路径 (MEP)、块正则模式 (BNM) 分析和引导/偏置/靶向分子动力学来确定可用晶体结构之间的转变路径。将计算与转变相关的平均力的势，这将给出与转变相关的自由能变化。我们将通过自由能模拟方法确定晶体结构对各种配体的亲和力，以确定不同配体如何稳定不同的构象。为了了解肌球蛋白 VI 和其他（向前迈进的）肌球蛋白之间的差异，我们将比较肌球蛋白 VI 和肌球蛋白 V 的机制（目前 Karplus 实验室正在对肌球蛋白 V 进行研究）。上面提到的许多方法已经在CHARMM程序中实现，我们将使用它来进行模拟和分析。结合我们对运动头的分析与肌动球蛋白复合物的现有冷冻电子显微镜结构、文献中的单分子研究以及弹性理论，我们将为这种不寻常的肌球蛋白开发一个粗粒度模型。 肌球蛋白 VI 功能障碍与遗传性听力损失有关，卵巢癌细胞中肌球蛋白 VI 的浓度远高于正常细胞。我们的研究结果可能会导致针对这些疾病的新疗法的设计。例如，了解肌球蛋白 VI 的机制可以确定调节该运动活动的方法。