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

描述（由申请人提供）：肌凝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。在脊椎动物肌肉中首次发现肌球蛋白II后，又发现了其他各种类型的肌球蛋白。VI类肌凝蛋白最近被证明在肌动蛋白上“向后”行走，即与其他肌凝蛋白相反的方向。随后的研究揭示了这种反向运动在多种细胞中的重要运输和锚定作用。近年来已经获得了几种不同构象的电动机晶体结构。在本研究中，我们打算利用这些结构和其他实验数据，通过数值模拟的方法在原子水平上阐明肌凝蛋白VI马达的完整循环和能量学。我们将使用最小能量路径（MEP）、块正态模式（BNM）分析和定向/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。将计算与过渡相关的平均力的势，这将给出与过渡相关的自由能变化。我们将通过自由能模拟方法确定各种配体的晶体结构的亲和力，以确定不同配体如何稳定不同的构象。为了了解肌凝蛋白VI和其他（向前推进的）肌凝蛋白之间的差异，我们将比较肌凝蛋白VI和肌凝蛋白V的作用机制（关于肌凝蛋白V的研究目前正在Karplus实验室进行）。上面提到的许多方法已经在CHARMM程序中实现，我们将使用该程序进行仿真和分析。结合我们对马达头的分析、现有的肌动蛋白-肌球蛋白复合物的冷冻电镜结构、文献中的单分子研究和弹性理论，我们将为这种不寻常的肌球蛋白开发一个粗粒度模型。

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.