Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
J Mol Biol. 2010 Jan 29;395(4):815-33. doi: 10.1016/j.jmb.2009.10.029. Epub 2009 Oct 21.
Myosin motor function depends on the interaction between different domains that transmit information from one part of the molecule to another. The interdomain coupling in myosin V is studied with restrained targeted molecular dynamics using an all-atom representation in explicit solvent. To elucidate the origin of the conformational change due to the binding of ATP, targeting forces are applied to small sets of atoms (the forcing sets, FSs) in the direction of their displacement from the rigor conformation, which has a closed actin-binding cleft, to the post-rigor conformation, in which the cleft is open. The "minimal" FS that results in extensive structural changes in the overall myosin conformation is composed of ATP, switch 1, and the nearby HF, HG, and HH helices. Addition of switch 2 to the FS is required to achieve a complete opening of the actin-binding cleft. The restrained targeted molecular dynamics simulations reveal the mechanical coupling pathways between (i) the nucleotide-binding pocket (NBP) and the actin-binding cleft, (ii) the NBP and the converter, and (iii) the actin-binding cleft and the converter. Closing of the NBP due to ATP binding is tightly coupled to the opening of the cleft and leads to the rupture of a key hydrogen bond (F441N/A684O) between switch 2 and the SH1 helix. The actin-binding cleft may mediate the rupture of this bond via a connection between the HW helix, the relay helix, and switch 2. The findings are consistent with experimental studies and a recent normal mode analysis. The present method is expected to be useful more generally in studies of interdomain coupling in proteins.
肌球蛋白的马达功能取决于不同结构域之间的相互作用，这些结构域将信息从分子的一部分传递到另一部分。使用全原子表示和显式溶剂的受限靶向分子动力学研究了肌球蛋白 V 中的结构域间耦合。为了阐明由于结合 ATP 而导致的构象变化的起源，靶向力被应用于一小部分原子（力施加集，FSs），其方向是从僵硬构象到后僵硬构象的位移方向，其中僵硬构象的肌动蛋白结合裂隙是关闭的，而后僵硬构象的肌动蛋白结合裂隙是打开的。导致整个肌球蛋白构象发生广泛结构变化的“最小”FS 由 ATP、开关 1 和附近的 HF、HG 和 HH 螺旋组成。需要将开关 2 添加到 FS 中才能实现肌动蛋白结合裂隙的完全打开。受限靶向分子动力学模拟揭示了核苷酸结合口袋 (NBP) 和肌动蛋白结合裂隙之间、NBP 和转换器之间以及肌动蛋白结合裂隙和转换器之间的机械耦合途径。由于 ATP 结合而导致的 NBP 关闭与裂隙的打开紧密耦合，并导致开关 2 和 SH1 螺旋之间的关键氢键（F441N/A684O）断裂。肌动蛋白结合裂隙可能通过 HW 螺旋、中继螺旋和开关 2 之间的连接来介导该键的断裂。这些发现与实验研究和最近的正常模式分析一致。本方法有望在蛋白质结构域间耦合的研究中更广泛地应用。
