Nie Qing-Miao, Togashi Akio, Sasaki Takeshi N, Takano Mitsunori, Sasai Masaki, Terada Tomoki P
Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan; Institute for Molecular Science, Okazaki, Japan; Department of Applied Physics, Zhejiang University of Technology, Hangzhou, P. R. China.
Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan.
PLoS Comput Biol. 2014 Apr 24;10(4):e1003552. doi: 10.1371/journal.pcbi.1003552. eCollection 2014 Apr.
An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (Pi) and ADP weakly binds to actin and that after releasing Pi and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5-11 nm displacement due to the biased Brownian motion and the 3-5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family.
与肌动球蛋白马达相关的一个重要未解决问题是布朗运动在力产生过程中的作用。基于对肌球蛋白和肌动蛋白的结构观察，人们提出了广泛认可的杠杆臂假说，该假说认为蛋白质在观察到的和假设的结构之间呈现顺序性结构变化以施加机械力。另一种假说，即布朗运动假说，得到了单分子实验的支持，并且更强调蛋白质波动运动的作用。在本研究中，我们通过对肌动球蛋白系统的计算机模拟观察来解决杠杆臂假说和布朗运动假说之间长期存在的争议。我们通过使用分子动力学方法计算肌动蛋白 - 肌球蛋白相互作用的自由能景观，并使用蒙特卡罗方法模拟动态变化的自由能景观之间的转变，来研究由肌球蛋白 II 和肌动蛋白丝组成的系统。通过这种组合的多尺度计算获得的结果表明，带有无机磷酸（Pi）和二磷酸腺苷（ADP）的肌球蛋白与肌动蛋白弱结合，并且在释放 Pi 和 ADP 后，肌球蛋白通过表现出有偏布朗运动沿着肌动蛋白丝向强结合位点移动，这种行为与观察到的肌球蛋白单分子行为一致。肌球蛋白与肌动蛋白亚基 N 端的肌动蛋白界面处环的构象灵活性对于布朗运动中的明显偏向是必要的。由有偏布朗运动引起的 5.5 - 11 纳米位移和由杠杆臂摆动引起的 3 - 5 纳米位移都有助于肌球蛋白的净位移。计算结果进一步表明，杠杆臂的恢复冲程在通过多个 ATP 水解循环增强肌球蛋白的位移方面起着重要作用，这表明了肌球蛋白家族各成员的统一运动机制。
