School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
J Phys Chem A. 2011 Jun 30;115(25):7267-74. doi: 10.1021/jp2005088. Epub 2011 Apr 1.
F(1)-ATPase is the catalytic domain of F(1)F(o)-ATP synthase and consists of a hexameric arrangement of three noncatalytic α and three catalytic β subunits. We have used unbiased molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic relaxation properties of isolated β-subunits as a step toward explaining the function of the integral F(1) unit. To this end, we simulated the open (β(E)) and the closed (β(TP)) conformations under unbiased conditions for up to 120 ns each using several samples. The simulations confirm that nucleotide-free β(E) retains its open configuration over the course of the simulations. The same is true when the neighboring α subunits are included. The nucleotide-depleted as well as the nucleotide-bound isolated β(TP) subunits show a significant trend toward the open conformation during our simulations, with one trajectory per case opening completely. Hence, our simulations suggest that the equilibrium conformation of a nucleotide-free β-subunit is the open conformation and that the transition from the closed to the open conformation can occur on a time scale of a few tens of nanoseconds.
F(1)-ATP 酶是 F(1)F(o)-ATP 合酶的催化结构域，由三个非催化的α和三个催化的β亚基组成六聚体排列。我们使用了无偏分子动力学模拟，总模拟时间为 900 纳秒，以研究分离的β亚基的动态弛豫特性，作为解释完整 F(1)单元功能的一步。为此，我们使用了几个样本，分别对开放（β(E))和闭合（β(TP))构象进行了长达 120 纳秒的无偏条件模拟。模拟结果证实，在整个模拟过程中，无核苷酸的β(E)保持其开放构象。当相邻的α亚基被包含在内时，情况也是如此。核苷酸耗尽以及结合核苷酸的分离β(TP)亚基在我们的模拟过程中显示出向开放构象的显著趋势，每个情况都有一个轨迹完全打开。因此，我们的模拟表明，无核苷酸的β-亚基的平衡构象是开放构象，并且从封闭到开放的构象转变可以在几十纳秒的时间尺度上发生。
