Detailed understanding of the action of biological molecular machines must overcome the challenge of gaining a clear knowledge of the corresponding free-energy landscape. An example for this is the elucidation of the nature of converting chemical energy to torque and work in the rotary molecular motor of F1-ATPase. A major part of the challenge involves understanding the rotary–chemical coupling from a non-phenomenological structure/energy description. Here we focused on using a coarse-grained model of F1-ATPase to generate a structure-based free-energy landscape of the rotary–chemical process of the whole system. In particular, we concentrated on exploring the possible impact of the position of the catalytic dwell on the efficiency and torque generation of the molecular machine. It was found that the experimentally observed torque can be reproduced with landscapes that have different positions for the catalytic dwell on the rotary–chemical surface. Thus, although the catalysis is undeniably required for torque generation, the experimentally observed position of the catalytic dwell at 80° might not have a clear advantage for the force generation by F1-ATPase. This further implies that the rotary–chemical couplings in these biological motors are quite robust and their efficiencies do not depend explicitly on the position of the catalytic dwells. Rather, the specific positioning of the dwells with respect to the rotational angle is a characteristic arising due to the structural construct of the molecular machine and might not bear any clear connection to the thermodynamic efficiency for the system.

中文翻译：

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分子马达的扭矩、化学和效率：F1-ATP酶中旋转-化学耦合的研究

详细了解生物分子机器的作用必须克服获得相应自由能景观的清晰知识的挑战。这方面的一个例子是阐明将化学能转化为扭矩并在 F 的旋转分子马达中做功的性质1-ATP酶。挑战的主要部分涉及从非现象学结构/能量描述中理解旋转化学耦合。在这里，我们专注于使用 F 的粗粒度模型1-ATP酶生成整个系统的旋转化学过程的基于结构的自由能景观。特别是，我们专注于探索催化停留位置对分子机器的效率和扭矩产生的可能影响。结果发现，实验观察到的扭矩可以用在旋转化学表面上具有不同催化停留位置的景观来重现。因此，尽管不可否认地需要催化来产生扭矩，但实验观察到的催化停留在 80° 的位置可能对 F 产生的力没有明显优势1-ATP酶。这进一步意味着这些生物马达中的旋转-化学耦合非常坚固，并且它们的效率并不明确取决于催化停留的位置。相反，停留点相对于旋转角的特定定位是由于分子机器的结构构造而产生的特征，并且可能与系统的热力学效率没有任何明确的联系。