Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase.
Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase.
复制标题
基于单分子成像数据的布伦斯特德斜率有助于揭示 F1-ATP 酶中的化学耦合旋转。
DOI：
10.1073/pnas.1519066112
复制
发表时间：
2015
影响因子：
11.1
通讯作者：
Warshel,Arieh
中科院分区：
文献类型：
--
作者：
Mukherjee,Shayantani;Warshel,Arieh
f1 - atp酶是为活细胞中的大多数过程提供动力的旋转马达，它对科学家、实验家和理论家都提出了挑战，要求他们更深入地了解它的作用。二十多年来，F1的工作包括阐明复杂的3D结构(1)和化学步骤的热力学和动力学分析(2)，从而揭示了其旋转化学作用(3)。这些进展通过直接观察F1中心柄（γ）旋转(4)得到加强，该旋转与ATP结合、水解和产物释放的化学步骤紧密耦合，发生在冠（α/β）的三个催化亚基中。观察到γ旋转发生在80/40的子步骤中，这些子步骤嵌入在等待子步骤中，即80子步骤之前的“ATP结合驻留”和40子步骤之前的“催化驻留”(5)。1）. 自从近20年前取得初步进展以来，对F1各个方面的研究继续占据中心地位，因为不断的努力提供了对系统结构、功能和动力学的更详细的见解（6,7）。虽然我们从开创性的实验研究中了解了很多，但当人们试图了解F1功能的物理基础时，仍然存在很大的真空。基于结构的计算研究揭示了酶功能的各个方面（8-11）。作为一个整体来研究这种酶的尝试被证明是有问题的，部分原因是F1的巨大尺寸及其复杂的多维功能，要求在广泛的时间尺度上了解它们。由于F1存在大量的三维结构、整体和实时单分子数据，因此该系统将挑战理论家，以破译决定其旋转化学作用的物理原理。尚未解决的核心问题之一与化学自由能（ATP结合，水解，ADP和Pi释放）与冠（α/β）和中心柄（γ）的催化亚基的构象变化耦合的方式的详细知识有关。这种耦合最终导致γ单元的单向旋转和扭矩产生，代价是ATP被冠水解。冠和柄之间耦合的性质也决定了子台阶的旋转行为，并在间歇停留和催化状态之间建立了精确的相关性(5)。在这里，至少在原则上，人们可以从从三维结构计算的功能相关的自由能面（图1B）（12-14）中探索旋转-化学耦合及其与驻留的关系。这种方法可以揭示耦合的潜在物理基础，并提供直接与实时实验观测相比较的理论预测。虽然通过计算方法获得结构-功能相关性是有希望的，但Volkán-Kacsó和Marcus在PNAS（15）上发表的研究开辟了一个令人兴奋和富有洞察力的方向。作者分析了耦合的旋转-化学过程，并通过扩展化学过程中动力学和能量学之间的统一关系（称为Brønsted关系）的知识，将化学（或结合）步骤的自由能与γ的旋转联系起来。如果这样一个广义的理论框架能够突出F1中耦合的本质（如参考文献15所做的那样），人们也可以通过了解化学和机械步骤之间的关系来提取关于功能自由能景观的关键信息。这种方法应该提供一个……
F1-ATPase, the rotary motor that powers most of the processes in living cells, has challenged scientists, experimentalists, and theoreticians alike to gain deeper understanding of its action. The work on F1 for more than two decades encompasses elucidation of the complex 3D structure (1) and the analysis of the thermodynamics and kinetics of the chemical steps (2) that led to the revelation of its rotary–chemical action (3). These advances were enhanced by direct observation of the F1 central stalk (γ) rotation (4) that is tightly coupled to the chemical steps of the ATP binding, hydrolysis, and product release, occurring in the three catalytic subunits of the crown (α/β). The γ rotation was observed to occur in substeps of 80/40 that were embedded within the waiting dwells, namely, the “ATP binding dwell” before the 80 substep and the “catalytic dwell” before the 40 substep (5)(Fig. 1). Since the initial progress made almost two decades ago, the study of various aspects of F1 continues to occupy a central position, as ongoing efforts offer more detailed insights into the structure, function, and dynamics of the system (6, 7). Although much is known from pioneering experimental studies, a large vacuum still persists when one attempts to understand the physical basis of F1 functionality. There have been insightful structure-based computational studies that revealed various facets of the enzyme’s functionality (8–11). Attempts to study the enzyme as a whole turned out to be problematic, due in part to the huge size of F1 and its complex multidimensional functionality that commands the need to understand them on wide ranges of timescales. Because a considerable body of 3D structural, ensemble, and real-time single-molecule data exists for F1, this system is poised to challenge theoreticians to decipher the physical principles that determine its rotary–chemical action. One of the central unresolved questions is associated with the detailed knowledge of the way the chemical free energies (ATP binding, hydrolysis, ADP, and Pi release) are coupled to the conformational changes in the catalytic subunits of the crown (α/β) and the central stalk (γ). This coupling eventually leads to unidirectional rotation and torque generation at the γ unit at the expense of the ATP hydrolysis by the crown. The nature of the coupling between the crown and the stalk also dictates the substep rotational behavior and establishes a precise correlation between the intermittent dwells and the catalytic states (5). Here, at least in principle, one can explore the rotary–chemical coupling and its relationships to the dwells from functionally relevant free-energy surfaces calculated from the 3D structure (Fig. 1B)(12–14). Such an approach can reveal the underlying physical basis of the coupling and also lends theoretical predictions directly comparable to real-time experimental observations.Although it is promising to obtain the structure–function correlation by computational approaches, an exciting and insightful direction has been opened by the study by Volkán-Kacsó and Marcus published in PNAS (15). The authors have analyzed the coupled rotary–chemical process and related the free energies of the chemical (or binding) steps to the rotation of γ by extending the knowledge of the unified relationship between the kinetics and energetics in chemical processes (known as the Brønsted relationship). If such a generalized theoretical framework is able to highlight the nature of the coupling in F1 (as done in ref. 15), one can also extract crucial information about the functional free-energy landscape by knowing the relationship between the chemical and mechanical steps. Such an approach should provide a …