Molecular Mechanisms of Energy Conversion in Respiratory Complex I

阐明生物能量转化的分子机制对于理解细胞的生物化学和开发新的仿生能源技术都是至关重要的。复合体I(NADH：泛醌氧化还原酶)作为电子在细菌和真核生物呼吸链中的初始进入点起作用。通过还原其可溶域中的苯二酚(Q)，络合物I将在此过程中释放的自由能耦合到其膜结构域中的质子转移。通过细菌内线粒体膜和细胞质膜的质子转移产生了一个电化学质子梯度，该质子梯度随后被FoF1-ATPase用于合成ATP和主动转运。值得注意的是，络合物I中的可滴定残基在远离Q-还原位置的~200°处突变，抑制了质子泵和Q还原。虽然这是热力学上可逆的质子耦合电子转移(PCET)机制的预期，但它对耦合机制施加了几个限制。为了解释络合物I中这种长程能量传播的原理，已经提出了直接(氧化还原驱动)和间接(构象驱动)机制，但分子细节仍然难以捉摸。在这个项目中，我们使用了最先进的量子和经典分子模拟技术来研究配合物I催化的长程质子耦合电子转移的分子机制。计算方法为探索复杂生化系统的机理假说提供了强有力的方法，从而从分子水平上深入了解催化机理。我们的分子模拟旨在研究络合物I中关键催化步骤的结构、动力学和能量学，从而为许多实验技术提供补充但也是不可访问的信息。在这个项目中，我们的目标是阐明(1)络合物I的反转运蛋白样膜结构域中质子转移过程的能量学和动力学，(2)导致络合物I可溶域中的苯二酚还原的电子转移过程的能量学，以及(3)氧化还原诱导的醌位置的变化是如何激活质子泵的。

Elucidating molecular mechanisms of biological energy conversion is crucial both for understanding the biochemistry of the cell and for developing new biomimetic energy technologies. Complex I (NADH:ubiquinone-oxidoreductase) functions as an initial entry point for electrons in the respiratory chains of bacteria and eukaryotes. By reducing quinones (Q) in its soluble domain, Complex I couples the free energy released in the process to the translocation of protons in its membrane domain. The proton transfer across the inner mitochondrial membrane and cytoplasmic membrane of bacteria generates an electrochemical proton gradient, which is subsequently used for synthesis of ATP by FoF1-ATPase and for active transport. Remarkably, mutation of titratable residues ~200 Å away from the site of Q-reduction in Complex I, inhibits both the proton-pumping and Q reduction. Although this is thermodynamically expected for a reversible proton-coupled electron transfer (PCET) machinery, it imposes several restrictions on the coupling mechanism. To explain the principles of this long-range energy propagation in Complex I, both direct (redox-driven) and indirect (conformationally-driven) mechanisms have been suggested, but the molecular details remains elusive. In this project, we employ a broad range of state-of-the-art quantum and classical molecular simulation techniques to study molecular mechanisms of the long-range proton-coupled electron transfer catalyzed by Complex I. The computational approaches provide powerful methodologies to probe mechanistic hypothesis of complex biochemical systems, and thus to get insight in the catalytic mechanisms on a molecular level. Our molecular simulations aim to address the structure, dynamics and energetics of key catalytic steps in Complex I, thus providing complementary, but also inaccessible information to many experimental techniques. In this project we aim to elucidate (1) the energetics and dynamics of the proton transfer process in the antiporter-like membrane domain of Complex I, (2) the energetics of the electron transfer process that lead to reduction of quinones in the soluble domain of Complex I, and (3) how the redox-induced changes at the quinone site are responsible for activating the proton pump.