Department Chemie, Technische Universität München, D-85748 Garching, Germany;Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520;
Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; and.
Proc Natl Acad Sci U S A. 2014 May 13;111(19):6988-93. doi: 10.1073/pnas.1319156111. Epub 2014 Apr 28.
Complex I serves as the primary electron entry point into the mitochondrial and bacterial respiratory chains. It catalyzes the reduction of quinones by electron transfer from NADH, and couples this exergonic reaction to the translocation of protons against an electrochemical proton gradient. The membrane domain of the enzyme extends ∼180 Å from the site of quinone reduction to the most distant proton pathway. To elucidate possible mechanisms of the long-range proton-coupled electron transfer process, we perform large-scale atomistic molecular dynamics simulations of the membrane domain of complex I from Escherichia coli. We observe spontaneous hydration of a putative proton entry channel at the NuoN/K interface, which is sensitive to the protonation state of buried glutamic acid residues. In hybrid quantum mechanics/classical mechanics simulations, we find that the observed water wires support rapid proton transfer from the protein surface to the center of the membrane domain. To explore the functional relevance of the pseudosymmetric inverted-repeat structures of the antiporter-like subunits NuoL/M/N, we constructed a symmetry-related structure of a possible alternate-access state. In molecular dynamics simulations, we find the resulting structural changes to be metastable and reversible at the protein backbone level. However, the increased hydration induced by the conformational change persists, with water molecules establishing enhanced lateral connectivity and pathways for proton transfer between conserved ionizable residues along the center of the membrane domain. Overall, the observed water-gated transitions establish conduits for the unidirectional proton translocation processes, and provide a possible coupling mechanism for the energy transduction in complex I.
复合体 I 作为线粒体和细菌呼吸链的主要电子进入点。它通过电子从 NADH 的转移来催化醌的还原，并将此放能反应与质子逆电化学质子梯度的转运偶联。酶的膜域从醌还原的部位延伸约 180Å，直到最远的质子途径。为了阐明长程质子偶联电子转移过程的可能机制，我们对来自大肠杆菌的复合体 I 的膜域进行了大规模原子分子动力学模拟。我们观察到在 NuoN/K 界面处假定质子进入通道的自发水合作用，这对埋藏的谷氨酸残基的质子化状态敏感。在混合量子力学/经典力学模拟中，我们发现观察到的水线支持从蛋白质表面到膜域中心的快速质子转移。为了探索反向转运蛋白样亚基 NuoL/M/N 的伪对称反转重复结构的功能相关性，我们构建了可能的交替访问状态的对称相关结构。在分子动力学模拟中，我们发现由此产生的结构变化在蛋白质骨架水平上是亚稳定和可逆的。然而，构象变化引起的水合作用增加仍然存在，水分子在膜域中心的保守可离子化残基之间建立了增强的横向连接和质子转移途径。总的来说，观察到的水门控转变为单向质子转运过程建立了通道，并为复合体 I 中的能量转导提供了可能的偶联机制。
