Quantum Chemistry of Proton Pumping by Cytochrome c Oxidases

描述（由申请人提供）：拟开展的工作涉及几何和电子结构的密度泛函理论（DFT）计算、静电计算以及量子力学\分子力学\分子动力学（QM/MM/MD）模拟，以提供对B型细胞色素c氧化酶中催化反应途径的详细机理理解，并与A型细胞色素c氧化酶（CcO）进行比较。目标1。建立一个量子/静电模型，解释化学键和质子/电子流到Fe-Cu双核配合物（DNC）中的分子氧如何导致质子泵跨膜。QM/MM/MD研究将提供深入了解质子转移的动态过程内和质子出口通道从DNC。目标2.过氧桥Fe-Cu物种的检测和表征将与DFT中相应的电子态相关。振动光谱和其他电子性质（穆斯堡尔和光学）的DFT计算将与实验光谱进行比较。目标3：用密度泛函/静电学和量子力学/MM/MD方法分析了质子转移到双核铁铜配合物中的K-途径。目标4。我们将进一步发展目前的方法，以提高这些大的活性位点模型的DFT计算的质量，分析与QM/MM/MD的动态过程，和剩余的蛋白质/膜/水溶剂环境的物理描述。线粒体的细胞色素c氧化酶（复合物IV）将通过电子传递链的电子传递与穿过线粒体内膜的质子泵送连接起来，并且类似地，在大多数需氧细菌中穿过质膜。这是用于ATP生产的质子动力。线粒体CcO在人类健康中起着至关重要的作用，因为大多数重要的代谢功能都需要足够的ATP供应。此外，电子或质子转移反应或在CcO处的氧结合的中断可导致包括羟基和超氧化物自由基以及过氧化氢的破坏性活性氧物质的产生。了解线粒体CcO的结构、机制和功能对于更好地分析许多遗传和代谢疾病和癌症是重要的，并且也与衰老的病理学有关。 公共卫生相关性：我们正在使用量子化学，静电学和分子动力学的方法，以获得详细的机械理解如何氧结合和电子/质子流入细胞色素c氧化酶导致质子泵在人类线粒体的内膜，并在大多数需氧细菌的质膜类似。产生的质子动力用于ATP的产生，这种酶的缺陷会损害能量的产生，也会产生活性氧自由基。线粒体代谢缺陷与许多代谢疾病、癌症和衰老病理学有关，因此分析这种分子机器具有重要意义。

DESCRIPTION (provided by applicant): The proposed work involves density functional theory (DFT) calculations of geometric and electronic structure, electrostatics calculations, and quantum mechanics\molecular mechanics\molecular dynamics (QM/MM/MD) simulations to provide a detailed mechanistic understanding of the catalytic reaction pathways in B-type cytochrome c oxidases, comparing also to A-type cytochrome c oxidases (CcO's). Aim 1. To develop a quantum/electrostatic model explaining how chemical bonding and proton/electron flow to molecular oxygen within the Fe-Cu dinuclear complex (DNC) leads to proton pumping across the membrane. QM/MM/MD studies will provide insights into dynamic processes of proton transfer within and the proton exit channel from the DNC. Aim 2. Detection and characterization of peroxo bridged Fe-Cu species will be related to corresponding electronic states from DFT. DFT calculations of vibrational spectra and other electronic properties (Mossbauer and optical) will be performed for comparisons with experimental spectroscopies. Aim 3. The K-pathway for proton transfer into the dinuclear Fe-Cu complex will be analyzed using DFT/electrostatics and QM/MM/MD methods. Aim 4. We will further develop current methodologies to improve the quality of DFT calculations for these large active site models, to analyze dynamic processes with QM/MM/MD, and for the physical description of the remaining protein/membrane/aqueous solvent environment. Cytochrome c oxidase (Complex IV) of mitochondria links electron transfer through the electron transport chain to proton pumping across the inner membrane of the mitochondria, and similarly, across the plasma membrane in most aerobic bacteria. This is the proton motive force utilized for ATP production. Mitochondrial CcO's play an essential role in human health because adequate ATP supplies are required for most important metabolic functions. Also, disruptions in electron or proton transfer reactions or oxygen binding at CcO can lead the production of damaging reactive oxygen species including hydroxyl and superoxide radicals, and hydrogen peroxide. Understanding the structures, mechanisms, and functions of mitochondrial CcO's is important for better analysis of many genetic and metabolic diseases and cancers, and is also relevant to pathologies of aging. PUBLIC HEALTH RELEVANCE: We are using methods from quantum chemistry, electrostatics, and molecular dynamics to obtain a detailed mechanistic understanding of how oxygen binding and electron/proton flow into cytochrome c oxidase leads to proton pumping across the inner membrane of mitochondria in humans, and similarly across the plasma membrane in most aerobic bacteria. The proton motive force generated is used for ATP production, and defects in this enzyme harm energy production, and also can generate reactive radical oxygen species. Defects in mitochondrial metabolism are associated with many metabolic diseases, cancers, and pathologies of aging, so analyzing this molecular machine has great significance.