QM/MM analysis of redox driven proton pumping

细胞色素COxidase(CEO)是参与电子传递的重要酶 细胞呼吸中的途径。CEO激活分子氧以防止释放 具有潜在毒性的氧中间体，同时使用来自 氧还原以化学计量的方式将质子泵过膜，创造 合成三磷酸腺苷所需的质子浓度梯度。CEO活动的妥协是 与各种神经退行性疾病等严重的人类健康威胁有关， 肌肉营养不良和结肠癌。因此，对其作用机理的探讨 在分子水平上的CEO不仅具有基本价值，而且还有助于 了解这些疾病的分子起源并帮助设计有效的 治疗策略。在这个项目中，我们建议使用量子力学/分子 机械(QM/MM)技术研究中几个热门的机械问题 首席执行官。具体来说，我们有以下目标：(I)。使用QM/MM的PKA计算 帮助确定最有可能的候选人(S)的方法抽水蓄能电站的装载地点 His334中的质子和丙酸的亚铁血红素共因子。(Ii)。通过对这一问题的分析 Glu286异构化的能量学(包括势垒)和关键的质子转移步骤 型首席执行官，确立防止回流的“门控元素(S)”的身份 质子。定义构象和静电对门控的贡献。 再加上实验分析，这些原子层面的研究将坚定地 确定对其功能至关重要的CEO的分子性质。续 近似密度泛函方法的发展将在研究中得到应用 广泛的生物分子，特别是那些涉及矢量化学的生物分子。

Cytochrome COxidase (CeO) is an important enzyme involved in the electron transfer pathway in cellular respiration. CeO activates molecular oxygen to prevent the release of potentially toxic oxygen intermediates and at the same time, uses the free energy from oxygen reduction to pump protons across the membrane in a stoichiometric fashion, creating the proton concentration gradient required for ATP synthesis. Compromise of CeO activity is implicated in serious human health threats such as various neurodegenerative diseases, muscular dystrophies and colon cancer. Therefore, investigation of the functional mechanism of CeO at a molecular level not only has fundamental value but also contributes to understanding the molecular origin of these diseases and aiding the design of effective therapeutic strategies. In this project, we propose to use quantum mechanical/molecular mechanical (QM/MM) techniques to study several actively debated mechanistic issues in CeO. Specifically, we have the following aims: (i). Use pKa calculations with QM/MM methods to help identify the most likely candidate(s) for the loading site of pumped protons among His334 and the propionates of the heme co-factor. (ii). Via analysis of the energetics (including barrier) of Glu286 isomerization and key proton transfer steps in wild type CeO, establish the identity of the "gating element(s)" that prevent the backflow of protons. Define conformational and electrostatic contributions to gating. Together with experimental analyses, these investigations at the atomic level will firmly establish the molecular properties of CeO that are essential to its function. Continued development of an approximate density functional approach will find application in the study of a broad range of biomolecules, especially those involve vectorial chemistry.