QM/MM analysis of redox driven proton pumping

细胞色素氧化酶（CeO）是参与电子传递的重要酶 细胞呼吸的途径。CeO激活分子氧以防止 同时，利用潜在的有毒氧中间体的自由能， 氧还原以化学计量方式泵送质子穿过膜， ATP合成所需的质子浓度梯度。首席执行官活动的损害是 涉及严重的人类健康威胁，如各种神经退行性疾病， 肌肉萎缩症和结肠癌。因此，研究其作用机制， 在分子水平上研究CeO不仅具有重要的价值， 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）技术研究几个积极辩论的机械问题， 首席执行官具体而言，我们有以下目标：（i）。使用QM/MM进行pKa计算 方法，以帮助确定最有可能的候选人为装载地点的泵 His334中的质子和血红素辅因子的丙酸酯。（ii）。通过分析 Glu286异构化的能量学（包括势垒）和关键的质子转移步骤 CeO型，确定防止回流的"门控元件"的特性 质子定义构象和静电对门控的影响。 结合实验分析，这些在原子水平上的研究将坚定地 确定CeO的分子特性，这对其功能至关重要。继续 一个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。

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.