QM/MM analysis of redox driven proton pumping

细胞色素氧化酶（CeO）是参与电子转移的重要酶 细胞呼吸的途径。 CeO 激活分子氧以防止释放 潜在有毒的氧中间体，同时使用来自的自由能 氧还原以化学计量方式将质子泵过膜，产生 ATP 合成所需的质子浓度梯度。 CeO 活性的折衷是 与严重的人类健康威胁有关，例如各种神经退行性疾病， 肌营养不良症和结肠癌。因此，对其作用机制的研究 CeO在分子水平上的研究不仅具有基础价值，而且有助于 了解这些疾病的分子起源并帮助设计有效的治疗方案 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）技术来研究几个活跃争论的机械问题 氧化铈。具体来说，我们有以下目标：（i）。使用 QM/MM 进行 pKa 计算 帮助确定泵送装载地点最有可能的候选者的方法 His334 中的质子和血红素辅因子的丙酸盐。 (二).通过分析 Glu286 异构化的能量学（包括势垒）和野外关键质子转移步骤 类型 CeO，建立防止回流的“门控元素”的身份 质子。定义构象和静电对门控的贡献。 与实验分析一起，这些原子水平的研究将坚定地 确定 CeO 对其功能至关重要的分子特性。续 近似密度函数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.