Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives.
Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives.
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DOI：
10.1016/j.bbabio.2007.01.015
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发表时间：
2007-03
期刊：
影响因子：
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通讯作者：
M. Olsson;P. Siegbahn;M. Blomberg;A. Warshel
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文献类型：
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作者：
M. Olsson;P. Siegbahn;M. Blomberg;A. Warshel
获得细胞色素c氧化酶（CcO）质子泵送过程能量学的详细理解是现代生物物理学的挑战之一。虽然目前有几个机制建议，但大多数这些想法都没有受到一致的结构-功能考虑。特别是大多数工作没有将不同机制建议的激活障碍与蛋白质结构联系起来。本工作描述了一种利用观察到的蛋白质结构、建立的模拟方法和改进的Marcus公式来探索CcO作用的不同可行模型的能量学的一般方法。我们首先回顾了评估不同质子易位路径能量图的方法，然后系统地分析了泵浦过程能量图上的各种约束条件。在一般分析之后，我们转向实际的计算研究，在那里我们使用估计的计算还原电位和所有相关位点（包括内部水分子）的pkvalue来构建向前和向后路径的能量图。然后，我们探讨了计算的能量图与关键实验约束之间的关系。这种比较使我们能够识别出一些不完全符合有效泵送总体要求的屏障。特别是我们确定了后泄漏通道，如果不停止前泄漏通道，则难以阻塞。这有助于确定需要进一步实验和理论研究的开放性问题。我们还考虑对可能导致泵工作的计算障碍进行合理调整。虽然目前的分析并没有为CcO的机制建立一个独特和可行的模型，但它提出了可能是目前对不同可行途径的障碍最一致的分析。也许更重要的是，这里开发的框架应该提供一种通用的方法来检查任何关于CcO作用的建议，以及分析关于这个迷人系统作用的进一步实验结果。
Gaining a detailed understanding of the energetics of the proton pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Although there are several current mechanistic proposals, most of these ideas have not been subjected to consistent structure–function considerations. In particular most works have not related the activation barriers for different mechanistic proposals to the protein structure. The present work describes a general approach for exploring the energetics of different feasible models of the action of CcO, using the observed protein structure, established simulation methods and a modified Marcus' formulation. We start by reviewing our methods for evaluation of the energy diagrams for different proton translocation paths and then present a systematic analysis of various constraints that should be imposed on any energy diagram for the pumping process. After the general analysis we turn to the actual computational study, where we construct energy diagrams for forward and backward paths, using the estimated calculated reduction potentials and pKavalues of all the relevant sites (including internal water molecules). We then explore the relationship between the calculated energy diagrams and key experimental constraints. This comparison allows us to identify some barriers that are not fully consistent with the overall requirement for an efficient pumping. In particular we identify back leakage channels, which are hard to block without stopping the forward channels. This helps to identify open problems that will require further experimental and theoretical studies. We also consider reasonable adjustments of the calculated barriers that may lead to a working pump. Although the present analysis does not establish a unique and workable model for the mechanism of CcO, it presents what is probably the most consistent current analysis of the barriers for different feasible pathways. Perhaps more importantly, the framework developed here should provide a general way for examining any proposal for the action of CcO as well as for the analysis of further experimental findings about the action of this fascinating system.