Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects
Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects
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DOI：
10.1016/j.bbabio.2011.01.004
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发表时间：
2011-04-01
影响因子：
4.3
通讯作者：
Warshel, Arieh
中科院分区：
文献类型：
--
作者：
Chakrabarty, Suman;Namslauer, Ida;Warshel, Arieh
深入了解细胞色素c氧化酶（CcO）中质子泵过程的能量学是当前备受关注的问题。尽管有一些有前景的机制假说，但到目前为止，还没有一个能重现构建一个工作泵所需的所有相关能垒的物理上自洽的模型被提出。此外，在阐明关键突变效应的起源以及理解与CcO中特定质子转移（PT）反应的pH依赖性相关的表观pKₐ值的性质方面还存在重大问题。这项工作在解决上述问题上迈出了关键的一步，通过考虑诸如Asn139Asp替换这样的突变，这种突变会阻断质子泵浦但不影响向催化位点的质子转移。我们首先引入一种公式，使得能够将Glu286的表观pKₐ与该残基的不同构象状态联系起来。然后我们使用新公式以及在这些不同构象下计算出的Glu286的pKₐ值来重现该残基经实验观测到的表观pKₐ。接下来，我们采用脱氮副球菌CcO的天然型和Asn139Asp突变体（在该体系中为N131D）的X射线结构，并基于从观测到的结构变化开始的模拟，首次重现了主要质子转移途径（以及其他关键特征）的变化。我们还考虑了质子向催化位点和泵位点运输之间的竞争，它是整体pH的函数，以及H/D同位素效应，并利用这些信息来探究两个能垒的相对高度。本文强调了包括质子转移过程在内的基于能量的考虑因素的关键作用，以及CcO中质子转移的精细调控。（C）2011爱思唯尔有限公司。保留所有权利。
Gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (CcO) is a problem of great current interest. Despite promising mechanistic proposals, so far, a physically consistent model that would reproduce all the relevant barriers needed to create a working pump has not been presented. In addition, there are major problems in elucidating the origin of key mutational effects and in understanding the nature of the apparent pK(a) values associated with the pH dependencies of specific proton transfer (PT) reactions in CcO. This work takes a key step in resolving the above problems, by considering mutations, such as the Asn139Asp replacement, that blocks proton pumping without affecting PT to the catalytic site. We first introduce a formulation that makes it possible to relate the apparent pK(a) of Glu286 to different conformational states of this residue. We then use the new formulation along with the calculated pK(a) values of Glu286 at these different conformations to reproduce the experimentally observed apparent pK(a) of the residue. Next, we take the X-ray structures of the native and Asn139Asp mutant of the Paracoccus denitrificans CcO (N131D in this system) and reproduce for the first time the change in the primary PT pathways (and other key features) based on simulations that start with the observed structural changes. We also consider the competition between proton transport to the catalytic site and the pump site, as a function of the bulk pH, as well as the H/D isotope effect, and use this information to explore the relative height of the two barriers. The paper emphasizes the crucial role of energy-based considerations that include the PT process, and the delicate control of PT in CcO. (C) 2011 Elsevier B.V. All rights reserved.