Pisliakov Andrei V, Sharma Pankaz K, Chu Zhen T, Haranczyk Maciej, Warshel Arieh
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA.
Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7726-31. doi: 10.1073/pnas.0800580105. Epub 2008 May 28.
Gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Despite promising mechanistic proposals, most works have not related the activation barriers of the different assumed steps to the protein structure, and there has not been a physically consistent model that reproduced the barriers needed to create a working pump. This work reevaluates the activation barriers for the primary proton transfer (PT) steps by calculations that reflect all relevant free energy contributions, including the electrostatic energies of the generated charges, the energies of water insertion, and large structural rearrangements of the donor and acceptor. The calculations have reproduced barriers that account for the directionality and sequence of events in the primary PT in CcO. It has also been found that the PT from Glu-286 (E) to the propionate of heme a(3) (Prd) provides a gate for an initial back leakage from the high pH side of the membrane. Interestingly, the rotation of E that brings it closer to Prd appears to provide a way for blocking competing pathways in the primary PT. Our study elucidates and quantifies the nature of the control of the directionality in the primary PT in CcO and provides instructive insight into the role of the water molecules in biological PT, showing that "bridges" of several water molecules in hydrophobic regions present a problem (rather than a solution) that is minimized in the primary PT.
深入了解细胞色素c氧化酶（CcO）中质子泵浦过程的能量学是现代生物物理学面临的挑战之一。尽管有一些很有前景的机理推测，但大多数研究并未将不同假设步骤的活化能垒与蛋白质结构联系起来，而且还没有一个物理上自洽的模型能够重现形成一个工作泵所需的能垒。这项工作通过计算重新评估了初级质子转移（PT）步骤的活化能垒，这些计算反映了所有相关的自由能贡献，包括所产生电荷的静电能、水插入的能量以及供体和受体的大结构重排。这些计算重现了能垒，这些能垒解释了CcO中初级PT事件的方向性和顺序。还发现从Glu-286（E）到血红素a3（Prd）的丙酸酯的PT为膜高pH侧的初始反向泄漏提供了一个通道。有趣的是，E的旋转使其更接近Prd，这似乎为阻断初级PT中的竞争途径提供了一种方式。我们的研究阐明并量化了CcO中初级PT方向性控制的本质，并为水分子在生物PT中的作用提供了有启发性的见解，表明疏水区域中几个水分子的“桥”带来了一个问题（而非解决方案），而在初级PT中这个问题被最小化了。
