Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase
Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase
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DOI：
10.1016/j.bbabio.2018.05.010
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发表时间：
2018-10-01
影响因子：
4.3
通讯作者：
Gunner, M. R.
中科院分区：
文献类型：
--
作者：
Cai, Xiuhong;Haider, Kamran;Gunner, M. R.
细胞色素c氧化酶(CcO)将氧气呼吸电子传递链中的末端电子受体O-2还原为水。O-2还原释放的能量是通过从膜的高pH值N侧去除8个质子来储存的，其中4个质子用于活性部位的化学作用，4个质子泵入低pH值的P侧。质子转移必须沿着可控制的质子路径进行，以防止能量耗散向N侧移动。CcoN-side已经很好地建立了D-和K-通道，将质子输送到蛋白质内部。P侧有一个被称为质子负载中心簇(PIS簇)的氢键可质子化残基的掩埋核心，在P侧表面有许多可质子化残基，没有明显的唯一出口。在Rb的分子动力学(MD)轨迹中确定了氢键路径。用不同质子化状态的血红素a(3)丙酸酯和Glu286在P-R状态下制备了球形CcO。轨道快照中水位置、极性质子位置和残基质子化状态的大典型蒙特卡罗采样确定了有限数量的水介导的质子通过(P-EXIT)残基簇从PLS团簇到表面的路径。关键的P-出口残基包括His93、Ser168、Thr100和Asn96。PLS团簇与P-Exit簇之间的氢键是由位于Thr100附近的空腔中的水线介导的，其水合作用可被疏水对Leu255B(靠近铜-A)和Ile99打断。D通道和通过Glu286的PLS之间的连接是由第二个可变的水化空腔控制的。意义陈述细胞色素C氧化酶在细胞呼吸和能量产生中起着关键作用。它将氧气还原为水，并利用释放的自由能在线粒体和细菌细胞膜上移动质子，增加了基本的电化学梯度。能量存储要求质子从膜的高pH、N侧被吸收，并释放到低pH、P侧。我们确定了一个潜在的质子从掩埋的极性残基簇(质子加载位置)通过水和保守残基组成的路径进入CCOO的P侧。只有在水合时，两个水腔才能将质子出射路径连接到表面。改变水化程度可能会控制从P侧回流的质子，否则对能量有利。
Cytochrome c Oxidase (CcO) reduces O-2, the terminal electron acceptor, to water in the aerobic, respiratory electron transport chain. The energy released by O-2 reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior. The P-side has a buried core of hydrogen-bonded protonatable residues designated the Proton Loading Site cluster (PIS cluster) and many protonatable residues on the P-side surface, providing no obvious unique exit. Hydrogen bond pathways were identified in Molecular Dynamics (MD) trajectories of Rb. sphaeroides CcO prepared in the P-R state with the heme a(3) propionate and Glu286 in different protonation states. Grand Canonical Monte Carlo sampling of water locations, polar proton positions and residue protonation states in trajectory snapshots identify a limited number of water mediated, proton paths from PLS cluster to the surface via a (P-exit) cluster of residues. Key P-exit residues include His93, Ser168, Thr100 and Asn96. The hydrogen bonds between PLS cluster and P-exit clusters are mediated by a water wire in a cavity centered near Thr100, whose hydration can be interrupted by a hydrophobic pair, Leu255B (near Cu-A) and Ile99. Connections between the D channel and PLS via Glu286 are controlled by a second, variably hydrated cavity.Significance statement Cytochrome C oxidase plays a crucial role in cellular respiration and energy generation. It reduces O-2 to water and uses the released free energy to move protons across mitochondrial and bacterial cell membranes adding to the essential electrochemical gradient. Energy storage requires that protons are taken up from the high pH, N-side and released to the low pH, P-side of the membrane. We identify a potential proton exit from a buried cluster of polar residues (the proton loading site) to the P-side of CcO via paths made up of waters and conserved residues. Two water cavities connect the proton exit pathway to the surface only when hydrated. Changing the degree of hydration may control otherwise energetically favorable proton backflow from the P-side.