Computer simulation of water in cytochrome c oxidase.
Computer simulation of water in cytochrome c oxidase.
复制标题
细胞色素c氧化酶中水的计算机模拟。
DOI：
10.1016/s0005-2728(03)00002-1
复制
发表时间：
2003
期刊：
影响因子：
--
通讯作者：
Stuchebrukhov,AlexeiA
中科院分区：
文献类型：
--
作者：
Zheng,Xuehe;Medvedev,DmitryM;Swanson,Jessica;Stuchebrukhov,AlexeiA
用统计力学和分子动力学方法模拟研究了牛心细胞色素c氧化酶（CcO）内部水分子的分布和动力学。发现CcO能够容纳大量的水，仅在亚基I中就有大约165个分子。这些水分子的动态特性进行。在血红素a3-CuB双核位点的氧化还原反应中产生的新生水分子形成了一种有趣的链状结构。该链起始于D通道末端Glu 242的位置，并具有叉状结构，其中一个分支通向双核中心，另一个通向血红素a3的丙酸盐d。通向双核中心的分支既可以动态地进入水形成的位点，也可以动态地进入His 291的δ-氮。从双核中心，链继续运行到K通道。这种氢键网络的稳定性进行了动态检查。催化位点位于疏水区，而新生水分子在能量山的顶部产生。能量梯度被用作从蛋白质中去除水的机制。采用高温动力学模拟探讨了水出口通道。已经确定了两个假定的通道，从催化位点的水出口。一个是直接通向Mg 2+位点。然而，该通道仅在His 291与CuB解离时打开。如果His 291与CuB结合，则水离开的唯一通道是起源于E242并通向膜中部的通道。这是可能用于氧气供应的相同通道。
Statistical mechanics and molecular dynamics simulations have been carried out to study the distribution and dynamics of internal water molecules in bovine heart cytochrome c oxidase (CcO). CcO is found to be capable of holding plenty of water, which in subunit I alone amounts to about 165 molecules. The dynamic characterization of these water molecules is carried out. The nascent water molecules produced in the redox reaction at the heme a3–CuB binuclear site form an intriguing chain structure. The chain begins at the position of Glu242 at the end of the D channel, and has a fork structure, one branch of which leads to the binuclear center, and the other to the propionate d of heme a3. The branch that leads to the binuclear center has dynamic access both to the site where the formation of water occurs, and to delta-nitrogen of His291. From the binuclear center, the chain continues to run into the K channel. The stability of this hydrogen bond network is examined dynamically. The catalytic site is located at the hydrophobic region, and the nascent water molecules are produced at the top of the energy hill. The energy gradient is utilized as the mechanism of water removal from the protein. The water exit channels are explored using high-temperature dynamics simulations. Two putative channels for water exit from the catalytic site have been identified. One is leading directly toward Mg2+site. However, this channel is only open when His291 is dissociated from CuB. If His291 is bound to CuB, the only channel for water exit is the one that originates at E242 and leads toward the middle of the membrane. This is the same channel that is presumably used for oxygen supply.
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DOI：
10.1016/s0005-2728(00)00066-9
发表时间：
2000-05
期刊：
Biochimica et biophysica acta
影响因子：
--
作者：
D. Zaslavsky;R. Gennis
通讯作者：
D. Zaslavsky;R. Gennis
DOI：
--
发表时间：
1999
期刊：
影响因子：
--
作者：
R. Pomès
通讯作者：
R. Pomès
细胞色素c氧化酶中质子穿梭的结构和动力学
DOI：
10.1016/s0005-2728(98)00077-2
发表时间：
1998
期刊：
Biochimica et Biophysica Acta
影响因子：
--
作者：
R. Pomès;G. Hummer;M. Wikström
通讯作者：
M. Wikström
细胞色素c氧化酶中的超快血红素-血红素电子转移。
DOI：
--
发表时间：
2001
期刊：
Biochimica et Biophysica Acta
影响因子：
--
作者：
M. Verkhovsky;A. Jasaitis;M. Wikström
通讯作者：
M. Wikström
影响因子：
3.5
作者：
S. Riistama;Gerhard Hummer;A. Puustinen;A. Puustinen;R. Dyer;William H. Woodruff;Mårten Wikström
通讯作者：
Mårten Wikström