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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Molecular Dynamics Simulations of Carbon Monoxide Dissociation from Heme a_3 in Cytochrome c Oxidase from Paracoccus Denitrificans
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Molecular Dynamics Simulations of Carbon Monoxide Dissociation from Heme a_3 in Cytochrome c Oxidase from Paracoccus Denitrificans

机译：副球菌属细胞色素c氧化酶中血红素a_3一氧化碳解离的分子动力学模拟

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摘要

We have investigated ligand motions the heme a_3-CuB binuclear active site of cytochrome c oxidase by molecular dynamics simulations. The starting structural model is based on the two-subunit structure from the Paracoccus denitrificans enzyme and contains carbon monoxide (CO) bound to heme a_3. Short (1 ps) trajectories of the enzyme were calculated, each initiated by the sudden breaking of the Fea_3-Co bond. A comparison of two sets of calculations suggests a functional mechanistic role of the covalent bond between Tyr280 and His276, the latter being one of the three histidines coordinating the copper atom CuB. In particular, the presence of this bond enhances the coupling of the CO motion to the environment and confines motion of CO on the picosecond time scale to the region close to CuB. On the time scale of a few hundred femtoseconds after dissociation, the most important movement of CO consists of rotation over approx 90 deg and the most favorable position for binding to CuB appears to be occupied after 300-400 fs. These results are discussed in the light of the recent suggestion that the reaction coordinate of coherent reaction dynamics of heme a_3 after photodissociation involves CO transfer to CuB (Liebl, U.; Lipowski, G.; Negrerie, M.; Lambry J.-C.; Martin, J.-L.; Vos, M. H. Nature 1999, 401, 181.).
机译：我们已经通过分子动力学模拟研究了细胞色素C氧化酶的血红素a_3-CuB双核活性位点的配体运动。起始结构模型基于反硝化副球菌酶的两个亚基结构，并包含与血红素a_3结合的一氧化碳（CO）。计算了酶的短轨迹（1 ps），每个轨迹均由Fea_3-Co键的突然断裂引发。两组计算的比较表明，Tyr280和His276之间的共价键具有功能性机械作用，后者是配位铜原子CuB的三个组氨酸之一。尤其是，该键的存在增强了CO运动与环境的耦合，并将CO在皮秒级的运动范围内限制在接近CuB的区域。在解离后几百飞秒的时间尺度上，CO的最重要运动是旋转约90度，并且在300-400 fs之后占据了最有利于与CuB结合的位置。根据最近的建议讨论了这些结果，即光解离后血红素a_3的相干反应动力学的反应坐标涉及将CO转移到CuB（Liebl，U .; Lipowski，G .; Negrerie，M .; Lambry J.-C 。; Martin，J.-L .; Vos，MH Nature 1999，401，181.）。

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