Theoretical insight in to hydrogen-bonding networks and proton wire for the CaMn4O5 cluster of photosystem II. Elongation of Mn–Mn distances with hydrogen bonds
Theoretical insight in to hydrogen-bonding networks and proton wire for the CaMn4O5 cluster of photosystem II. Elongation of Mn–Mn distances with hydrogen bonds
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对光系统 II 的 CaMn4O5 簇的氢键网络和质子线的理论见解 通过氢键延长 Mn-Mn 距离。
DOI：
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
K. Yamaguchi
中科院分区：
文献类型：
--
作者：
M. Shoji;H. Isobe;S. Yamanaka;Y. Umena;K. Kawakami;N. Kamiya;Jian;K. Yamaguchi
利用量子力学（QM）和量子力学/分子力学（MM）计算了光系统II （PSII）演化氧络合物（OEC）水氧化反应中质子释放途径（PRP）的氢键网络和质子线。对PSII OEC活性位CaMn4O5配合物的扩展QM模型III（包括第二配位球）中所有氢原子的位置进行了优化，假设PSII最近的高分辨率x射线衍射（XRD）实验确定的重原子几何形状精细到1.9 A分辨率。为了阐明蛋白质对CaMn4O5簇几何参数的约束效应，我们还对嵌入在模型III和QM (QM模型I加7个水分子，即QM模型II)/MM模型中的第一个配位球模型（QM模型I）进行了全几何优化。这些方法的计算结果已经阐明了质子释放路径（PRP） I和II中氢键的O⋯O(N)， O⋯H距离和O(N) -H⋯O角度，这些路径构建了从Asp61到His190的质子线。揭示的氢键结构也被检查与桥氧离子质子化的可能性在CaMn4O5簇。通过QM模型I和模型III以及QM（模型II）/MM对原子间距离的优化，揭示了Mn-Mn距离随氢键的延长以及mn - o(5)长度随蛋白质约束效应的变化。结合现有的EXAFS实验，以及高分辨率（SP8） XRD的内、半内、外还原Mn离子和Mn - Mn长距离，合理设计水氧化人工催化剂，讨论了计算结果的意义。这些都是目前PSII OEC领域的研究热点。
Quantum mechanical (QM) and QM/molecular mechanics (MM) calculations of three different cluster models have been performed to shed light on hydrogen bonding networks and proton wires for proton release pathways (PRP) of water oxidation reactions in the oxygen evolving complex (OEC) of photosystem II (PSII). Positions of all the hydrogen atoms in an extended QM Model III including the second coordination sphere for the active-site CaMn4O5 complex of OEC of PSII have been optimized assuming the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 A resolution. Full geometry optimizations of the first coordination sphere model (QM Model I) embedded in the Model III and QM (QM Model I plus seven water molecules, namely QM Model II)/MM models, together with full QM Model III, have also been conducted to elucidate confinement effects for geometrical parameters of the CaMn4O5 cluster by proteins. Computational results by these methods have elucidated the O⋯O(N), O⋯H distances and O(N)–H⋯O angles for hydrogen bonds in proton release paths (PRP) I and II that construct a proton wire from Asp61 toward His190. The hydrogen-bonding structures revealed have also been examined in relation to the possibilities of protonation of bridge oxygen dianions within the CaMn4O5 cluster. The optimized inter-atomic distances by QM Models I and III, together with QM(Model II)/MM, have elucidated the elongation of the Mn–Mn distances with hydrogen bonds and variations of the Mnd–O(5) length with confinement effects by protein. Implications of the computational results are discussed in relation to the available EXAFS experiments, and internal, semi-internal and external reductions of Mn ions and long Mn–Mn distances of the high-resolution (SP8) XRD, and rational design of artificial catalysts for water oxidation that are current topics in the field of OEC of PSII.
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DOI：
10.1016/s0005-2728(00)00217-6
发表时间：
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期刊：
Biochimica et biophysica acta
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DOI：
10.1073/pnas.1204598109
发表时间：
2012-06-19
影响因子：
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