Theoretical modeling of biomolecular system I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II
Theoretical modeling of biomolecular system I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II
复制标题
生物分子系统的理论建模 I. 光系统放氧复合体氢键网络的大规模 QM/MM 计算 II
DOI：
10.1080/00268976.2014.960021
复制
发表时间：
2015
影响因子：
1.7
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;J.-R. Shen;T. Nakajima;K. Yamaguchi
利用量子力学(QM)/分子力学（MM）的大尺度量子力学模型（QM模型V）对光系统II （PSII）的析氧络合物（OEC）中水氧化反应的质子释放途径（PRP）的氢键网络和质子线进行了计算。用QM/MM模型对PRP进行了全面的几何优化，从PSII最近的高分辨率x射线衍射（XRD）实验确定的重原子几何开始，精确到1.9 Å分辨率。通过QM/MM计算得到PRP中氢键O··O(N)和O··H的距离和O(N) -H·O的角，以及氯离子的Cl - O(N)和Cl··H的距离和O(N) -H·Cl的角。优化后的氢键网络与XRD结果和扩展x射线吸收精细结构等现有实验结果吻合较好，表明了XRD实验揭示的PSII OEC通道结构的可靠性。QM/MM计算已经阐明了氯离子在PSII OEC中的可能作用。QM/MM计算结果为理解和解释PSII OEC中关键氨基酸残基的累积突变实验提供了有用的信息。讨论了目前结果的含义，涉及PSII OEC中水氧化理论建模的三个步骤，以及利用三维过渡金属配合物开发人工水氧化系统的生物启发工作假设。
Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O···O(N) and O···H distances and O(N)–H···O angles in PRP, together with the Cl–O(N) and Cl···H distances and O(N)–H···Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.