Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II

Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Jian Ren Shen, Takahito Nakajima, Kizashi Yamaguchi

研究成果査読

28 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)359-384
ページ数26
ジャーナルMolecular Physics
113
DOI
出版ステータスPublished - 2月 16 2015

ASJC Scopus subject areas

  • 生物理学
  • 分子生物学
  • 凝縮系物理学
  • 物理化学および理論化学

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