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

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)359-384
Number of pages26
JournalMolecular Physics
Volume113
DOIs
Publication statusPublished - Feb 16 2015

Fingerprint

Molecular mechanics
Photosystem II Protein Complex
Hydrogen Bonding
Mechanics
Hydrogen bonds
Oxygen
Protons
oxygen
hydrogen
X-Ray Diffraction
protons
oxidation
X ray diffraction
x rays
Oxidation
computational mechanics
chlorides
Anions
diffraction
Water

Keywords

  • CaMn4O5
  • hydrogen bonds networks
  • mutations
  • photosystem II
  • QM/MM

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Condensed Matter Physics
  • Biophysics
  • Molecular Biology

Cite this

Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II. / Shoji, Mitsuo; Isobe, Hiroshi; Yamanaka, Shusuke; Umena, Yasufumi; Kawakami, Keisuke; Kamiya, Nobuo; Shen, Jian-Ren; Nakajima, Takahito; Yamaguchi, Kizashi.

In: Molecular Physics, Vol. 113, 16.02.2015, p. 359-384.

Research output: Contribution to journalArticle

Shoji, Mitsuo ; Isobe, Hiroshi ; Yamanaka, Shusuke ; Umena, Yasufumi ; Kawakami, Keisuke ; Kamiya, Nobuo ; Shen, Jian-Ren ; Nakajima, Takahito ; Yamaguchi, Kizashi. / Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II. In: Molecular Physics. 2015 ; Vol. 113. pp. 359-384.
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