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Isobe H, Shoji M, Suzuki T, Shen JR, Yamaguchi K. Roles of the Flexible Primary Coordination Sphere of the Mn 4CaO x Cluster: What Are the Immediate Decay Products of the S3 State? J Phys Chem B 2022; 126:7212-7228. [DOI: 10.1021/acs.jpcb.2c02596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Mitsuo Shoji
- Center for Computational Science, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takayoshi Suzuki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-0043, Japan
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2
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Boussac A, Sugiura M, Sellés J. Probing the proton release by Photosystem II in the S 1 to S 2 high-spin transition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148546. [PMID: 35337840 DOI: 10.1016/j.bbabio.2022.148546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The stoichiometry and kinetics of the proton release were investigated during each transition of the S-state cycle in Photosystem II (PSII) from Thermosynechococcus elongatus containing either a Mn4CaO5 (PSII/Ca) or a Mn4SrO5 (PSII/Sr) cluster. The measurements were done at pH 6.0 and pH 7.0 knowing that, in PSII/Ca at pH 6.0 and pH 7.0 and in PSII/Sr at pH 6.0, the flash-induced S2-state is in a low-spin configuration (S2LS) whereas in PSII/Sr at pH 7.0, the S2-state is in a high-spin configuration (S2HS) in half of the centers. Two measurements were done; the time-resolved flash dependent i) absorption of either bromocresol purple at pH 6.0 or neutral red at pH 7.0 and ii) electrochromism in the Soret band of PD1 at 440 nm. The fittings of the oscillations with a period of four indicate that one proton is released in the S1 to S2HS transition in PSII/Sr at pH 7.0. It has previously been suggested that the proton released in the S2LS to S3 transition would be released in a S2LSTyrZ• → S2HSTyrZ• transition before the electron transfer from the cluster to TyrZ• occurs. The release of a proton in the S1TyrZ• → S2HSTyrZ transition would logically imply that this proton release is missing in the S2HSTyrZ• to S3TyrZ transition. Instead, the proton release in the S1 to S2HS transition in PSII/Sr at pH 7.0 was mainly done at the expense of the proton release in the S3 to S0 and S0 to S1 transitions. However, at pH 7.0, the electrochromism of PD1 seems larger in PSII/Sr when compared to PSII/Ca in the S3 state. This points to the complex link between proton movements in and immediately around the Mn4 cluster and the mechanism leading to the release of protons into the bulk.
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Affiliation(s)
- Alain Boussac
- I(2)BC, UMR CNRS 9198, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | - Miwa Sugiura
- Proteo-Science Research Center, Department of Chemistry, Graduate School of Science and Technology, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Julien Sellés
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 and Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France
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3
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Drosou M, Zahariou G, Pantazis DA. Orientational Jahn-Teller Isomerism in the Dark-Stable State of Nature's Water Oxidase. Angew Chem Int Ed Engl 2021; 60:13493-13499. [PMID: 33830630 PMCID: PMC8252073 DOI: 10.1002/anie.202103425] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 01/31/2023]
Abstract
The tetramanganese–calcium cluster of the oxygen‐evolving complex of photosystem II adopts electronically and magnetically distinct but interconvertible valence isomeric forms in its first light‐driven oxidized catalytic state, S2. This bistability is implicated in gating the final catalytic states preceding O−O bond formation, but it is unknown how the biological system enables its emergence and controls its effect. Here we show that the Mn4CaO5 cluster in the resting (dark‐stable) S1 state adopts orientational Jahn–Teller isomeric forms arising from a directional change in electronic configuration of the “dangler” MnIII ion. The isomers are consistent with available structural data and explain previously unresolved electron paramagnetic resonance spectroscopic observations on the S1 state. This unique isomerism in the resting state is shown to be the electronic origin of valence isomerism in the S2 state, establishing a functional role of orientational Jahn–Teller isomerism unprecedented in biological or artificial catalysis.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Greece
| | - Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Athens, 15310, Greece
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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4
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Drosou M, Zahariou G, Pantazis DA. Orientational Jahn–Teller Isomerism in the Dark‐Stable State of Nature's Water Oxidase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Maria Drosou
- Inorganic Chemistry Laboratory National and Kapodistrian University of Athens, Panepistimiopolis Zografou 15771 Greece
| | - Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos” Athens 15310 Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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5
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Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Kawakami T. Theory of chemical bonds in metalloenzymes XXIII fundamental principles for the photo-induced water oxidation in oxygen evolving complex of photosystem II. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1725168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K. Yamaguchi
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- Institute for Nanoscience Design, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Japan
| | - K. Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - T. Kawakami
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
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6
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Water-oxidizing complex in Photosystem II: Its structure and relation to manganese-oxide based catalysts. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213183] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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7
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Shoji M, Isobe H, Shen JR, Suga M, Akita F, Miyagawa K, Shigeta Y, Yamaguchi K. Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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8
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Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Yamaguchi K. Theoretical Elucidation of Geometrical Structures of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn–Teller Effects. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Shoji M, Isobe H, Tanaka A, Fukushima Y, Kawakami K, Umena Y, Kamiya N, Nakajima T, Yamaguchi K. Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem II: Applicability of the Jahn-Teller Deformation Formula. CHEMPHOTOCHEM 2018; 2:257-270. [PMID: 29577075 PMCID: PMC5861676 DOI: 10.1002/cptc.201700162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/02/2017] [Indexed: 11/11/2022]
Abstract
Tanaka et al. (J. Am. Chem. Soc., 2017, 139, 1718) recently reported the three-dimensional (3D) structure of the oxygen evolving complex (OEC) of photosystem II (PSII) by X-ray diffraction (XRD) using extremely low X-ray doses of 0.03 and 0.12 MGy. They observed two different 3D structures of the CaMn4O5 cluster with different hydrogen-bonding interactions in the S1 state of OEC keeping the surrounding polypeptide frameworks of PSII the same. Our Jahn-Teller (JT) deformation formula based on large-scale quantum mechanics/molecular mechanics (QM/MM) was applied for these low-dose XRD structures, elucidating important roles of JT effects of the MnIII ion for subtle geometric distortions of the CaMn4O5 cluster in OEC of PSII. The JT deformation formula revealed the similarity between the low-dose XRD and damage-free serial femtosecond X-ray diffraction (SFX) structures of the CaMn4O5 cluster in the dark stable state. The extremely low-dose XRD structures were not damaged by X-ray irradiation. Implications of the present results are discussed in relation to recent SFX results and a blue print for the design of artificial photocatalysts for water oxidation.
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Affiliation(s)
- Mitsuo Shoji
- Center of Computational SciencesTsukuba University, TsukubaIbaraki305–8577Japan
| | - Hiroshi Isobe
- Graduate School of Natural Science and TechnologyOkayama UniversityOkayama700–8530Japan
| | - Ayako Tanaka
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Yoshimasa Fukushima
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Keisuke Kawakami
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Yasufumi Umena
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Nobuo Kamiya
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Takahito Nakajima
- Riken Advanced Institute for Computational Science, Chuo-KuKobe, Hyogo650-0047Japan
| | - Kizashi Yamaguchi
- Riken Advanced Institute for Computational Science, Chuo-KuKobe, Hyogo650-0047Japan
- Institute for Nanoscience DesignOsaka University, ToyonakaOsaka560–8531Japan
- Handairigaku Techno-Research, ToyonakaOsaka560-0043Japan
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10
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Sakashita N, Watanabe HC, Ikeda T, Saito K, Ishikita H. Origins of Water Molecules in the Photosystem II Crystal Structure. Biochemistry 2017; 56:3049-3057. [DOI: 10.1021/acs.biochem.7b00220] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoki Sakashita
- Department
of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi C. Watanabe
- Department
of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takuya Ikeda
- Department
of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department
of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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11
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Paul S, Cox N, Pantazis DA. What Can We Learn from a Biomimetic Model of Nature’s Oxygen-Evolving Complex? Inorg Chem 2017; 56:3875-3888. [DOI: 10.1021/acs.inorgchem.6b02777] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Satadal Paul
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Dimitrios A. Pantazis
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
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12
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Shoji M, Isobe H, Shen JR, Yamaguchi K. Geometric and electronic structures of the synthetic Mn₄CaO₄ model compound mimicking the photosynthetic oxygen-evolving complex. Phys Chem Chem Phys 2017; 18:11330-40. [PMID: 27055567 DOI: 10.1039/c5cp07226c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(Bu(t)COO)8(py)(Bu(t)COOH)2] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan and Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan.
| | - Hiroshi Isobe
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-0043, Japan and Handairigaku Techno-Research (NPO), Toyonaka, Osaka 560-0043, Japan
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13
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Yamaguchi K, Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N. On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn–Teller effects. Mol Phys 2017. [DOI: 10.1080/00268976.2016.1278476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- K. Yamaguchi
- Institute for Nanoscience Design, Osaka University, Toyonaka, Japan
- Handairigaku Techno-Research , Toyonaka, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University , Tsukuba, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University , Okayama, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University , Osaka, Japan
| | - Y. Umena
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University , Osaka, Japan
| | - K. Kawakami
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University , Osaka, Japan
| | - N. Kamiya
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University , Osaka, Japan
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14
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Isobe H. Functional significance of the “distorted chair” topology of the Mn cluster for oxygen evolution in photosynthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.4019/bjscc.70.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University
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15
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Shoji M, Isobe H, Nakajima T, Shigeta Y, Suga M, Akita F, Shen JR, Yamaguchi K. Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures. Faraday Discuss 2017; 198:83-106. [DOI: 10.1039/c6fd00230g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mna(4)–Mnd(1) distance determined by QM/MM was about 5.0 Å for the S3 structure without an inserted hydroxide anion, but this is elongated by 0.2–0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O–O bond formation in water oxidation by the OEC of PSII.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
- Graduate School of Pure and Applied Sciences
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | | | - Yasuteru Shigeta
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
- Graduate School of Pure and Applied Sciences
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | - Kizashi Yamaguchi
- Riken Advanced Institute for Computational Science
- Kobe
- Japan
- Institute for NanoScience Design
- Osaka University
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Guo Y, Li H, He LL, Zhao DX, Gong LD, Yang ZZ. The open-cubane oxo–oxyl coupling mechanism dominates photosynthetic oxygen evolution: a comprehensive DFT investigation on O–O bond formation in the S4state. Phys Chem Chem Phys 2017; 19:13909-13923. [DOI: 10.1039/c7cp01617d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How is O2created in nature? Comprehensive DFT investigations determine the dominance of the open-cubane oxo–oxyl coupling mechanism over alternative possibilities.
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Affiliation(s)
- Yu Guo
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Hui Li
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Lan-Lan He
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
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17
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Chernev P, Zaharieva I, Rossini E, Galstyan A, Dau H, Knapp EW. Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII. J Phys Chem B 2016; 120:10899-10922. [DOI: 10.1021/acs.jpcb.6b05800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Petko Chernev
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ivelina Zaharieva
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Emanuele Rossini
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Artur Galstyan
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Holger Dau
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
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18
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Gerey B, Gouré E, Fortage J, Pécaut J, Collomb MN. Manganese-calcium/strontium heterometallic compounds and their relevance for the oxygen-evolving center of photosystem II. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Chuah WY, Stranger R, Pace RJ, Krausz E, Frankcombe TJ. Deprotonation of Water/Hydroxo Ligands in Clusters Mimicking the Water Oxidizing Complex of PSII and Its Effect on the Vibrational Frequencies of Ligated Carboxylate Groups. J Phys Chem B 2016; 120:377-85. [PMID: 26727127 DOI: 10.1021/acs.jpcb.5b09987] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The IR absorptions of several first-shell carboxylate ligands of the water oxidizing complex (WOC) have been experimentally shown to be unaffected by oxidation state changes in the WOC during its catalytic cycle. Several model clusters that mimic the Mn4O5Ca core of the WOC in the S1 state, with electronic configurations that correspond to both the so-called "high" and "low" oxidation paradigms, were investigated. Deprotonation at W2, W1, or O3 sites was found to strongly reduce carboxylate ligand frequency shifts on oxidation of the metal cluster. The frequency shifts were smallest in neutrally charged clusters where the initial mean Mn oxidation state was +3, with W2 as an hydroxide and O5 a water. Deprotonation also reduced and balanced the oxidation energy of all clusters in successive oxidations.
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Affiliation(s)
- Wooi Yee Chuah
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Rob Stranger
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Elmars Krausz
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Terry J Frankcombe
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia.,School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra, Australian Capital Territory 2600, Australia
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21
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Najafpour MM, Renger G, Hołyńska M, Moghaddam AN, Aro EM, Carpentier R, Nishihara H, Eaton-Rye JJ, Shen JR, Allakhverdiev SI. Manganese Compounds as Water-Oxidizing Catalysts: From the Natural Water-Oxidizing Complex to Nanosized Manganese Oxide Structures. Chem Rev 2016; 116:2886-936. [PMID: 26812090 DOI: 10.1021/acs.chemrev.5b00340] [Citation(s) in RCA: 337] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn-Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25-90 molecules of O2 released per second. In this Review, we discuss the atomic structure of the Mn-Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn complexes decomposing to Mn oxide. We then provide a detailed assessment of the chemistry of Mn oxides by considering how their bulk and nanoscale properties contribute to their effectiveness as water-oxidizing catalysts.
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Affiliation(s)
| | - Gernot Renger
- Institute of Chemistry, Max-Volmer-Laboratory of Biophysical Chemistry, Technical University Berlin , Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Małgorzata Hołyńska
- Fachbereich Chemie und Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg , Hans-Meerwein-Straße, D-35032 Marburg, Germany
| | | | - Eva-Mari Aro
- Department of Biochemistry and Food Chemistry, University of Turku , 20014 Turku, Finland
| | - Robert Carpentier
- Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières , C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - Hiroshi Nishihara
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1, Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Julian J Eaton-Rye
- Department of Biochemistry, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Faculty of Science, Okayama University , Okayama 700-8530, Japan.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
| | - Suleyman I Allakhverdiev
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences , Botanicheskaya Street 35, Moscow 127276, Russia.,Institute of Basic Biological Problems, Russian Academy of Sciences , Pushchino, Moscow Region 142290, Russia.,Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University , Leninskie Gory 1-12, Moscow 119991, Russia
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22
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Yamaguchi K, Isobe H, Shoji M, Yamanaka S, Okumura M. Theory of chemical bonds in metalloenzymes XX: magneto-structural correlations in the CaMn4O5cluster in oxygen-evolving complex of photosystem II. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1114162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Shoji M, Isobe H, Nakajima T, Yamaguchi K. Full geometry optimizations of the CaMn4O4 model cluster for the oxygen evolving complex of photosystem II. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Beckwith MA, Ames W, Vila FD, Krewald V, Pantazis DA, Mantel C, Pécaut J, Gennari M, Duboc C, Collomb MN, Yano J, Rehr JJ, Neese F, DeBeer S. How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II. J Am Chem Soc 2015; 137:12815-34. [PMID: 26352328 DOI: 10.1021/jacs.5b00783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
First principle calculations of extended X-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S0(2) and Debye-Waller values as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first-principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.
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Affiliation(s)
- Martha A Beckwith
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - William Ames
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Fernando D Vila
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Vera Krewald
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Claire Mantel
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Jacques Pécaut
- Laboratoire de Reconnaissance Ionique et Chimie de Coordination, Service de Chimie Inorganique et Biologique, (UMR E-3 CEA/UJF, FRE3200 CNRS), CEA-Grenoble, INAC , 17 rue des Martyrs 38054 Grenoble cedex 9, France
| | - Marcello Gennari
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Carole Duboc
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Marie-Noëlle Collomb
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - John J Rehr
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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