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Guo Y, He L, Ding Y, Kloo L, Pantazis DA, Messinger J, Sun L. Closing Kok's cycle of nature's water oxidation catalysis. Nat Commun 2024; 15:5982. [PMID: 39013902 PMCID: PMC11252165 DOI: 10.1038/s41467-024-50210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0-4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature's water oxidation catalysis.
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Affiliation(s)
- Yu Guo
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Lanlan He
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Yunxuan Ding
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Lars Kloo
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10044, Stockholm, Sweden
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr, 45470, Germany
| | - Johannes Messinger
- Department of Plant Physiology, Umeå University, Linnaeus väg 6 (KBC huset), SE-90187, Umeå, Sweden
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, SE-75120, Uppsala, Sweden
| | - Licheng Sun
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou, 310024, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China.
- Division of Solar Energy Conversion and Catalysis at Westlake University, Zhejiang Baima Lake Laboratory Co., Ltd., Hangzhou, 310000, Zhejiang, China.
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Abstract
Photosystem II (PSII) uses water as the terminal electron donor, producing oxygen in the Mn4CaO5 oxygen evolving complex (OEC), while cytochrome c oxidase (CcO) reduces O2 to water in its heme–Cu binuclear center (BNC). Each protein is oriented in the membrane to add to the proton gradient. The OEC, which releases protons, is located near the P-side (positive, at low-pH) of the membrane. In contrast, the BNC is in the middle of CcO, so the protons needed for O2 reduction must be transferred from the N-side (negative, at high pH). In addition, CcO pumps protons from N- to P-side, coupled to the O2 reduction chemistry, to store additional energy. Thus, proton transfers are directly coupled to the OEC and BNC redox chemistry, as well as needed for CcO proton pumping. The simulations that study the changes in proton affinity of the redox active sites and the surrounding protein at different states of the reaction cycle, as well as the changes in hydration that modulate proton transfer paths, are described.
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3
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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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Affiliation(s)
- Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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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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6
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Rossini E, Knapp EW. Protonation equilibria of transition metal complexes: From model systems toward the Mn-complex in photosystem II. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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7
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Nakamura S, Noguchi T. Infrared Determination of the Protonation State of a Key Histidine Residue in the Photosynthetic Water Oxidizing Center. J Am Chem Soc 2017. [DOI: 10.1021/jacs.7b04924] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shin Nakamura
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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8
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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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Takaoka T, Sakashita N, Saito K, Ishikita H. pK(a) of a Proton-Conducting Water Chain in Photosystem II. J Phys Chem Lett 2016; 7:1925-32. [PMID: 27128410 DOI: 10.1021/acs.jpclett.6b00656] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent high-resolution crystal structures of the water-oxidizing enzyme photosystem II (PSII) show that O4 of the catalytic Mn4CaO5 cluster forms an H-bond with a water molecule W539, which belongs to a chain of water molecules (O4-water chain). Oxidation of Mn4CaO5 to S1 resulted in elongation of the O-H bonds and decrease in pKa(O-H/O(-)) in the [O4-H···OW539-H···OW538-H···OW393] region along the O4-water chain. In S1, removal of all water molecules from the O4-water chain, except W539, resulted in a significant pKa upshift at O4; this suggests that the proton-conducting water chain serves as a conducting media for protons and significantly decreases the donor pKa, leading to a downhill proton transfer. The absence of a corresponding proton-conducting channel is disadvantageous for release of protons from the proton-releasing site, as in the case of O5 that has no H-bond partner.
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Affiliation(s)
- Tomohiro Takaoka
- Department of Applied Chemistry, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Naoki Sakashita
- 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
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, 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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Redox-coupled substrate water reorganization in the active site of Photosystem II-The role of calcium in substrate water delivery. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:740-8. [PMID: 26826591 DOI: 10.1016/j.bbabio.2016.01.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/10/2015] [Accepted: 01/26/2016] [Indexed: 01/08/2023]
Abstract
Photosystem II (PSII) catalyzes light-driven water splitting in nature and is the key enzyme for energy input into the biosphere. Important details of its mechanism are not well understood. In order to understand the mechanism of water splitting, we perform here large-scale density functional theory (DFT) calculations on the active site of PSII in different oxidation, spin and ligand states. Prior to formation of the O-O bond, we find that all manganese atoms are oxidized to Mn(IV) in the S3 state, consistent with earlier studies. We find here, however, that the formation of the S3 state is coupled to the movement of a calcium-bound hydroxide (W3) from the Ca to a Mn (Mn1 or Mn4) in a process that is triggered by the formation of a tyrosyl radical (Tyr-161) and its protonated base, His-190. We find that subsequent oxidation and deprotonation of this hydroxide on Mn1 result in formation of an oxyl-radical that can exergonically couple with one of the oxo-bridges (O5), forming an O-O bond. When O(2) leaves the active site, a second Ca-bound water molecule reorients to bridge the gap between the manganese ions Mn1 and Mn4, forming a new oxo-bridge for the next reaction cycle. Our findings are consistent with experimental data, and suggest that the calcium ion may control substrate water access to the water oxidation sites.
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11
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Retegan M, Krewald V, Mamedov F, Neese F, Lubitz W, Cox N, Pantazis DA. A five-coordinate Mn(iv) intermediate in biological water oxidation: spectroscopic signature and a pivot mechanism for water binding. Chem Sci 2015; 7:72-84. [PMID: 29861966 PMCID: PMC5950799 DOI: 10.1039/c5sc03124a] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 11/17/2015] [Indexed: 01/16/2023] Open
Abstract
Among the four photo-driven transitions of the water-oxidizing tetramanganese-calcium cofactor of biological photosynthesis, the second-last step of the catalytic cycle, that is the S2 to S3 state transition, is the crucial step that poises the catalyst for the final O-O bond formation. This transition, whose intermediates are not yet fully understood, is a multi-step process that involves the redox-active tyrosine residue and includes oxidation and deprotonation of the catalytic cluster, as well as the binding of a water molecule. Spectroscopic data has the potential to shed light on the sequence of events that comprise this catalytic step, which still lacks a structural interpretation. In this work the S2-S3 state transition is studied and a key intermediate species is characterized: it contains a Mn3O4Ca cubane subunit linked to a five-coordinate Mn(iv) ion that adopts an approximately trigonal bipyramidal ligand field. It is shown using high-level density functional and multireference wave function calculations that this species accounts for the near-infrared absorption and electron paramagnetic resonance observations on metastable S2-S3 intermediates. The results confirm that deprotonation and Mn oxidation of the cofactor must precede the coordination of a water molecule, and lead to identification of a novel low-energy water binding mode that has important implications for the identity of the substrates in the mechanism of biological water oxidation.
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Affiliation(s)
- Marius Retegan
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Vera Krewald
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Fikret Mamedov
- Molecular Biomimetics , Department of Chemistry - Ångstrom Laboratory , Uppsala University , Box 523 , 75120 Uppsala , Sweden
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Wolfgang Lubitz
- 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 . ;
| | - 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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Meyer T, Knapp EW. pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories. J Chem Theory Comput 2015; 11:2827-40. [PMID: 26575575 DOI: 10.1021/acs.jctc.5b00123] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For a benchmark set of 194 measured pKa values in 13 proteins, electrostatic energy computations are performed in which pKa values are computed by solving the Poisson-Boltzmann equation. In contrast to the previous approach of Karlsberg(+) (KB(+)) that essentially used protein crystal structures with variations in their side chain conformations, the present approach (KB2(+)MD) uses protein conformations from four molecular dynamics (MD) simulations of 10 ns each. These MD simulations are performed with different specific but fixed protonation patterns, selected to sample the conformational space for the different protonation patterns faithfully. The root-mean-square deviation between computed and measured pKa values (pKa RMSD) is shown to be reduced from 1.17 pH units using KB(+) to 0.96 pH units using KB2(+)MD. The pKa RMSD can be further reduced to 0.79 pH units, if each conformation is energy-minimized with a dielectric constant of εmin = 4 prior to calculating the electrostatic energy. The electrostatic energy expressions upon which the computations are based have been reformulated such that they do not involve terms that mix protein and solvent environment contributions and no thermodynamic cycle is needed. As a consequence, conformations of the titratable residues can be treated independently in the protein and solvent environments. In addition, the energy terms used here avoid the so-called intrinsic pKa and can therefore be interpreted without reference to arbitrary protonation states and conformations.
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Affiliation(s)
- Tim Meyer
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Fabeckstrasse 36A, 14195 Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Fabeckstrasse 36A, 14195 Berlin, Germany
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13
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Amin M, Vogt L, Szejgis W, Vassiliev S, Brudvig GW, Bruce D, Gunner MR. Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II. J Phys Chem B 2015; 119:7366-77. [PMID: 25575266 DOI: 10.1021/jp510948e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The oxygen-evolving complex (OEC) of photosystem II (PSII) is a unique Mn4O5Ca cluster that catalyzes water oxidation via four photoactivated electron transfer steps. As the protein influence on the redox and protonation chemistry of the OEC remains an open question, we present a classical valence model of the OEC that allows the redox state of each Mn and the protonation state of bridging μ-oxos and terminal waters to remain in equilibrium with the PSII protein throughout the redox cycle. We find that the last bridging oxygen loses its proton during the transition from S0 to S1. Two possible S2 states are found depending on the OEC geometry: S2 has Mn4(IV) with a proton lost from a terminal water (W1) trapped by the nearby D1-D61 if O5 is closer to Mn4, or Mn1(IV), with partial deprotonation of D1-H337 and D1-E329 if O5 is closer to Mn1. In S3, the OEC is Mn4(IV) with W2 deprotonated. The estimated OEC Em's range from +0.7 to +1.3 V, enabling oxidation by P680(+), the primary electron donor in PSII. In chloride-depleted PSII, the proton release increases during the S1 to S2 transition, leaving the OEC unable to properly advance through the water-splitting cycle.
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Affiliation(s)
- Muhamed Amin
- †Department of Physics, J-419, City College of New York, 138th Street, Convent Avenue, New York, New York 10031, United States
| | - Leslie Vogt
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Witold Szejgis
- †Department of Physics, J-419, City College of New York, 138th Street, Convent Avenue, New York, New York 10031, United States
| | - Serguei Vassiliev
- §Department of Biological Sciences, Brock University, 500 Glenridge Ave., St. Catherines, ON LS2 3A1, Canada
| | - Gary W Brudvig
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Doug Bruce
- §Department of Biological Sciences, Brock University, 500 Glenridge Ave., St. Catherines, ON LS2 3A1, Canada
| | - M R Gunner
- †Department of Physics, J-419, City College of New York, 138th Street, Convent Avenue, New York, New York 10031, United States
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Vogt L, Ertem MZ, Pal R, Brudvig GW, Batista VS. Computational Insights on Crystal Structures of the Oxygen-Evolving Complex of Photosystem II with Either Ca2+ or Ca2+ Substituted by Sr2+. Biochemistry 2015; 54:820-5. [DOI: 10.1021/bi5011706] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leslie Vogt
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Mehmed Z. Ertem
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Rhitankar Pal
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Gary W. Brudvig
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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15
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Krewald V, Retegan M, Cox N, Messinger J, Lubitz W, DeBeer S, Neese F, Pantazis DA. Metal oxidation states in biological water splitting. Chem Sci 2015; 6:1676-1695. [PMID: 29308133 PMCID: PMC5639794 DOI: 10.1039/c4sc03720k] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/31/2014] [Indexed: 12/20/2022] Open
Abstract
A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II.
A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five Si states (i = 0–4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called “high-valent scheme”—where, for example, the Mn oxidation states in the S2 state are assigned as III, IV, IV, IV—the competing “low-valent scheme” that differs by a total of two metal unpaired electrons (i.e. III, III, III, IV in the S2 state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi)stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K 55Mn ENDOR data of the S2 state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S0 (III, III, III, IV) to S3 (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S states and the states involved in the assembly of the catalytically active water oxidizing cluster.
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Affiliation(s)
- Vera Krewald
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Johannes Messinger
- Department of Chemistry , Chemical Biological Center (KBC) , Umeå University , 90187 Umeå , Sweden
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
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Shen JR. The Structure of Photosystem II and the Mechanism of Water Oxidation in Photosynthesis. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:23-48. [PMID: 25746448 DOI: 10.1146/annurev-arplant-050312-120129] [Citation(s) in RCA: 450] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Oxygenic photosynthesis forms the basis of aerobic life on earth by converting light energy into biologically useful chemical energy and by splitting water to generate molecular oxygen. The water-splitting and oxygen-evolving reaction is catalyzed by photosystem II (PSII), a huge, multisubunit membrane-protein complex located in the thylakoid membranes of organisms ranging from cyanobacteria to higher plants. The structure of PSII has been analyzed at 1.9-Å resolution by X-ray crystallography, revealing a clear picture of the Mn4CaO5 cluster, the catalytic center for water oxidation. This article provides an overview of the overall structure of PSII followed by detailed descriptions of the specific structure of the Mn4CaO5 cluster and its surrounding protein environment. Based on the geometric organization of the Mn4CaO5 cluster revealed by the crystallographic analysis, in combination with the results of a vast number of experimental studies involving spectroscopic and other techniques as well as various theoretical studies, the article also discusses possible mechanisms for water splitting that are currently under consideration.
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Affiliation(s)
- Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan;
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Galstyan G, Knapp EW. Computing pK(A) values of hexa-aqua transition metal complexes. J Comput Chem 2014; 36:69-78. [PMID: 25328033 DOI: 10.1002/jcc.23764] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/24/2014] [Accepted: 10/09/2014] [Indexed: 01/13/2023]
Abstract
Aqueous pKA values for 15 hexa-aqua transition metal complexes were computed using a combination of quantum chemical and electrostatic methods. Two different structure models were considered optimizing the isolated complexes in vacuum or in presence of explicit solvent using a QM/MM approach. They yield very good agreement with experimentally measured pKA values with an overall root mean square deviation of about 1 pH unit, excluding a single but different outlier for each of the two structure models. These outliers are hexa-aqua Cr(III) for the vacuum and hexa-aqua Mn(III) for the QM/MM structure model. Reasons leading to the deviations of the outlier complexes are partially explained. Compared to previous approaches from the same lab the precision of the method was systematically improved as discussed in this study. The refined methods to obtain the appropriate geometries of the complexes, developed in this work, may allow also the computation of accurate pKA values for multicore transition metal complexes in different oxidation states.
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Affiliation(s)
- Gegham Galstyan
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, D-14195, Berlin, Germany
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