1
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Capone M, Parisse G, Narzi D, Guidoni L. Unravelling Mn 4Ca cluster vibrations in the S 1, S 2 and S 3 states of the Kok-Joliot cycle of photosystem II. Phys Chem Chem Phys 2024; 26:20598-20609. [PMID: 39037338 PMCID: PMC11290063 DOI: 10.1039/d4cp01307g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Vibrational spectroscopy serves as a powerful tool for characterizing intermediate states within the Kok-Joliot cycle. In this study, we employ a QM/MM molecular dynamics framework to calculate the room temperature infrared absorption spectra of the S1, S2, and S3 states via the Fourier transform of the dipole time auto-correlation function. To better analyze the computational data and assign spectral peaks, we introduce an approach based on dipole-dipole correlation function of cluster moieties of the reaction center. Our analysis reveals variation in the infrared signature of the Mn4Ca cluster along the Kok-Joliot cycle, attributed to its increasing symmetry and rigidity resulting from the rising oxidation state of the Mn ions. Furthermore, we successfully assign the debated contributions in the frequency range around 600 cm-1. This computational methodology provides valuable insights for deciphering experimental infrared spectra and understanding the water oxidation process in both biological and artificial systems.
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Affiliation(s)
- Matteo Capone
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Gianluca Parisse
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Daniele Narzi
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Leonardo Guidoni
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
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2
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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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3
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Krysiak S, Burda K. The Effect of Removal of External Proteins PsbO, PsbP and PsbQ on Flash-Induced Molecular Oxygen Evolution and Its Biphasicity in Tobacco PSII. Curr Issues Mol Biol 2024; 46:7187-7218. [PMID: 39057069 PMCID: PMC11276211 DOI: 10.3390/cimb46070428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The oxygen evolution within photosystem II (PSII) is one of the most enigmatic processes occurring in nature. It is suggested that external proteins surrounding the oxygen-evolving complex (OEC) not only stabilize it and provide an appropriate ionic environment but also create water channels, which could be involved in triggering the ingress of water and the removal of O2 and protons outside the system. To investigate the influence of these proteins on the rate of oxygen release and the efficiency of OEC function, we developed a measurement protocol for the direct measurement of the kinetics of oxygen release from PSII using a Joliot-type electrode. PSII-enriched tobacco thylakoids were used in the experiments. The results revealed the existence of slow and fast modes of oxygen evolution. This observation is model-independent and requires no specific assumptions about the initial distribution of the OEC states. The gradual removal of exogenous proteins resulted in a slowdown of the rapid phase (~ms) of O2 release and its gradual disappearance while the slow phase (~tens of ms) accelerated. The role of external proteins in regulating the biphasicity and efficiency of oxygen release is discussed based on observed phenomena and current knowledge.
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Affiliation(s)
| | - Kvetoslava Burda
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, al. Mickiewicza 30, 30-059 Krakow, Poland;
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4
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Ariafard A, Longhurst M, Swiegers GF, Stranger R. Mechanisms of Mn(V)-Oxo to Mn(IV)-Oxyl Conversion: From Closed-Cubane Photosystem II to Mn(V) Catalysts and the Role of the Entering Ligands. Chemistry 2024; 30:e202400396. [PMID: 38659321 DOI: 10.1002/chem.202400396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/02/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
The low activation barrier for O-O coupling in the closed-cubane Oxygen-Evolving Centre (OEC) of Photosystem II (PSII) requires water coordination with the Mn4 'dangler' ion in the Mn(V)-oxo fragment. This coordination transforms the Mn(V)-oxo complex into a more reactive Mn4(IV)-oxyl species, enhancing O-O coupling. This study explains the mechanism behind the coordination and indicates that in the most stable form of the OEC, the Mn4 fragment adopts a trigonal bipyramidal geometry but needs to transition to a square pyramidal form to be activated for O-O coupling. This transition stabilizes the Mn4 dxy orbital, enabling electron transfer from the oxo ligand to the dxy orbital, converting the oxo ligand into an oxyl species. The role of the water is to coordinate with the square pyramidal structure, reducing the energy gap between the oxo and oxyl forms, thereby lowering the activation energy for O-O coupling. This mechanism applies not only to the OEC system but also to other Mn(V)-based catalysts. For other catalysts, ligands such as OH- stabilize the Mn(IV)-oxyl species better than water, improving catalyst activation for reactions like C-H bond activation. This study is the first to explain the Mn(V)-oxo to Mn(IV)-oxyl conversion, providing a new foundation for Mn-based catalyst design.
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Affiliation(s)
- Alireza Ariafard
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Matthew Longhurst
- Intelligent Polymer Research Institute, University of Wollongong, Wollongong, Australia
| | - Gerhard F Swiegers
- Intelligent Polymer Research Institute, University of Wollongong, Wollongong, Australia
| | - Robert Stranger
- Research School of Chemistry, Australian National University, Canberra, Australia
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5
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Debus RJ, Oyala PH. Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O 2-Evolving Mn 4CaO 5 Cluster in Photosystem II. J Phys Chem B 2024; 128:3870-3884. [PMID: 38602496 DOI: 10.1021/acs.jpcb.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The O2-evolving Mn4CaO5 cluster in photosystem II is ligated by six carboxylate residues. One of these is D170 of the D1 subunit. This carboxylate bridges between one Mn ion (Mn4) and the Ca ion. A second carboxylate ligand is D342 of the D1 subunit. This carboxylate bridges between two Mn ions (Mn1 and Mn2). D170 and D342 are located on opposite sides of the Mn4CaO5 cluster. Recently, it was shown that the D170E mutation perturbs both the intricate networks of H-bonds that surround the Mn4CaO5 cluster and the equilibrium between different conformers of the cluster in two of its lower oxidation states, S1 and S2, while still supporting O2 evolution at approximately 50% the rate of the wild type. In this study, we show that the D342E mutation produces much the same alterations to the cluster's FTIR and EPR spectra as D170E, while still supporting O2 evolution at approximately 20% the rate of the wild type. Furthermore, the double mutation, D170E + D342E, behaves similarly to the two single mutations. We conclude that D342E alters the equilibrium between different conformers of the cluster in its S1 and S2 states in the same manner as D170E and perturbs the H-bond networks in a similar fashion. This is the second identification of a Mn4CaO5 metal ligand whose mutation influences the equilibrium between the different conformers of the S1 and S2 states without eliminating O2 evolution. This finding has implications for our understanding of the mechanism of O2 formation in terms of catalytically active/inactive conformations of the Mn4CaO5 cluster in its lower oxidation states.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106, United States
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6
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Yamaguchi K, Miyagawa K, Shoji M, Kawakami T, Isobe H, Yamanaka S, Nakajima T. Theoretical elucidation of the structure, bonding, and reactivity of the CaMn 4O x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01053-7. [PMID: 37945776 DOI: 10.1007/s11120-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.
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Affiliation(s)
- Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
| | - Koichi Miyagawa
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takashi Kawakami
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
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7
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Gates C, Williams JM, Ananyev G, Dismukes GC. How chloride functions to enable proton conduction in photosynthetic water oxidation: Time-resolved kinetics of intermediates (S-states) in vivo and bromide substitution. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148998. [PMID: 37499962 DOI: 10.1016/j.bbabio.2023.148998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Chloride (Cl-) is essential for O2 evolution during photosynthetic water oxidation. Two chlorides near the water-oxidizing complex (WOC) in Photosystem II (PSII) structures from Thermosynechococcus elongatus (and T. vulcanus) have been postulated to transfer protons generated from water oxidation. We monitored four criteria: primary charge separation flash yield (P* → P+QA-), rates of water oxidation steps (S-states), rate of proton evolution, and flash O2 yield oscillations by measuring chlorophyll variable fluorescence (P* quenching), pH-sensitive dye changes, and oximetry. Br-substitution slows and destabilizes cellular growth, resulting from lower light-saturated O2 evolution rate (-20 %) and proton release (-36 % ΔpH gradient). The latter implies less ATP production. In Br- cultures, protonogenic S-state transitions (S2 → S3 → S0') slow with increasing light intensity and during O2/water exchange (S0' → S0 → S1), while the non-protonogenic S1 → S2 transition is kinetically unaffected. As flash rate increases in Cl- cultures, both rate and extent of acidification of the lumen increase, while charge recombination is suppressed relative to Br-. The Cl- advantage in rapid proton escape from the WOC to lumen is attributed to correlated ion-pair movement of H3O+Cl- in dry water channels vs. separated Br- and H+ ion movement through different regions (>200-fold difference in Bronsted acidities). By contrast, at low flash rates a previously unreported reversal occurs that favors Br- cultures for both proton evolution and less PSII charge recombination. In Br- cultures, slower proton transfer rate is attributed to stronger ion-pairing of Br- with AA residues lining the water channels. Both anions charge-neutralize protons and shepherd them to the lumen using dry aqueous channels.
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Affiliation(s)
- Colin Gates
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Computational Biology and Molecular Biophysics, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Biochemistry, Loyola University Chicago, IL 60660, USA
| | - Jonah M Williams
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Gennady Ananyev
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - G Charles Dismukes
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA.
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8
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Drosou M, Comas-Vilà G, Neese F, Salvador P, Pantazis DA. Does Serial Femtosecond Crystallography Depict State-Specific Catalytic Intermediates of the Oxygen-Evolving Complex? J Am Chem Soc 2023; 145:10604-10621. [PMID: 37137865 DOI: 10.1021/jacs.3c00489] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent advances in serial femtosecond crystallography (SFX) of photosystem II (PSII), enabled by X-ray free electron lasers (XFEL), provided the first geometric models of distinct intermediates in the catalytic S-state cycle of the oxygen-evolving complex (OEC). These models are obtained by flash-advancing the OEC from the dark-stable state (S1) to more oxidized intermediates (S2 and S3), eventually cycling back to the most reduced S0. However, the interpretation of these models is controversial because geometric parameters within the Mn4CaO5 cluster of the OEC do not exactly match those expected from coordination chemistry for the spectroscopically verified manganese oxidation states of the distinct S-state intermediates. Here we focus on the first catalytic transition, S1 → S2, which represents a one-electron oxidation of the OEC. Combining geometric and electronic structure criteria, including a novel effective oxidation state approach, we analyze existing 1-flash (1F) SFX-XFEL crystallographic models that should depict the S2 state of the OEC. We show that the 1F/S2 equivalence is not obvious, because the Mn oxidation states and total unpaired electron counts encoded in these models are not fully consistent with those of a pure S2 state and with the nature of the S1 → S2 transition. Furthermore, the oxidation state definition in two-flashed (2F) structural models is practically impossible to elucidate. Our results advise caution in the extraction of electronic structure information solely from the literal interpretation of crystallographic models and call for re-evaluation of structural and mechanistic interpretations that presume exact correspondence of such models to specific catalytic intermediates of the OEC.
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Affiliation(s)
- Maria Drosou
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Gerard Comas-Vilà
- Institute of Computational Chemistry and Catalysis, Chemistry Department, University of Girona, Montilivi Campus, Girona, Catalonia 17003, Spain
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Pedro Salvador
- Institute of Computational Chemistry and Catalysis, Chemistry Department, University of Girona, Montilivi Campus, Girona, Catalonia 17003, Spain
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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9
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Greife P, Schönborn M, Capone M, Assunção R, Narzi D, Guidoni L, Dau H. The electron-proton bottleneck of photosynthetic oxygen evolution. Nature 2023; 617:623-628. [PMID: 37138082 DOI: 10.1038/s41586-023-06008-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today's oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S4 state-which was postulated half a century ago1 and remains largely uncharacterized. Here we resolve this key stage of photosynthetic O2 formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combining these results with computational chemistry reveals that a crucial proton vacancy is initally created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in a single-electron, multi-proton transfer event. This is the slowest step in photosynthetic O2 formation, with a moderate energetic barrier and marked entropic slowdown. We identify the S4 state as the oxygen-radical state; its formation is followed by fast O-O bonding and O2 release. In conjunction with previous breakthroughs in experimental and computational investigations, a compelling atomistic picture of photosynthetic O2 formation emerges. Our results provide insights into a biological process that is likely to have occurred unchanged for the past three billion years, which we expect to support the knowledge-based design of artificial water-splitting systems.
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Affiliation(s)
- Paul Greife
- Department of Physics, Freie Universität, Berlin, Germany
| | | | - Matteo Capone
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, L'Aquila, Italy
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Daniele Narzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Holger Dau
- Department of Physics, Freie Universität, Berlin, Germany.
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10
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Guo Y, Messinger J, Kloo L, Sun L. Alternative Mechanism for O 2 Formation in Natural Photosynthesis via Nucleophilic Oxo-Oxo Coupling. J Am Chem Soc 2023; 145:4129-4141. [PMID: 36763485 DOI: 10.1021/jacs.2c12174] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
O2 formation in photosystem II (PSII) is a vital event on Earth, but the exact mechanism remains unclear. The presently prevailing theoretical model is "radical coupling" (RC) involving a Mn(IV)-oxyl unit in an "open-cubane" Mn4CaO6 cluster, which is supported experimentally by the S3 state of cyanobacterial PSII featuring an additional Mn-bound oxygenic ligand. However, it was recently proposed that the major structural form of the S3 state of higher plants lacks this extra ligand, and that the resulting S4 state would feature instead a penta-coordinate dangler Mn(V)=oxo, covalently linked to a "closed-cubane" Mn3CaO4 cluster. For this proposal, we explore here a large number of possible pathways of O-O bond formation and demonstrate that the "nucleophilic oxo-oxo coupling" (NOOC) between Mn(V)=oxo and μ3-oxo is the only eligible mechanism in such a system. The reaction is facilitated by a specific conformation of the cluster and concomitant water binding, which is delayed compared to the RC mechanism. An energetically feasible process is described starting from the valid S4 state through the sequential formation of peroxide and superoxide, followed by O2 release and a second water insertion. The newly found mechanism is consistent with available experimental thermodynamic and kinetic data and thus a viable alternative pathway for O2 formation in natural photosynthesis, in particular for higher plants.
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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
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), Umeå SE-90187, Sweden
- Molecular Biomimetics, Department of Chemistry─Ångström Laboratory, Uppsala University, Uppsala SE-75120, Sweden
| | - Lars Kloo
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm SE-10044, 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
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11
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Guo Y, Messinger J, Kloo L, Sun L. Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation. J Am Chem Soc 2022; 144:11736-11747. [PMID: 35748306 PMCID: PMC9264352 DOI: 10.1021/jacs.2c03528] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Photosynthetic water
oxidation is catalyzed by a manganese–calcium
oxide cluster, which experiences five “S-states” during
a light-driven reaction cycle. The unique “distorted chair”-like
geometry of the Mn4CaO5(6) cluster shows structural
flexibility that has been frequently proposed to involve “open”
and “closed”-cubane forms from the S1 to
S3 states. The isomers are interconvertible in the S1 and S2 states, while in the S3 state,
the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples.
In this work, using density functional theory calculations, we go
beyond the S3+Yz state to the S3nYz• → S4+Yz step, and report for the first time
that the reversible isomerism, which is suppressed in the S3+Yz state, is fully recovered
in the ensuing S3nYz• state due to the proton release
from a manganese-bound water ligand. The altered coordination strength
of the manganese–ligand facilitates formation of the closed-cubane
form, in a dynamic equilibrium with the open-cubane form. This tautomerism
immediately preceding dioxygen formation may constitute the rate limiting
step for O2 formation, and exert a significant influence
on the water oxidation mechanism in photosystem II.
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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
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), SE-90187 Umeå, Sweden.,Molecular Biomimetics, Department of Chemistry─Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | - Lars Kloo
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10044 Stockholm, 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
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12
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Allgöwer F, Gamiz-Hernandez AP, Rutherford AW, Kaila VRI. Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II. J Am Chem Soc 2022; 144:7171-7180. [PMID: 35421304 PMCID: PMC9052759 DOI: 10.1021/jacs.1c13041] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O2 into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn4O5Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyrz (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca2+-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624-12,635]. Further oxidation of the Mn4O5Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn4O5Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O2 formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.
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Affiliation(s)
- Friederike Allgöwer
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - A William Rutherford
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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13
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Debus RJ. Alteration of the O 2-Producing Mn 4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand. Biochemistry 2021; 60:3841-3855. [PMID: 34898175 DOI: 10.1021/acs.biochem.1c00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The O2-evolving Mn4Ca cluster in photosystem II (PSII) is arranged as a distorted Mn3Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn4Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn4Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn4Ca cluster in the dark-stable S1 state so that a high-spin form of the S2 state is produced during the S1-to-S2 transition instead of the low-spin form that gives rise to the S2 state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn4Ca cluster without substantially eliminating O2 evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn4Ca cluster in the mechanism of O2 formation.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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14
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Wang M, Zhang Y, Chen C, Zhang C, Jiang J, Weng Y. Structural Reorganization of a Synthetic Mimic of the Oxygen-Evolving Center in Multiple Redox Transitions Revealed by Electrochemical FTIR Spectra. J Phys Chem Lett 2021; 12:9830-9839. [PMID: 34605651 DOI: 10.1021/acs.jpclett.1c02689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In photosynthesis, the protein-bound natural oxygen-evolving center (OEC) undergoes multiple oxidation-state transitions in the light-driven water splitting reactions with a stepwise change in the oxidation potential. Because the protein is vulnerable to electrochemical oxidation, the multiple oxidation/reduction-state transitions can hardly be achieved by electrochemical oxidation with a continuous change in the oxidation potential. An OEC mimic that can undergo four redox transitions has been synthesized (Zhang, C., Science, 2015, 348, 690-693). Here we report an electrochemical FTIR spectroscopic study of this synthetic complex at its multiple oxidation states in the low-frequency region for Mn-O bonds. Compared with those of the native OEC induced by pulsed laser flashes, our results also show the existence of two structural isomers in the S2 state, with the closed cubane conformer being more stable than the open cubane conformer, in contrast to that of the native OEC in which the open form is more stable.
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Affiliation(s)
- Mohan Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changhui Chen
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunxi Zhang
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Yuxiang Weng
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523000, China
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15
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Drosou M, Pantazis DA. Redox Isomerism in the S 3 State of the Oxygen-Evolving Complex Resolved by Coupled Cluster Theory. Chemistry 2021; 27:12815-12825. [PMID: 34288176 PMCID: PMC8518824 DOI: 10.1002/chem.202101567] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Indexed: 01/19/2023]
Abstract
The electronic and geometric structures of the water-oxidizing complex of photosystem II in the steps of the catalytic cycle that precede dioxygen evolution remain hotly debated. Recent structural and spectroscopic investigations support contradictory redox formulations for the active-site Mn4 CaOx cofactor in the final metastable S3 state. These range from the widely accepted MnIV 4 oxo-hydroxo model, which presumes that O-O bond formation occurs in the ultimate transient intermediate (S4 ) of the catalytic cycle, to a MnIII 2 MnIV 2 peroxo model representative of the contrasting "early-onset" O-O bond formation hypothesis. Density functional theory energetics of suggested S3 redox isomers are inconclusive because of extreme functional dependence. Here, we use the power of the domain-based local pair natural orbital approach to coupled cluster theory, DLPNO-CCSD(T), to present the first correlated wave function theory calculations of relative stabilities for distinct redox-isomeric forms of the S3 state. Our results enabled us to evaluate conflicting models for the S3 state of the oxygen-evolving complex (OEC) and to quantify the accuracy of lower-level theoretical approaches. Our assessment of the relevance of distinct redox-isomeric forms for the mechanism of biological water oxidation strongly disfavors the scenario of early-onset O-O formation advanced by literal interpretations of certain crystallographic models. This work serves as a case study in the application of modern coupled cluster implementations to redox isomerism problems in oligonuclear transition metal systems.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry LaboratoryNational and Kapodistrian University of AthensPanepistimiopolisZografou15771Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an derRuhrGermany
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16
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Capone M, Narzi D, Guidoni L. Mechanism of Oxygen Evolution and Mn 4CaO 5 Cluster Restoration in the Natural Water-Oxidizing Catalyst. Biochemistry 2021; 60:2341-2348. [PMID: 34283569 DOI: 10.1021/acs.biochem.1c00226] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water oxidation occurring in the first steps of natural oxygenic photosynthesis is catalyzed by the pigment/protein complex Photosystem II. This process takes place on the Mn4Ca cluster located in the core of Photosystem II and proceeds along the five steps (S0-S4) of the so-called Kok-Joliot cycle until the release of molecular oxygen. The catalytic cycle can therefore be started afresh through insertion of a new water molecule. Here, combining quantum mechanics/molecular mechanics simulations and minimum energy path calculations, we characterized on different spin surfaces the events occurring in the last sector of the catalytic cycle from structural, electronic, and thermodynamic points of view. We found that the process of oxygen evolution and water insertion can be described well by a two-step mechanism, with oxygen release being the rate-limiting step of the process. Moreover, our results allow us to identify the upcoming water molecule required to regenerate the initial structure of the Mn4Ca cluster in the S0 state. The insertion of the water molecule was found to be coupled with the transfer of a proton to a neighboring hydroxide ion, thus resulting in the reconstitution of the most widely accepted model of the S0 state.
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Affiliation(s)
- Matteo Capone
- Dipartimento di Scienze Fisiche e Chimiche, Universitá degli studi dell'Aquila, Via Vetoio (Coppito), 67100 L'Aquila, Italy
| | - Daniele Narzi
- Dipartimento di Scienze Fisiche e Chimiche, Universitá degli studi dell'Aquila, Via Vetoio (Coppito), 67100 L'Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Universitá degli studi dell'Aquila, Via Vetoio (Coppito), 67100 L'Aquila, Italy
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17
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Zahariou G, Ioannidis N, Sanakis Y, Pantazis DA. Arrested Substrate Binding Resolves Catalytic Intermediates in Higher-Plant Water Oxidation. Angew Chem Int Ed Engl 2021; 60:3156-3162. [PMID: 33030775 PMCID: PMC7898718 DOI: 10.1002/anie.202012304] [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: 09/09/2020] [Indexed: 12/05/2022]
Abstract
Among the intermediate catalytic steps of the water-oxidizing Mn4 CaO5 cluster of photosystem II (PSII), the final metastable S3 state is critically important because it binds one substrate and precedes O2 evolution. Herein, we combine X- and Q-band EPR experiments on native and methanol-treated PSII of Spinacia oleracea and show that methanol-treated PSII preparations of the S3 state correspond to a previously uncharacterized high-spin (S=6) species. This is confirmed as a major component also in intact photosynthetic membranes, coexisting with the previously known intermediate-spin conformation (S=3). The high-spin intermediate is assigned to a water-unbound form, with a MnIV3 subunit interacting ferromagnetically via anisotropic exchange with a coordinatively unsaturated MnIV ion. These results resolve and define the structural heterogeneity of the S3 state, providing constraints on the S3 to S4 transition, on substrate identity and delivery pathways, and on the mechanism of O-O bond formation.
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Affiliation(s)
- Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos”Athens15310Greece
| | - Nikolaos Ioannidis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos”Athens15310Greece
| | - Yiannis Sanakis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos”Athens15310Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
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18
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Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S3 state of the oxygen evolving complex of photosystem II. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Zahariou G, Ioannidis N, Sanakis Y, Pantazis DA. Arrested Substrate Binding Resolves Catalytic Intermediates in Higher‐Plant Water Oxidation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos” Athens 15310 Greece
| | - Nikolaos Ioannidis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos” Athens 15310 Greece
| | - Yiannis Sanakis
- 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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20
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Kim CJ, Debus RJ. Roles of D1-Glu189 and D1-Glu329 in O2 Formation by the Water-Splitting Mn4Ca Cluster in Photosystem II. Biochemistry 2020; 59:3902-3917. [DOI: 10.1021/acs.biochem.0c00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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21
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Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A 2020; 117:12624-12635. [PMID: 32434915 PMCID: PMC7293653 DOI: 10.1073/pnas.2000529117] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
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Affiliation(s)
- Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Casper de Lichtenberg
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Petko Chernev
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, OX11 0FA Didcot, United Kingdom
| | - Nicholas Saichek
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Trent Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
| | - Shigeki Owada
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bolotovsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany;
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden;
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
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22
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Structural and dynamical characterization of the S4 state of the Kok-Joliot’s cycle by means of QM/MM Molecular Dynamics Simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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23
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de Lichtenberg C, Messinger J. Substrate water exchange in the S2 state of photosystem II is dependent on the conformation of the Mn4Ca cluster. Phys Chem Chem Phys 2020; 22:12894-12908. [DOI: 10.1039/d0cp01380c] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural flexibility of the Mn4Ca cluster in photosystem II supports the exchange of the central O5 bridge.
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24
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Nakamura S, Capone M, Narzi D, Guidoni L. Pivotal role of the redox-active tyrosine in driving the water splitting catalyzed by photosystem II. Phys Chem Chem Phys 2020; 22:273-285. [DOI: 10.1039/c9cp04605d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
TyrZ oxidation state triggers hydrogen bond modification in the water oxidation catalysis.
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Affiliation(s)
- Shin Nakamura
- Department of Biochemical Sciences “A. Rossi Fanelli”
- University of Rome “Sapienza”
- Rome
- Italy
| | - Matteo Capone
- Department of Information Engineering, Computational Science, and Mathematics
- Università dell’Aquila
- L’Aquila
- Italy
| | - Daniele Narzi
- Institute of Chemical Sciences and Engineering Ecole Polytechnique Federale de Lausanne Av. F.-A. Forel 2
- 1015 Lausanne
- Switzerland
| | - Leonardo Guidoni
- Department of Physical and Chemical Science
- Università dell’Aquila
- L’Aquila
- Italy
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25
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Tychengulova A, Capone M, Pitari F, Guidoni L. Molecular Vibrations of an Oxygen-Evolving Complex and Its Synthetic Mimic. Chemistry 2019; 25:13385-13395. [PMID: 31340068 DOI: 10.1002/chem.201902621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/18/2019] [Indexed: 11/07/2022]
Abstract
Bio-inspired catalysis for artificial photosynthesis has been widely studied for decades, in particular, with the purpose of using bio-disposable and non-toxic metals as building blocks. The characterisation of such catalysts has been achieved by using different kinds of spectroscopic methods, from X-ray crystallography to NMR spectroscopy. An artificial Mn4 CaO4 cubane cluster with dangling Mn4 was synthesised in 2015 [Zhang et al. Science 2015, 348, 690-693]; this cluster showed many structural similarities to that of the natural oxygen-evolving complex. An accurate structural and spectroscopic comparison between the natural and artificial systems is highly relevant to understand the catalytic mechanism. Among data from different techniques, the differential FTIR spectra (Sn+1 -Sn ) of photosystem II are still lacking a complete interpretation. The availability of IR data of the artificial cluster offers a unique opportunity to assign absolute absorption spectra on a well-defined and easier to interpret analogous moiety. The present work aims to investigate the novel inorganic compound as a model system for an oxygen-evolving complex through measurement of its spectroscopic properties. The experimental results are compared with calculations by using a variety of theoretical methods (normal mode analysis, effective normal mode analysis) in the S1 state. We underline the similarities and the differences in the computational spectra based on atomistic models of Mn4 CaO5 and Mn4 CaO4 complexes.
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Affiliation(s)
- Aliya Tychengulova
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via Scarpa 16, 00161, Rome, Italy
| | - Mateo Capone
- Department of Engineering, Computer Science and Mathematics, University of L'Aquila, Via Vetoio Coppito, 67100, L'Aquila, Italy
| | - Fabio Pitari
- Department of Engineering, Computer Science and Mathematics, University of L'Aquila, Via Vetoio Coppito, 67100, L'Aquila, Italy
- Current address: CINECA High Performance Computing Department, Via Magnanelli, 40033, Casalecchio di Reno, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Science, University of L'Aquila, Via Vetoio Coppito, 67100, L'Aquila, Italy
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26
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Five-coordinate Mn IV intermediate in the activation of nature's water splitting cofactor. Proc Natl Acad Sci U S A 2019; 116:16841-16846. [PMID: 31391299 DOI: 10.1073/pnas.1817526116] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature's water splitting cofactor passes through a series of catalytic intermediates (S0-S4) before O-O bond formation and O2 release. In the second last transition (S2 to S3) cofactor oxidation is coupled to water molecule binding to Mn1. It is this activated, water-enriched all MnIV form of the cofactor that goes on to form the O-O bond, after the next light-induced oxidation to S4 How cofactor activation proceeds remains an open question. Here, we report a so far not described intermediate (S3') in which cofactor oxidation has occurred without water insertion. This intermediate can be trapped in a significant fraction of centers (>50%) in (i) chemical-modified cofactors in which Ca2+ is exchanged with Sr2+; the Mn4O5Sr cofactor remains active, but the S2-S3 and S3-S0 transitions are slower than for the Mn4O5Ca cofactor; and (ii) upon addition of 3% vol/vol methanol; methanol is thought to act as a substrate water analog. The S3' electron paramagnetic resonance (EPR) signal is significantly broader than the untreated S3 signal (2.5 T vs. 1.5 T), indicating the cofactor still contains a 5-coordinate Mn ion, as seen in the preceding S2 state. Magnetic double resonance data extend these findings revealing the electronic connectivity of the S3' cofactor is similar to the high spin form of the preceding S2 state, which contains a cuboidal Mn3O4Ca unit tethered to an external, 5-coordinate Mn ion (Mn4). These results demonstrate that cofactor oxidation regulates water molecule insertion via binding to Mn4. The interaction of ammonia with the cofactor is also discussed.
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27
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Krewald V, Neese F, Pantazis DA. Implications of structural heterogeneity for the electronic structure of the final oxygen-evolving intermediate in photosystem II. J Inorg Biochem 2019; 199:110797. [PMID: 31404888 DOI: 10.1016/j.jinorgbio.2019.110797] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Heterogeneity in intermediate catalytic states of the oxygen-evolving complex (OEC) of Photosystem II is known from a wide range of experimental and theoretical data, but its potential implications for the mechanism of water oxidation remain unexplored. We delineate the consequences of structural heterogeneity for the final step of the catalytic cycle by tracing the evolution of three spectroscopically relevant and structurally distinct components of the last metastable S3 state to the transient O2-evolving S4 state of the OEC. Using quantum chemical calculations, we show that each S3 isomer leads to a different electronic structure formulation for the active S4 state. Crucially, in addition to previously hypothesized Mn(IV)-oxyl species, we establish for the first time, how a genuine Mn(V)-oxo can be obtained in the catalytically active S4 state: this takes the form of a five-coordinate and locally high-spin (SMn = 1) Mn(V) site. This formulation for the S4 state evolves naturally from a preceding S3-state structural intermediate that contains a quasi-trigonal-bipyramidal Mn(IV) ion. The results strongly suggest that water binding in the S3 state is not prerequisite for reaching the oxygen-evolving S4 state of the complex, supporting the notion that both substrates are preloaded at the beginning of the catalytic cycle. This scenario allows true four-electron metal-centered hole accumulation to precede OO bond formation and hence the latter can proceed via a genuine even-electron mechanism. This can occur as intramolecular nucleophilic coupling of two oxo units synchronously with the binding of a water substrate for the next catalytic cycle.
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Affiliation(s)
- Vera Krewald
- Theoretische Chemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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28
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Kim CJ, Debus RJ. One of the Substrate Waters for O2 Formation in Photosystem II Is Provided by the Water-Splitting Mn4CaO5 Cluster’s Ca2+ Ion. Biochemistry 2019; 58:3185-3192. [DOI: 10.1021/acs.biochem.9b00418] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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29
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Capone M, Narzi D, Tychengulova A, Guidoni L. On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:33-43. [PMID: 30801735 DOI: 10.1111/ppl.12949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Understanding the structural modification experienced by the Mn4 CaO5 oxygen-evolving complex of photosystem II along the Kok-Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction center, to catch spectral changes between different S-states along the catalytic cycle. Because of the complexity of the signals, only a limited quantity of identified peaks have been assigned so far, also because of the difficulty of a direct comparison with theoretical calculations. In the present work, we critically reconsider the comparison between differential vibrational spectroscopy and theoretical calculations performed on the structural models of the photosystem II active site and an inorganic structural mimic. Several factors are currently limiting the reliability of a quantitative comparison, such as intrinsic errors associated to theoretical methods, and most of all, the uncertainty attributed to the lack of knowledge about the localization of the underlying structural changes. Critical points in this comparison are extensively discussed. Comparing several computational data of differential S2 /S1 infrared spectroscopy, we have identified weak and strong points in their interpretation when compared with experimental spectra.
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Affiliation(s)
- Matteo Capone
- Department of Information Engineering, Computational Science and Mathematics, Università dell'Aquila, 67100, L'Aquila, Italy
| | - Daniele Narzi
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Aliya Tychengulova
- Department of Basic Sciences Applied for Engineering, "Sapienza" Università di Roma, 00185, Rome, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Science, Università dell'Aquila, 67100, L'Aquila, Italy
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30
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Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Nakajima T, Kawakami T, Okumura M. Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn 4 O X (X = 5, 6) cluster in the Kok cycle S i (i = 0-3) of oxygen evolving complex of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:44-59. [PMID: 30847925 DOI: 10.1111/ppl.12960] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The optimized geometries of the CaMn4 OX (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the Si (i = 0-3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the Si intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S3 state are investigated in detail in relation to recent SFX and XES experiments for the S3 state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S3 state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII.
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Affiliation(s)
- Kizashi Yamaguchi
- Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 567-0047, Japan
- Riken Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shusuke Yamanaka
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Okayama 700-8530, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki 305-8577, Japan
| | - Kouichi Miyagawa
- Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 567-0047, Japan
| | | | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
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31
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The S3 State of the Oxygen-Evolving Complex: Overview of Spectroscopy and XFEL Crystallography with a Critical Evaluation of Early-Onset Models for O–O Bond Formation. INORGANICS 2019. [DOI: 10.3390/inorganics7040055] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The catalytic cycle of the oxygen-evolving complex (OEC) of photosystem II (PSII) comprises five intermediate states Si (i = 0–4), from the most reduced S0 state to the most oxidized S4, which spontaneously evolves dioxygen. The precise geometric and electronic structure of the Si states, and hence the mechanism of O–O bond formation in the OEC, remain under investigation, particularly for the final steps of the catalytic cycle. Recent advances in protein crystallography based on X-ray free-electron lasers (XFELs) have produced new structural models for the S3 state, which indicate that two of the oxygen atoms of the inorganic Mn4CaO6 core of the OEC are in very close proximity. This has been interpreted as possible evidence for “early-onset” O–O bond formation in the S3 state, as opposed to the more widely accepted view that the O–O bond is formed in the final state of the cycle, S4. Peroxo or superoxo formation in S3 has received partial support from computational studies. Here, a brief overview is provided of spectroscopic information, recent crystallographic results, and computational models for the S3 state. Emphasis is placed on computational S3 models that involve O–O formation, which are discussed with respect to their agreement with structural information, experimental evidence from various spectroscopic studies, and substrate exchange kinetics. Despite seemingly better agreement with some of the available crystallographic interpretations for the S3 state, models that implicate early-onset O–O bond formation are hard to reconcile with the complete line of experimental evidence, especially with X-ray absorption, X-ray emission, and magnetic resonance spectroscopic observations. Specifically with respect to quantum chemical studies, the inconclusive energetics for the possible isoforms of S3 is an acute problem that is probably beyond the capabilities of standard density functional theory.
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32
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Isobe H, Shoji M, Suzuki T, Shen JR, Yamaguchi K. Spin, Valence, and Structural Isomerism in the S 3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity. J Chem Theory Comput 2019; 15:2375-2391. [PMID: 30855953 DOI: 10.1021/acs.jctc.8b01055] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S3 state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal-ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn···Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state ( Stotal = 6) of the oxyl-oxo species can be causative for catalytic function, which manifests through mixing of the metal-ligand character in magnetic orbitals at relatively short O5···O6 distances (<2.0 Å) and long MnA···O5 distances (>2.0 Å). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique "distorted chair" topology of the cluster through cooperative Jahn-Teller effects on multimetallic centers.
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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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33
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Yamaguchi K, Shoji M, Isobe H, Miyagawa K, Nakatani K. Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1552799] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Yamaguchi
- Institute for Nanoscience Design, Osaka University, Toyonaka, Osaka, Japan
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
- Handairigaku Techno-Research, Toyonaka, Osaka, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - K. Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - K. Nakatani
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
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34
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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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35
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Kim CJ, Bao H, Burnap RL, Debus RJ. Impact of D1-V185 on the Water Molecules That Facilitate O2 Formation by the Catalytic Mn4CaO5 Cluster in Photosystem II. Biochemistry 2018; 57:4299-4311. [DOI: 10.1021/acs.biochem.8b00630] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Han Bao
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Robert L. Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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36
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Narzi D, Capone M, Bovi D, Guidoni L. Evolution from S3
to S4
States of the Oxygen-Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics. Chemistry 2018; 24:10820-10828. [DOI: 10.1002/chem.201801709] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Daniele Narzi
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Federale de Lausanne; Av. F.-A. Forel 2 1015 Lausanne Switzerland
| | - Matteo Capone
- Dipartimento di Ingegneria e Scienze dell'Informazione e Matematica; Universita degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
| | - Daniele Bovi
- Dipartimento di Scienze Fisiche e Chimiche; Universita degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche; Universita degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
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37
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The low spin - high spin equilibrium in the S2-state of the water oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:342-356. [DOI: 10.1016/j.bbabio.2018.02.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 11/17/2022]
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38
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Yamaguchi K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Yamada S, Katouda M, Nakajima T. Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1428375] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Kizashi Yamaguchi
- Institute for Nanoscience Design, Osaka University, Osaka, Japan
- Handairigaku Techno-Research, Osaka Univeristy, Osaka, Japan
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Hiroshi Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Takashi Kawakami
- Graduate School of Science, Osaka University, Osaka, Japan
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Satoru Yamada
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Michio Katouda
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Takahito Nakajima
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
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39
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Siegbahn PEM. The S2 to S3 transition for water oxidation in PSII (photosystem II), revisited. Phys Chem Chem Phys 2018; 20:22926-22931. [DOI: 10.1039/c8cp03720e] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The formation of O2 from water requires four transitions, each one after the absorption of one light flash.
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Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry
- Arrhenius Laboratory
- Stockholm University
- Stockholm
- Sweden
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40
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Schilling M, Hodel FH, Luber S. Discovery of Open Cubane Core Structures for Biomimetic LnCo 3 (OR) 4 Water Oxidation Catalysts. CHEMSUSCHEM 2017; 10:4561-4569. [PMID: 28941193 DOI: 10.1002/cssc.201701527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Indexed: 06/07/2023]
Abstract
Bio-mimetic catalysts such as LnCo3 (OR)4 (Ln=Er, Tm; OR=alkoxide) cubanes have recently been in the focus of research for artificial water oxidation processes. Previously, the remarkable adaptability with respect to ligand shell, nuclear structure as well as protonation and oxidation states of those catalysts has been shown to be beneficial for the water oxidation process. We further explored the structural flexibility of those catalysts and present here a series of novel structures in which one metal center is pulled out of the cubane cage. This leads to an open cubane core, which is to some extent reminiscent of observed open/closed cubane-core forms of the oxygen-evolving complex in nature's photosystem II. We investigate how those open cubane core models alter the thermodynamics of the water oxidation cycle and how different solvation approaches influence their stability.
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Affiliation(s)
- Mauro Schilling
- Department of Chemistry C, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Florian H Hodel
- Department of Chemistry C, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry C, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
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41
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Narzi D, Coccia E, Manzoli M, Guidoni L. Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II. Biophys Chem 2017; 229:93-98. [DOI: 10.1016/j.bpc.2017.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023]
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42
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Guo Y, Li H, He LL, Zhao DX, Gong LD, Yang ZZ. Theoretical reflections on the structural polymorphism of the oxygen-evolving complex in the S2 state and the correlations to substrate water exchange and water oxidation mechanism in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:833-846. [DOI: 10.1016/j.bbabio.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/25/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022]
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43
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Kim CJ, Debus RJ. Evidence from FTIR Difference Spectroscopy That a Substrate H2O Molecule for O2 Formation in Photosystem II Is Provided by the Ca Ion of the Catalytic Mn4CaO5 Cluster. Biochemistry 2017; 56:2558-2570. [DOI: 10.1021/acs.biochem.6b01278] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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44
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Narzi D, Mattioli G, Bovi D, Guidoni L. A Spotlight on the Compatibility between XFEL and Ab Initio Structures of the Oxygen Evolving Complex in Photosystem II. Chemistry 2017; 23:6969-6973. [DOI: 10.1002/chem.201700722] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Daniele Narzi
- Institute of Chemical Sciences and Engineering; École polytechnique fédérale de Lausanne; Av. F.-A. Forel 2 1015 Lausanne Switzerland
| | | | - Daniele Bovi
- Pangea Formazione s.r.l.; via Gaspare Gozzi, 55 00145 Rome Italy
- Dipartimento di Scienze Fisiche e Chimiche; Università degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche; Università degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
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45
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Najafpour MM, Heidari S, Balaghi SE, Hołyńska M, Sadr MH, Soltani B, Khatamian M, Larkum AW, Allakhverdiev SI. Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:156-174. [DOI: 10.1016/j.bbabio.2016.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022]
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46
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Askerka M, Brudvig GW, Batista VS. The O 2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data. Acc Chem Res 2017; 50:41-48. [PMID: 28001034 DOI: 10.1021/acs.accounts.6b00405] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn4O5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S1 state is exposed to light, the S1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S1 → S2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the "narrow" channel through a "carousel" rearrangement of waters around Mn4 upon the S2 → S3 transition. An alternative hypothesis suggests water delivery through the "large" channel on the Ca side. However, both water delivery paths lead to a similar S3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O2 evolution.
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Affiliation(s)
- Mikhail Askerka
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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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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Zahariou G, Ioannidis N. Theoretical study of the EPR spectrum of the S 3TyrZ • metalloradical intermediate state of the O 2-evolving complex of photosystem II. PHOTOSYNTHESIS RESEARCH 2016; 130:417-426. [PMID: 27166961 DOI: 10.1007/s11120-016-0274-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 05/03/2016] [Indexed: 05/21/2023]
Abstract
The intermediates trapped during the transitions between the consecutive S-states of the oxygen-evolving complex (OEC) of photosystem II (PSII) contain the free radical TyrZ• interacting magnetically with the Mn-cluster (Mn4Ca). In this paper, we present a theoretical study of the EPR spectrum of the S3TyrZ• metalloradical intermediate state, which has been recently detected in MeOH-containing PSII preparations. For this analysis, we use two different approximations: the first, simpler one, is the point-dipole approach, where the two interacting spins are the S = 1/2 of TyrZ• and the ground spin state of S = 3 of the OEC being in the S3 state. The second approximation is based on previous proposals indicating that the ground spin state (S G = 3) of the S3 state arises from an antiferromagnetic exchange coupling between the S = 9/2 of the Mn(IV)3CaO4 and the S = 3/2 of the external Mn(IV) of the OEC. Under the above assumption, the second approximation involves three interacting spins, denoted S A(Mn(IV)3Ca) = 9/2, S B(Mn(IV)) = 3/2 and S C(TyrZ•) = 1/2. Accordingly, the tyrosine radical is exposed to dipolar interactions with both fragments of the OEC, while an antiferromagnetic exchange coupling within the "3 + 1" structural motif of the OEC is also considered. By application of the first-point-dipole approach, the inter-spin distance that simulates the experimental spectrum is not consistent with the theoretical models that were recently reported for the OEC in the S3 state. Instead, the recent models are consistent with the results of the analysis that is performed by using the second, more detailed, approach.
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Affiliation(s)
- Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", 15310, Athens, Greece.
| | - Nikolaos Ioannidis
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", 15310, Athens, Greece
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Bovi D, Capone M, Narzi D, Guidoni L. Vibrational fingerprints of the Mn 4 CaO 5 cluster in Photosystem II by mixed quantum-classical molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1669-77. [DOI: 10.1016/j.bbabio.2016.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/16/2016] [Accepted: 07/12/2016] [Indexed: 11/16/2022]
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50
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Hodel FH, Luber S. Redox-Inert Cations Enhancing Water Oxidation Activity: The Crucial Role of Flexibility. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01218] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian H. Hodel
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Sandra Luber
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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