1
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Saito K, Chen Y, Ishikita H. Exploring the Deprotonation Process during Incorporation of a Ligand Water Molecule at the Dangling Mn Site in Photosystem II. J Phys Chem B 2024; 128:4728-4734. [PMID: 38693711 PMCID: PMC11104351 DOI: 10.1021/acs.jpcb.4c01997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
The Mn4CaO5 cluster, featuring four ligand water molecules (W1 to W4), serves as the water-splitting site in photosystem II (PSII). X-ray free electron laser (XFEL) structures exhibit an additional oxygen site (O6) adjacent to the O5 site in the fourth lowest oxidation state, S3, forming Mn4CaO6. Here, we investigate the mechanism of the second water ligand molecule at the dangling Mn (W2) as a potential incorporating species, using a quantum mechanical/molecular mechanical (QM/MM) approach. Previous QM/MM calculations demonstrated that W1 releases two protons through a low-barrier H-bond toward D1-Asp61 and subsequently releases an electron during the S2 to S3 transition, resulting in O•- at W1 and protonated D1-Asp61. During the process of Mn4CaO6 formation, O•-, rather than H2O or OH-, best reproduced the O5···O6 distance. Although the catalytic cluster with O•- at O6 is more stable than that with O•- at W1 in S3, it does not occur spontaneously due to the significantly uphill deprotonation process. Assuming O•- at W2 incorporates into the O6 site, an exergonic conversion from Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (equivalent to the open-cubane S2 valence state) to Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (equivalent to the closed-cubane S2 valence state) occurs. These findings provide energetic insights into the deprotonation and structural conversion events required for the Mn4CaO6 formation.
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Affiliation(s)
- Keisuke Saito
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Yang Chen
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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2
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Guo M, Braun A, Sokaras D, Kroll T. Iron Kβ X-ray Emission Spectroscopy: The Origin of Spectral Features from Atomic to Molecular Systems Using Multi-configurational Calculations. J Phys Chem A 2024; 128:1260-1273. [PMID: 38329897 DOI: 10.1021/acs.jpca.3c07949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Kβ X-ray emission spectroscopy (XES) is widely used to fingerprint the local spin of transition-metal ions, including in pump-probe experiments, to identify excited states or in chemical and biological reactions to characterize short-lived intermediates. In this study, the spectra of ferrous and ferric complexes for various spin states were measured experimentally and described theoretically through restricted active space (RAS) calculations including dynamic correlations. Through the RAS calculations from simple atomic models to complex molecular systems, spectral effects such as the exchange interactions, crystal-field strength, and covalent orbital mixing were evaluated and discussed. The calculations find that only the spectral features of low-spin cases show a dependence on the crystal-field strength, particularly for ferrous low spin. The effect of the covalent orbital mixing strength on the first moment of the Kβ1,3 main line and the Kβ1,3-Kβ' energy splitting is quantitatively described. Clear relationships are found within a given nominal spin but less between different spin states, which calls for careful selection of reference spectra in future experiments. This study further advances our understanding of the correlation between changes in experimental spectral features and their corresponding electronic structure information.
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Affiliation(s)
- Meiyuan Guo
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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3
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Drosou M, Pantazis DA. Comprehensive Evaluation of Models for Ammonia Binding to the Oxygen Evolving Complex of Photosystem II. J Phys Chem B 2024; 128:1333-1349. [PMID: 38299511 PMCID: PMC10875651 DOI: 10.1021/acs.jpcb.3c06304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
The identity and insertion pathway of the substrate oxygen atoms that are coupled to dioxygen by the oxygen-evolving complex (OEC) remains a central question toward understanding Nature's water oxidation mechanism. In several studies, ammonia has been used as a small "water analogue" to elucidate the pathway of substrate access to the OEC and to aid in determining which of the oxygen ligands of the tetramanganese cluster are substrates for O-O bond formation. On the basis of structural and spectroscopic investigations, five first-sphere binding modes of ammonia have been suggested, involving either substitution of an existing H2O/OH-/O2- group or addition as an extra ligand to a metal ion of the Mn4CaO5 cluster. Some of these modes, specifically the ones involving substitution, have already been subject to spectroscopy-oriented quantum chemical investigations, whereas more recent suggestions that postulate the addition of ammonia have not been examined so far with quantum chemistry for their agreement with spectroscopic data. Herein, we use a common structural framework and theoretical methodology to evaluate structural models of the OEC that represent all proposed modes of first-sphere ammonia interaction with the OEC in its S2 state. Criteria include energetic, magnetic, kinetic, and spectroscopic properties compared against available experimental EPR, ENDOR, ESEEM, and EDNMR data. Our results show that models featuring ammonia replacing one of the two terminal water ligands on Mn4 align best with experimental data, while they definitively exclude substitution of a bridging μ-oxo ligand as well as incorporation of ammonia as a sixth ligand on Mn1 or Mn4.
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Affiliation(s)
- Maria Drosou
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
- Inorganic
Chemistry Laboratory, National and Kapodistrian
University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
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4
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Chrysina M, Drosou M, Castillo RG, Reus M, Neese F, Krewald V, Pantazis DA, DeBeer S. Nature of S-States in the Oxygen-Evolving Complex Resolved by High-Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy. J Am Chem Soc 2023; 145:25579-25594. [PMID: 37970825 PMCID: PMC10690802 DOI: 10.1021/jacs.3c06046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023]
Abstract
Photosystem II, the water splitting enzyme of photosynthesis, utilizes the energy of sunlight to drive the four-electron oxidation of water to dioxygen at the oxygen-evolving complex (OEC). The OEC harbors a Mn4CaO5 cluster that cycles through five oxidation states Si (i = 0-4). The S3 state is the last metastable state before the O2 evolution. Its electronic structure and nature of the S2 → S3 transition are key topics of persisting controversy. Most spectroscopic studies suggest that the S3 state consists of four Mn(IV) ions, compared to the Mn(III)Mn(IV)3 of the S2 state. However, recent crystallographic data have received conflicting interpretations, suggesting either metal- or ligand-based oxidation, the latter leading to an oxyl radical or a peroxo moiety in the S3 state. Herein, we utilize high-energy resolution fluorescence detected (HERFD) X-ray absorption spectroscopy to obtain a highly resolved description of the Mn K pre-edge region for all S-states, paying special attention to use chemically unperturbed S3 state samples. In combination with quantum chemical calculations, we achieve assignment of specific spectroscopic features to geometric and electronic structures for all S-states. These data are used to confidently discriminate between the various suggestions concerning the electronic structure and the nature of oxidation events in all observable catalytic intermediates of the OEC. Our results do not support the presence of either peroxo or oxyl in the active configuration of the S3 state. This establishes Mn-centered storage of oxidative equivalents in all observable catalytic transitions and constrains the onset of the O-O bond formation until after the final light-driven oxidation event.
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Affiliation(s)
- Maria Chrysina
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
- Institute
of Nanoscience & Nanotechnology, NCSR “Demokritos”, Athens 15310, Greece
| | - Maria Drosou
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Rebeca G. Castillo
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
- Laboratory
of Ultrafast Spectroscopy (LSU) and Lausanne Centre for Ultrafast
Science, École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Michael Reus
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Vera Krewald
- Department
of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Str. 4, Darmstadt 64287, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Serena DeBeer
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
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5
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Tamasaku K, Taguchi M, Inoue I, Osaka T, Inubushi Y, Yabashi M, Ishikawa T. Two-dimensional Kβ-Kα fluorescence spectrum by nonlinear resonant inelastic X-ray scattering. Nat Commun 2023; 14:4262. [PMID: 37460582 PMCID: PMC10352240 DOI: 10.1038/s41467-023-39967-4] [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: 12/20/2022] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
High sensitivity of the Kβ fluorescence spectrum to electronic state is widely used to investigate spin and oxidation state of first-row transition-metal compounds. However, the complex electronic structure results in overlapping spectral features, and the interpretation may be hampered by ambiguity in resolving the spectrum into components representing different electronic states. Here, we tackle this difficulty with a nonlinear resonant inelastic X-ray scattering (RIXS) scheme, where we leverage sequential two-photon absorption to realize an inverse process of the Kβ emission, and measure the successive Kα emission. The nonlinear RIXS reveals two-dimensional (2D) Kβ-Kα fluorescence spectrum of copper metal, leading to better understanding of the spectral feature. We isolate 3d-related satellite peaks in the 2D spectrum, and find good agreement with our multiplet ligand field calculation. Our work not only advances the fluorescence spectroscopy, but opens the door to extend RIXS into the nonlinear regime.
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Affiliation(s)
- Kenji Tamasaku
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.
| | - Munetaka Taguchi
- Toshiba Nanoanalysis Corporation, 8 Shinsugita-cho, Isogo-ku, Yokohama, Kanagawa, 235-8522, Japan.
| | - Ichiro Inoue
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Taito Osaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yuichi Inubushi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Tetsuya Ishikawa
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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6
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Shevela D, Kern JF, Govindjee G, Messinger J. Solar energy conversion by photosystem II: principles and structures. PHOTOSYNTHESIS RESEARCH 2023; 156:279-307. [PMID: 36826741 PMCID: PMC10203033 DOI: 10.1007/s11120-022-00991-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/01/2022] [Indexed: 05/23/2023]
Abstract
Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.
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Affiliation(s)
- Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Govindjee Govindjee
- Department of Plant Biology, Department of Biochemistry and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Johannes Messinger
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden.
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7
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Cutsail III GE, DeBeer S. Challenges and Opportunities for Applications of Advanced X-ray Spectroscopy in Catalysis Research. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- George E. Cutsail III
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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8
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Cząstka K, Oughli AA, Rüdiger O, DeBeer S. Enzymatic X-ray absorption spectroelectrochemistry. Faraday Discuss 2022; 234:214-231. [PMID: 35142778 DOI: 10.1039/d1fd00079a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to observe the changes that occur at an enzyme active site during electrocatalysis can provide very valuable information for understanding the mechanism and ultimately aid in catalyst design. Herein, we discuss the development of X-ray absorption spectroscopy (XAS) in combination with electrochemistry for operando studies of enzymatic systems. XAS has had a long history of enabling geometric and electronic structural insights into the catalytic active sites of enzymes, however, XAS combined with electrochemistry (XA-SEC) has been exceedingly rare in bioinorganic applications. Herein, we discuss the challenges and opportunities of applying operando XAS to enzymatic electrocatalysts. The challenges due to the low concentration of the photoabsorber and the instability of the protein in the X-ray beam are discussed. Methods for immobilizing enzymes on the electrodes, while maintaining full redox control are highlighted. A case study of combined XAS and electrochemistry applied to a [NiFe] hydrogenase is presented. By entrapping the [NiFe] hydrogenase in a redox polymer, relatively high protein concentrations can be achieved on the electrode surface, while maintaining redox control. Overall, it is demonstrated that the experiments are feasible, but require precise redox control over the majority of the absorber atoms and careful controls to discriminate between electrochemically-driven changes and beam damage. Opportunities for future applications are discussed.
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Affiliation(s)
- Karolina Cząstka
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
| | - Alaa A Oughli
- Technical University Munich, Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315 Straubing, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
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9
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Han G, Chernev P, Styring S, Messinger J, Mamedov F. Molecular basis for turnover inefficiencies (misses) during water oxidation in photosystem II. Chem Sci 2022; 13:8667-8678. [PMID: 35974765 PMCID: PMC9337725 DOI: 10.1039/d2sc00854h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Photosynthesis stores solar light as chemical energy and efficiency of this process is highly important. The electrons required for CO2 reduction are extracted from water in a reaction driven by light-induced charge separations in the Photosystem II reaction center and catalyzed by the CaMn4O5-cluster. This cyclic process involves five redox intermediates known as the S0–S4 states. In this study, we quantify the flash-induced turnover efficiency of each S state by electron paramagnetic resonance spectroscopy. Measurements were performed in photosystem II membrane preparations from spinach in the presence of an exogenous electron acceptor at selected temperatures between −10 °C and +20 °C and at flash frequencies of 1.25, 5 and 10 Hz. The results show that at optimal conditions the turnover efficiencies are limited by reactions occurring in the water oxidizing complex, allowing the extraction of their S state dependence and correlating low efficiencies to structural changes and chemical events during the reaction cycle. At temperatures 10 °C and below, the highest efficiency (i.e. lowest miss parameter) was found for the S1 → S2 transition, while the S2 → S3 transition was least efficient (highest miss parameter) over the whole temperature range. These electron paramagnetic resonance results were confirmed by measurements of flash-induced oxygen release patterns in thylakoid membranes and are explained on the basis of S state dependent structural changes at the CaMn4O5-cluster that were determined recently by femtosecond X-ray crystallography. Thereby, possible “molecular errors” connected to the e− transfer, H+ transfer, H2O binding and O2 release are identified. Temperature dependence of the transition inefficiencies (misses) for the water oxidation process in photosystem II were studied by EPR spectroscopy and are explained on the basis of S state dependent structural changes at the CaMn4O5-cluster.![]()
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Affiliation(s)
- Guangye Han
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 751 20 Uppsala, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 751 20 Uppsala, Sweden
| | - Stenbjörn Styring
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 751 20 Uppsala, Sweden
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 751 20 Uppsala, Sweden
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 751 20 Uppsala, Sweden
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10
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Mandal M, Saito K, Ishikita H. Requirement of Chloride for the Downhill Electron Transfer Pathway from the Water-Splitting Center in Natural Photosynthesis. J Phys Chem B 2021; 126:123-131. [PMID: 34955014 DOI: 10.1021/acs.jpcb.1c09176] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In photosystem II (PSII), Cl- is a prerequisite for the second flash-induced oxidation of the Mn4CaO5 cluster (the S2 to S3 transition). We report proton transfer from the substrate water molecule via D1-Asp61 and electron transfer via redox-active D1-Tyr161 (TyrZ) to the chlorophyll pair in Cl--depleted PSII using a quantum mechanical/molecular mechanical approach. The low-barrier H-bond formation between the substrate water molecule and D1-Asp61 remained unaffected upon the depletion of Cl-. However, the binding site, D2-Lys317, formed a salt bridge with D1-Asp61, leading to the inhibition of the subsequent proton transfer. Remarkably, the redox potential (Em) of S2/S3 increased significantly, making electron transfer from S2 to TyrZ energetically uphill, as observed in Ca2+-depleted PSII. The uphill electron transfer pathway was induced by the significant increase in Em(S2/S3) caused by the loss of charge compensation for D2-Lys317 upon the depletion of Cl-, whereas it was induced by the significant decrease in Em(TyrZ) caused by the rearrangement of the water molecules at the Ca2+ binding moiety upon the depletion of Ca2+.
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Affiliation(s)
- Manoj Mandal
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, West Bengal 700106, India
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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11
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Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:064302. [PMID: 34849380 PMCID: PMC8610604 DOI: 10.1063/4.0000130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/24/2021] [Indexed: 05/21/2023]
Abstract
In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
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Affiliation(s)
- Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Mohamed Ibrahim
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Miao Zhang
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ramzi Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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12
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Cavaletto SM, Nascimento DR, Zhang Y, Govind N, Mukamel S. Resonant Stimulated X-ray Raman Spectroscopy of Mixed-Valence Manganese Complexes. J Phys Chem Lett 2021; 12:5925-5931. [PMID: 34156863 DOI: 10.1021/acs.jpclett.1c01190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Resonant stimulated X-ray Raman spectroscopy of the bimetallic [MnIIIMnIV(μ-O)2(μ-OAC)(tacn)2]2+ manganese complex is investigated in a simulation study. Essential biological processes, including water oxidation in photosynthesis, involve charge transfer between manganese sites of different oxidation states. We study a prototypical binuclear mixed-valence transition-metal complex with two Mn atoms in different oxidation states surrounded by ligand structures and employ a pump-probe sequence of resonant X-ray Raman excitations to follow the charge transfer occurring in the molecule. This allows us to generate and monitor valence-electron wave packets at selected regions in the molecule by exploiting element-specific core-excited states. A two-color protocol is presented, with pump and probe pulses tuned to the Mn and N K-edges. A natural orbital decomposition allows the visualization of the electron dynamics underlying the signal.
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Affiliation(s)
- Stefano M Cavaletto
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Daniel R Nascimento
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yu Zhang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
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13
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Mandal M, Saito K, Ishikita H. Two Distinct Oxygen-Radical Conformations in the X-ray Free Electron Laser Structures of Photosystem II. J Phys Chem Lett 2021; 12:4032-4037. [PMID: 33881870 DOI: 10.1021/acs.jpclett.1c00814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report the existence of two distinct oxygen-radical-containing Mn4CaO5/6 conformations with short O···O bonds in the crystal structures of the oxygen-evolving enzyme photosystem II (PSII), obtained using an X-ray free electron laser (XFEL). A short O···O distance of <2.3 Å between the O4 site of the Mn4CaO5 complex and the adjacent water molecule (W539) in the proton-conducting O4-water chain was observed in the second flash-induced (2F) XFEL structure (2F-XFEL), which may correspond to S3. By use of a quantum mechanical/molecular mechanical approach, the OH• formation at W539 and the short O4···OW539 distance (<2.3 Å) were reproduced in S2 and S3 with reduced Mn1(III), which lacks the additional sixth water molecule O6. As the O•- formation at O6 and the short O5···O6 distance (1.9 Å) have been reported in another 2F-XFEL structure with reduced Mn4(III), two distinct oxygen-radical conformations exist in the 2F-XFEL crystals.
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Affiliation(s)
- Manoj Mandal
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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14
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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15
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Mandal M, Saito K, Ishikita H. The Nature of the Short Oxygen-Oxygen Distance in the Mn 4CaO 6 Complex of Photosystem II Crystals. J Phys Chem Lett 2020; 11:10262-10268. [PMID: 33210928 DOI: 10.1021/acs.jpclett.0c02868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The O···O distance for a typical H-bond is ∼2.8 Å, whereas the radiation-damage-free structures of photosystem II (PSII), obtained using the X-ray free electron laser (XFEL), shows remarkably short O···O distances of ∼2 Å in the oxygen-evolving Mn4CaO5/6 complex. Herein, we report the protonation/oxidation states of the short O···O atoms in the XFEL structures using a quantum mechanical/molecular mechanical approach. The O5···O6 distance of 1.9 Å is reproduced only when O6 is an unprotonated O radical (O•-) with Mn(IV)3Mn(III), i.e., the S3 state. The potential energy profile shows a barrier-less energy minimum region when O5···O6 = 1.90-2.05 Å (O•- ↓) or 2.05-2.20 Å (O•- ↑). Formation of such a short O5···O6 distance is not possible when O6 is OH- with Mn(IV)4. In the case in which the O5···O6 distance is 1.9 Å, it seems likely that the O radical species exists in the oxygen-evolving complex of the XFEL-S3 crystals.
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Affiliation(s)
- Manoj Mandal
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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16
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Lafuerza S, Retegan M, Detlefs B, Chatterjee R, Yachandra V, Yano J, Glatzel P. New reflections on hard X-ray photon-in/photon-out spectroscopy. NANOSCALE 2020; 12:16270-16284. [PMID: 32760987 PMCID: PMC7808884 DOI: 10.1039/d0nr01983f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Analysis of the electronic structure and local coordination of an element is an important aspect in the study of the chemical and physical properties of materials. This is particularly relevant at the nanoscale where new phases of matter may emerge below a critical size. X-ray emission spectroscopy (XES) at synchrotron radiation sources and free electron lasers has enriched the field of X-ray spectroscopy. The spectroscopic techniques derived from the combination of X-ray absorption and emission spectroscopy (XAS-XES), such as resonant inelastic X-ray scattering (RIXS) and high energy resolution fluorescence detected (HERFD) XAS, are an ideal tool for the study of nanomaterials. New installations and beamline upgrades now often include wavelength dispersive instruments for the analysis of the emitted X-rays. With the growing use of XAS-XES, scientists are learning about the possibilities and pitfalls. We discuss some experimental aspects, assess the feasibility of measuring weak fluorescence lines in dilute, radiation sensitive samples, and present new experimental approaches for studying magnetic properties of colloidal nanoparticles directly in the liquid phase.
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Affiliation(s)
- Sara Lafuerza
- European Synchrotron Radiation Facility, 71 Avenue des Martyres, 38000 Grenoble, France.
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17
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Cox N, Pantazis DA, Lubitz W. Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data. Annu Rev Biochem 2020; 89:795-820. [DOI: 10.1146/annurev-biochem-011520-104801] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOxcomplex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.
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Affiliation(s)
- Nicholas Cox
- Research School of Chemistry, The Australian National University, Canberra ACT 2601, Australia
| | | | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim an der Ruhr, Germany
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18
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Water-oxidizing complex in Photosystem II: Its structure and relation to manganese-oxide based catalysts. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213183] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Melder J, Bogdanoff P, Zaharieva I, Fiechter S, Dau H, Kurz P. Water-Oxidation Electrocatalysis by Manganese Oxides: Syntheses, Electrode Preparations, Electrolytes and Two Fundamental Questions. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2019-1491] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Abstract
The efficient catalysis of the four-electron oxidation of water to molecular oxygen is a central challenge for the development of devices for the production of solar fuels. This is equally true for artificial leaf-type structures and electrolyzer systems. Inspired by the oxygen evolving complex of Photosystem II, the biological catalyst for this reaction, scientists around the globe have investigated the possibility to use manganese oxides (“MnOx”) for this task. This perspective article will look at selected examples from the last about 10 years of research in this field. At first, three aspects are addressed in detail which have emerged as crucial for the development of efficient electrocatalysts for the anodic oxygen evolution reaction (OER): (1) the structure and composition of the “MnOx” is of central importance for catalytic performance and it seems that amorphous, MnIII/IV oxides with layered or tunnelled structures are especially good choices; (2) the type of support material (e.g. conducting oxides or nanostructured carbon) as well as the methods used to immobilize the MnOx catalysts on them greatly influence OER overpotentials, current densities and long-term stabilities of the electrodes and (3) when operating MnOx-based water-oxidizing anodes in electrolyzers, it has often been observed that the electrocatalytic performance is also largely dependent on the electrolyte’s composition and pH and that a number of equilibria accompany the catalytic process, resulting in “adaptive changes” of the MnOx material over time. Overall, it thus has become clear over the last years that efficient and stable water-oxidation electrolysis by manganese oxides can only be achieved if at least four parameters are optimized in combination: the oxide catalyst itself, the immobilization method, the catalyst support and last but not least the composition of the electrolyte. Furthermore, these parameters are not only important for the electrode optimization process alone but must also be considered if different electrode types are to be compared with each other or with literature values from literature. Because, as without their consideration it is almost impossible to draw the right scientific conclusions. On the other hand, it currently seems unlikely that even carefully optimized MnOx anodes will ever reach the superb OER rates observed for iridium, ruthenium or nickel-iron oxide anodes in acidic or alkaline solutions, respectively. So at the end of the article, two fundamental questions will be addressed: (1) are there technical applications where MnOx materials could actually be the first choice as OER electrocatalysts? and (2) do the results from the last decade of intensive research in this field help to solve a puzzle already formulated in 2008: “Why did nature choose manganese to make oxygen?”.
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Affiliation(s)
- Jens Melder
- Institut für Anorganische und Analytische Chemie und Freiburger Materialforschungszentrum (FMF) , Albert-Ludwigs-Universität Freiburg , Albertstraße 21, 79104 Freiburg , Germany
| | - Peter Bogdanoff
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Solar Fuels , 14109 Berlin , Germany
| | - Ivelina Zaharieva
- Freie Universität Berlin, Fachbereich Physik , Arnimallee 14, 14195 Berlin , Germany
| | - Sebastian Fiechter
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Solar Fuels , 14109 Berlin , Germany
| | - Holger Dau
- Freie Universität Berlin, Fachbereich Physik , Arnimallee 14, 14195 Berlin , Germany
| | - Philipp Kurz
- Institut für Anorganische und Analytische Chemie und Freiburger Materialforschungszentrum (FMF) , Albert-Ludwigs-Universität Freiburg , Albertstraße 21, 79104 Freiburg , Germany
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20
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Gagrani A, Alsultan M, Swiegers GF, Tsuzuki T. Comparative evaluation of the structural and other features governing photo-electrochemical oxygen evolution by Ca/Mn oxides. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00105h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bio-inspired calcium manganate ceramics induce higher photocurrents than MnO2 in photo-electrochemical water splitting.
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Affiliation(s)
- Ankita Gagrani
- Research School of Electrical, Energy and Materials Engineering
- The Australian National University
- Canberra
- Australia
| | - Mohammed Alsultan
- Intelligent Polymer Research Institute
- University of Wollongong
- Wollongong
- Australia
- Department of Science
| | - Gerhard F. Swiegers
- Intelligent Polymer Research Institute
- University of Wollongong
- Wollongong
- Australia
| | - Takuya Tsuzuki
- Research School of Electrical, Energy and Materials Engineering
- The Australian National University
- Canberra
- Australia
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21
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Assessment of the manganese cluster's oxidation state via photoactivation of photosystem II microcrystals. Proc Natl Acad Sci U S A 2019; 117:141-145. [PMID: 31848244 DOI: 10.1073/pnas.1915879117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Knowledge of the manganese oxidation states of the oxygen-evolving Mn4CaO5 cluster in photosystem II (PSII) is crucial toward understanding the mechanism of biological water oxidation. There is a 4 decade long debate on this topic that historically originates from the observation of a multiline electron paramagnetic resonance (EPR) signal with effective total spin of S = 1/2 in the singly oxidized S2 state of this cluster. This signal implies an overall oxidation state of either Mn(III)3Mn(IV) or Mn(III)Mn(IV)3 for the S2 state. These 2 competing assignments are commonly known as "low oxidation (LO)" and "high oxidation (HO)" models of the Mn4CaO5 cluster. Recent advanced EPR and Mn K-edge X-ray spectroscopy studies converge upon the HO model. However, doubts about these assignments have been voiced, fueled especially by studies counting the number of flash-driven electron removals required for the assembly of an active Mn4CaO5 cluster starting from Mn(II) and Mn-free PSII. This process, known as photoactivation, appeared to support the LO model since the first oxygen is reported to evolve already after 7 flashes. In this study, we improved the quantum yield and sensitivity of the photoactivation experiment by employing PSII microcrystals that retained all protein subunits after complete manganese removal and by oxygen detection via a custom built thin-layer cell connected to a membrane inlet mass spectrometer. We demonstrate that 9 flashes by a nanosecond laser are required for the production of the first oxygen, which proves that the HO model provides the correct description of the Mn4CaO5 cluster's oxidation states.
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22
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23
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Lubitz W, Chrysina M, Cox N. Water oxidation in photosystem II. PHOTOSYNTHESIS RESEARCH 2019; 142:105-125. [PMID: 31187340 PMCID: PMC6763417 DOI: 10.1007/s11120-019-00648-3] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/20/2019] [Indexed: 05/18/2023]
Abstract
Biological water oxidation, performed by a single enzyme, photosystem II, is a central research topic not only in understanding the photosynthetic apparatus but also for the development of water splitting catalysts for technological applications. Great progress has been made in this endeavor following the report of a high-resolution X-ray crystallographic structure in 2011 resolving the cofactor site (Umena et al. in Nature 473:55-60, 2011), a tetra-manganese calcium complex. The electronic properties of the protein-bound water oxidizing Mn4OxCa complex are crucial to understand its catalytic activity. These properties include: its redox state(s) which are tuned by the protein matrix, the distribution of the manganese valence and spin states and the complex interactions that exist between the four manganese ions. In this short review we describe how magnetic resonance techniques, particularly EPR, complemented by quantum chemical calculations, have played an important role in understanding the electronic structure of the cofactor. Together with isotope labeling, these techniques have also been instrumental in deciphering the binding of the two substrate water molecules to the cluster. These results are briefly described in the context of the history of biological water oxidation with special emphasis on recent work using time resolved X-ray diffraction with free electron lasers. It is shown that these data are instrumental for developing a model of the biological water oxidation cycle.
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Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim/Ruhr, Germany
| | - Maria Chrysina
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim/Ruhr, Germany
| | - Nicholas Cox
- Research School of Chemistry, The Australian National University, Canberra, Australia
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24
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Pushkar Y, K Ravari A, Jensen SC, Palenik M. Early Binding of Substrate Oxygen Is Responsible for a Spectroscopically Distinct S 2 State in Photosystem II. J Phys Chem Lett 2019; 10:5284-5291. [PMID: 31419136 DOI: 10.1021/acs.jpclett.9b01255] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The biological generation of oxygen by the oxygen-evolving complex (OEC) in photosystem II (PS II) is one of nature's most important reactions. The OEC is a Mn4Ca cluster that has multiple Mn-O-Mn and Mn-O-Ca bridges and binds four water molecules. Previously, binding of an additional oxygen was detected in the S2 to S3 transition. Here we demonstrate that early binding of the substrate oxygen to the five-coordinate Mn1 center in the S2 state is likely responsible for the S2 high-spin EPR signal. Substrate binding in the Mn1-OH form explains the prevalence of the high-spin S2 state at higher pH and its low-temperature conversion into the S3 state. The given interpretation was confirmed by X-ray absorption spectroscopic measurements, DFT, and broken symmetry DFT calculations of structures and magnetic properties. Structural, electronic, and spectroscopic properties of the high-spin S2 state model are provided and compared with the available S3 state models. New interpretation of the high-spin S2 state opens opportunity for analysis of factors controlling the oxygen substrate binding in PS II.
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Affiliation(s)
- Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Alireza K Ravari
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark Palenik
- Code 6189, Chemistry Division, Naval Research Laboratory, Washington, DC 20375, United States
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25
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Jensen SC, Sullivan B, Hartzler DA, Pushkar Y. DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system. X-RAY SPECTROMETRY : XRS 2019; 48:336-344. [PMID: 32606482 PMCID: PMC7326317 DOI: 10.1002/xrs.3005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 06/11/2023]
Abstract
The application of X-ray emission spectroscopy (XES) has grown substantially with the development of X-ray free electron lasers, third and fourth generation synchrotron sources and high-power benchtop sources. By providing the high X-ray flux required for XES, these sources broaden the availability and application of this method of probing electronic structure. As the number of sources increase, so does the demand for X-ray emission detection and sample delivery systems that are cost effective and customizable. Here, we present a detailed fabrication protocol for von Hamos X-ray optics and give details for a 3D-printed spectrometer design. Additionally, we outline an automated, externally triggered liquid sample delivery system that can be used to repeatedly deliver nanoliter droplets onto a plastic substrate for measurement. These systems are both low cost, efficient and easy to recreate or modify depending on the application. A low cost multiple X-ray analyzer system enables measurement of dilute samples, whereas the sample delivery limits sample loss and replaces spent sample with fresh sample in the same position. While both systems can be used in a wide range of applications, the design addresses several challenges associated specifically with time-resolved XES (TRXES). As an example application, we show results from TRXES measurements of photosystem II, a dilute, photoactive protein.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Daniel A Hartzler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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26
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Hayashi M, Takahashi Y, Yoshida Y, Sugimoto K, Kitagawa H. Role of d-Elements in a Proton–Electron Coupling of d–π Hybridized Electron Systems. J Am Chem Soc 2019; 141:11686-11693. [DOI: 10.1021/jacs.9b04937] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mikihiro Hayashi
- Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Faculty of Education, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yuki Takahashi
- Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yukihiro Yoshida
- Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Hiroshi Kitagawa
- Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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27
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Stabilization of reactive Co 4O 4 cubane oxygen-evolution catalysts within porous frameworks. Proc Natl Acad Sci U S A 2019; 116:11630-11639. [PMID: 31142656 DOI: 10.1073/pnas.1815013116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A major challenge to the implementation of artificial photosynthesis (AP), in which fuels are produced from abundant materials (water and carbon dioxide) in an electrochemical cell through the action of sunlight, is the discovery of active, inexpensive, safe, and stable catalysts for the oxygen evolution reaction (OER). Multimetallic molecular catalysts, inspired by the natural photosynthetic enzyme, can provide important guidance for catalyst design, but the necessary mechanistic understanding has been elusive. In particular, fundamental transformations for reactive intermediates are difficult to observe, and well-defined molecular models of such species are highly prone to decomposition by intermolecular aggregation. Here, we present a general strategy for stabilization of the molecular cobalt-oxo cubane core (Co4O4) by immobilizing it as part of metal-organic frameworks, thus preventing intermolecular pathways of catalyst decomposition. These materials retain the OER activity and mechanism of the molecular Co4O4 analog yet demonstrate unprecedented long-term stability at pH 14. The organic linkers of the framework allow for chemical fine-tuning of activity and stability and, perhaps most importantly, provide "matrix isolation" that allows for observation and stabilization of intermediates in the water-splitting pathway.
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28
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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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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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30
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Jensen SC, Sullivan B, Hartzler D, Aguilar JM, Awel S, Bajt S, Basu S, Bean R, Chapman H, Conrad C, Frank M, Fromme R, Martin-Garcia JM, Grant TD, Heymann M, Hunter MS, Ketawala G, Kirian RA, Knoska J, Kupitz C, Li X, Liang M, Lisova S, Mariani V, Mazalova V, Messerschmidt M, Moran M, Nelson G, Oberthür D, Schaffer A, Sierra RG, Vaughn N, Weierstall U, Wiedorn MO, Xavier L, Yang JH, Yefanov O, Zatsepin NA, Aquila A, Fromme P, Boutet S, Seidler GT, Pushkar Y. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. J Phys Chem Lett 2019; 10:441-446. [PMID: 30566358 PMCID: PMC7047744 DOI: 10.1021/acs.jpclett.8b03595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
X-ray free electron lasers (XFELs) provide ultrashort intense X-ray pulses suitable to probe electron dynamics but can also induce a multitude of nonlinear excitation processes. These affect spectroscopic measurements and interpretation, particularly for upcoming brighter XFELs. Here we identify and discuss the limits to observing classical spectroscopy, where only one photon is absorbed per atom for a Mn2+ in a light element (O, C, H) environment. X-ray emission spectroscopy (XES) with different incident photon energies, pulse intensities, and pulse durations is presented. A rate equation model based on sequential ionization and relaxation events is used to calculate populations of multiply ionized states during a single pulse and to explain the observed X-ray induced spectral lines shifts. This model provides easy estimation of spectral shifts, which is essential for experimental designs at XFELs and illustrates that shorter X-ray pulses will not overcome sequential ionization but can reduce electron cascade effects.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Daniel Hartzler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Jose Meza Aguilar
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Saša Bajt
- Photon Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Shibom Basu
- Paul Sherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Raimund Fromme
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | | | - Thomas D Grant
- Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY 14203
- BioXFEL Science and Technology Center, Buffalo, NY 14203, USA
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, 82152 Planegg, Germany
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gihan Ketawala
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Richard A Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Xuanxuan Li
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Mengning Liang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | | | - Michael Moran
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Alex Schaffer
- Department of Biochemistry, University of California Davis, Davis, CA 95616, USA
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Natalie Vaughn
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Uwe Weierstall
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jay-How Yang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Petra Fromme
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ85287-1604
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gerald T Seidler
- Department of Physics, University of Washington, Seattle, Washington 98195-1560, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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Abstract
AbstractCyanobacteria and plants carry out oxygenic photosynthesis. They use water to generate the atmospheric oxygen we breathe and carbon dioxide to produce the biomass serving as food, feed, fibre and fuel. This paper scans the emergence of structural and mechanistic understanding of oxygen evolution over the past 50 years. It reviews speculative concepts and the stepped insight provided by novel experimental and theoretical techniques. Driven by sunlight photosystem II oxidizes the catalyst of water oxidation, a hetero-metallic Mn4CaO5(H2O)4 cluster. Mn3Ca are arranged in cubanoid and one Mn dangles out. By accumulation of four oxidizing equivalents before initiating dioxygen formation it matches the four-electron chemistry from water to dioxygen to the one-electron chemistry of the photo-sensitizer. Potentially harmful intermediates are thereby occluded in space and time. Kinetic signatures of the catalytic cluster and its partners in the photo-reaction centre have been resolved, in the frequency domain ranging from acoustic waves via infra-red to X-ray radiation, and in the time domain from nano- to milli-seconds. X-ray structures to a resolution of 1.9 Å are available. Even time resolved X-ray structures have been obtained by clocking the reaction cycle by flashes of light and diffraction with femtosecond X-ray pulses. The terminal reaction cascade from two molecules of water to dioxygen involves the transfer of four electrons, two protons, one dioxygen and one water. A rigorous mechanistic analysis is challenging because of the kinetic enslaving at millisecond duration of six partial reactions (4e−, 1H+, 1O2). For the time being a peroxide-intermediate in the reaction cascade to dioxygen has been in focus, both experimentally and by quantum chemistry. Homo sapiens has relied on burning the products of oxygenic photosynthesis, recent and fossil. Mankind's total energy consumption amounts to almost one-fourth of the global photosynthetic productivity. If the average power consumption equalled one of those nations with the highest consumption per capita it was four times greater and matched the total productivity. It is obvious that biomass should be harvested for food, feed, fibre and platform chemicals rather than for fuel.
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32
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Shamsipur M, Pashabadi A. Latest advances in PSII features and mechanism of water oxidation. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Corry TA, O'Malley PJ. Evidence of O-O Bond Formation in the Final Metastable S 3 State of Nature's Water Oxidizing Complex Implying a Novel Mechanism of Water Oxidation. J Phys Chem Lett 2018; 9:6269-6274. [PMID: 30336040 DOI: 10.1021/acs.jpclett.8b02793] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A novel mechanism for the final stages of Nature's photosynthetic water oxidation to molecular oxygen is proposed. This is based on a comparison of experimental and broken symmetry density functional theory (BS-DFT) calculated geometries and magnetic resonance properties of water oxidizing complex models in the final metastable oxidation state, S3. We show that peroxo models of the S3 state are in vastly superior agreement with the current experimental structural determinations compared with oxo-hydroxo models. Comparison of experimental and BS-DFT calculated 55Mn hyperfine couplings for the electron paramagnetic resonance (EPR) visible form shows better agreement for the oxo-hydroxo model. An equilibrium between oxo-hydroxo and peroxo models is proposed for the S3 state and the major implications for the final steps in the water oxidation mechanism are analyzed and discussed.
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Affiliation(s)
- Thomas A Corry
- School of Chemistry , The University of Manchester , Manchester , M13 9PL , U.K
| | - Patrick J O'Malley
- School of Chemistry , The University of Manchester , Manchester , M13 9PL , U.K
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34
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Petrie S, Stranger R, Pace RJ. Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S 3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å. Chemphyschem 2018; 19:3296-3309. [PMID: 30290080 DOI: 10.1002/cphc.201800686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 11/10/2022]
Abstract
Recently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 Å and 2.35 Å resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 Å structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 Å XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 Å structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and an O5-O6 separation of ∼1.5 Å, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 Å structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 Å structure. We show that the Suga et al. 2.35 Å structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
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35
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Davis KM, Sullivan BT, Palenik MC, Yan L, Purohit V, Robison G, Kosheleva I, Henning RW, Seidler GT, Pushkar Y. Rapid evolution of the Photosystem II electronic structure during water splitting. PHYSICAL REVIEW. X 2018; 8:041014. [PMID: 31231592 PMCID: PMC6588194 DOI: 10.1103/physrevx.8.041014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Photosynthetic water oxidation is a fundamental process that sustains the biosphere. A Mn4Ca cluster embedded in the photosystem II protein environment is responsible for the production of atmospheric oxygen. Here, time-resolved x-ray emission spectroscopy (XES) was used to observe the process of oxygen formation in real time. These experiments reveal that the oxygen evolution step, initiated by three sequential laser flashes, is accompanied by rapid (within 50 μs) changes to the Mn Kβ XES spectrum. However, no oxidation of the Mn4Ca core above the all MnIV state was detected to precede O-O bond formation, and the observed changes were therefore assigned to O-O bond formation dynamics. We propose that O-O bond formation occurs prior to the transfer of the final (4th) electron from the Mn4Ca cluster to the oxidized tyrosine YZ residue. This model resolves the kinetic limitations associated with O-O bond formation, and suggests an evolutionary adaptation to avoid releasing of harmful peroxide species.
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Affiliation(s)
- Katherine M. Davis
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan T. Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lifen Yan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Vatsal Purohit
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Gregory Robison
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Robert W. Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Gerald T. Seidler
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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36
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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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37
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Schuth N, Zaharieva I, Chernev P, Berggren G, Anderlund M, Styring S, Dau H, Haumann M. Kα X-ray Emission Spectroscopy on the Photosynthetic Oxygen-Evolving Complex Supports Manganese Oxidation and Water Binding in the S3 State. Inorg Chem 2018; 57:10424-10430. [DOI: 10.1021/acs.inorgchem.8b01674] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nils Schuth
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ivelina Zaharieva
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Petko Chernev
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Gustav Berggren
- Ångström Laboratory, Department of Chemistry, Uppsala University, 75120 Uppsala, Sweden
| | - Magnus Anderlund
- Ångström Laboratory, Department of Chemistry, Uppsala University, 75120 Uppsala, Sweden
| | - Stenbjörn Styring
- Ångström Laboratory, Department of Chemistry, Uppsala University, 75120 Uppsala, Sweden
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
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38
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Kawashima K, Saito K, Ishikita H. Mechanism of Radical Formation in the H-Bond Network of D1-Asn298 in Photosystem II. Biochemistry 2018; 57:4997-5004. [DOI: 10.1021/acs.biochem.8b00574] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Keisuke Kawashima
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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39
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Fransson T, Chatterjee R, Fuller FD, Gul S, Weninger C, Sokaras D, Kroll T, Alonso-Mori R, Bergmann U, Kern J, Yachandra VK, Yano J. X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry 2018; 57:4629-4637. [PMID: 29906115 DOI: 10.1021/acs.biochem.8b00325] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kβ1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.
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Affiliation(s)
- Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
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40
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Pushkar Y, Davis KM, Palenik MC. Model of the Oxygen Evolving Complex Which Is Highly Predisposed to O-O Bond Formation. J Phys Chem Lett 2018; 9:3525-3531. [PMID: 29863871 DOI: 10.1021/acs.jpclett.8b00800] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Light-driven water oxidation is a fundamental reaction in the biosphere. The Mn4Ca cluster of photosystem II cycles through five redox states termed S0-S4, after which oxygen is evolved. Critically, the timing of O-O bond formation within the Kok cycle remains unknown. By combining recent crystallographic, spectroscopic, and DFT results, we demonstrate an atomistic S3 state model with the possibility of a low barrier to O-O bond formation prior to the final oxidation step. Furthermore, the associated one electron oxidized S4 state does not provide more advantages in terms of spin alignment or the energy of O-O bond formation. We propose that a high energy peroxide isoform of the S3 state can preferentially be oxidized by Tyr zox in the course of final electron transfer leading to O2 evolution. Such a mechanism may explain the peculiar kinetic behavior of O2 evolution as well as serve as an evolutionary adaptation to avoid release of the harmful peroxides.
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Affiliation(s)
- Yulia Pushkar
- Department of Physics and Astronomy , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Katherine M Davis
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Mark C Palenik
- Chemistry Division , Naval Research Laboratory , NRC Research Associate, Code 6189, 4555 Overlook Avenue SW , Washington, DC 20375 , United States
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41
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Kawashima K, Takaoka T, Kimura H, Saito K, Ishikita H. O 2 evolution and recovery of the water-oxidizing enzyme. Nat Commun 2018; 9:1247. [PMID: 29593210 PMCID: PMC5871790 DOI: 10.1038/s41467-018-03545-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/20/2018] [Indexed: 01/14/2023] Open
Abstract
In photosystem II, light-induced water oxidation occurs at the Mn4CaO5 cluster. Here we demonstrate proton releases, dioxygen formation, and substrate water incorporation in response to Mn4CaO5 oxidation in the protein environment, using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. In S2, H2O at the W1 site forms a low-barrier H-bond with D1-Asp61. In the S2-to-S3 transition, oxidation of OW1H– to OW1•–, concerted proton transfer from OW1H– to D1-Asp61, and binding of a water molecule Wn-W1 at OW1•– are observed. In S4, Wn-W1 facilitates oxo-oxyl radical coupling between OW1•– and corner μ-oxo O4. Deprotonation via D1-Asp61 leads to formation of OW1=O4. As OW1=O4 moves away from Mn, H2O at W539 is incorporated into the vacant O4 site of the O2-evolved Mn4CaO4 cluster, forming a μ-oxo bridge (Mn3–OW539–Mn4) in an exergonic process. Simultaneously, Wn-W1 is incorporated as W1, recovering the Mn4CaO5 cluster. Water splitting during photosynthesis results in the combination of two oxygen atoms to form O2. Here, based on computational simulations, the authors develop a possible mechanism for this reaction, which is different from the mechanisms previous studies have suggested.
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Affiliation(s)
- Keisuke Kawashima
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Tomohiro Takaoka
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiroki Kimura
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan. .,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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42
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Petrie S, Stranger R, Pace RJ. What Mn K β spectroscopy reveals concerning the oxidation states of the Mn cluster in photosystem II. Phys Chem Chem Phys 2018; 19:27682-27693. [PMID: 28983541 DOI: 10.1039/c7cp04797e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The oxygen evolving complex, (OEC) in Photosystem II contains a Mn4Ca cluster and catalyses oxidation of water to molecular oxygen and protons, the most energetically demanding reaction in nature. The catalytic mechanism remains unresolved and the precise Mn oxidation levels through which the cluster cycles during functional turnover are controversial. Two proposals for these redox levels exist; the 'high' and 'low' oxidation state paradigms, which differ systematically by two oxidation equivalents throughout the redox accumulating catalytic S state cycle (states S0…S3). Presently the 'high' paradigm is more favored. For S1 the assumed mean redox levels of Mn are 3.5 (high) and 3.0 (low) respectively. Mn K region X-ray spectroscopy has been extensively used to examine the OEC Mn oxidation levels, with Kβ emission spectroscopy increasingly the method of choice. Here we review the results from application of this and closely related techniques to PS II, building on our earlier examination of these and other data on the OEC oxidation states (Pace et al., Dalton Trans., 2012, 41, 11145). We compare the most recent results with a range of earlier Mn Kβ experiments on the photosystem and related model Mn systems. New analyses of these data are given, highlighting certain key spectral considerations which appear not to have been sufficiently appreciated earlier. These show that the recent and earlier PS II Kβ results have a natural internal consistency, leading to the strong conclusion that the low paradigm oxidation state assignment for the functional OEC is favoured.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical & Mathematical Sciences, College of Science, Australian National University, Canberra, ACT 0200, Australia.
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43
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Schuth N, Liang Z, Schönborn M, Kussicke A, Assunção R, Zaharieva I, Zilliges Y, Dau H. Inhibitory and Non-Inhibitory NH 3 Binding at the Water-Oxidizing Manganese Complex of Photosystem II Suggests Possible Sites and a Rearrangement Mode of Substrate Water Molecules. Biochemistry 2017; 56:6240-6256. [PMID: 29086556 DOI: 10.1021/acs.biochem.7b00743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The identity and rearrangements of substrate water molecules in photosystem II (PSII) water oxidation are of great mechanistic interest and addressed herein by comprehensive analysis of NH4+/NH3 binding. Time-resolved detection of O2 formation and recombination fluorescence as well as Fourier transform infrared (FTIR) difference spectroscopy on plant PSII membrane particles reveals the following. (1) Partial inhibition in NH4Cl buffer occurs with a pH-independent binding constant of ∼25 mM, which does not result from decelerated O2 formation, but from complete blockage of a major PSII fraction (∼60%) after reaching the Mn(IV)4 (S3) state. (2) The non-inhibited PSII fraction advances through the reaction cycle, but modified nuclear rearrangements are suggested by FTIR difference spectroscopy. (3) Partial inhibition can be explained by anticooperative (mutually exclusive) NH3 binding to one inhibitory and one non-inhibitory site; these two sites may correspond to two water molecules terminally bound to the "dangling" Mn ion. (4) Unexpectedly strong modifications of the FTIR difference spectra suggest that in the non-inhibited PSII, ammonia binding obliterates the need for some of the nuclear rearrangements occurring in the S2-S3 transition as well as their reversal in the O2 formation transition, in line with the carousel mechanism [Askerka, M., et al. (2015) Biochemistry 54, 5783]. (5) We observe the same partial inhibition of PSII by NH4Cl also for thylakoid membranes prepared from mesophilic and thermophilic cyanobacteria, suggesting that the results described above are valid for plant and cyanobacterial PSII.
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Affiliation(s)
- Nils Schuth
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
| | - Zhiyong Liang
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
| | | | - André Kussicke
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
| | - Ricardo Assunção
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
| | - Ivelina Zaharieva
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
| | - Yvonne Zilliges
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
| | - Holger Dau
- Freie Universität Berlin , Department of Physics, 14195 Berlin, Germany
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44
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Jensen SC, Davis KM, Sullivan B, Hartzler DA, Seidler GT, Casa DM, Kasman E, Colmer HE, Massie AA, Jackson TA, Pushkar Y. X-ray Emission Spectroscopy of Biomimetic Mn Coordination Complexes. J Phys Chem Lett 2017; 8:2584-2589. [PMID: 28524662 DOI: 10.1021/acs.jpclett.7b01209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the function of Mn ions in biological and chemical redox catalysis requires precise knowledge of their electronic structure. X-ray emission spectroscopy (XES) is an emerging technique with a growing application to biological and biomimetic systems. Here, we report an improved, cost-effective spectrometer used to analyze two biomimetic coordination compounds, [MnIV(OH)2(Me2EBC)]2+ and [MnIV(O)(OH)(Me2EBC)]+, the second of which contains a key MnIV═O structural fragment. Despite having the same formal oxidation state (MnIV) and tetradentate ligands, XES spectra from these two compounds demonstrate different electronic structures. Experimental measurements and DFT calculations yield different localized spin densities for the two complexes resulting from MnIV-OH conversion to MnIV═O. The relevance of the observed spectroscopic changes is discussed for applications in analyzing complex biological systems such as photosystem II. A model of the S3 intermediate state of photosystem II containing a MnIV═O fragment is compared to recent time-resolved X-ray diffraction data of the same state.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Katherine M Davis
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Daniel A Hartzler
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Gerald T Seidler
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Diego M Casa
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Elina Kasman
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Hannah E Colmer
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Allyssa A Massie
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Timothy A Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
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45
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 PMCID: PMC5376230 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ernest S. Burgie
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Christopher J. Pollock
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation
Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, 12489
Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
- Department of Biochemistry, University of Oxford, South Parks Road,
Oxford OX1 3QU, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Christian G. Roessler
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raymond G. Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Peter T. Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - James M. Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Department of Chemistry – Ångström,
Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
- Department of Chemistry, Stanford University, Stanford, CA 94305,
USA
| | - George N. Phillips
- Department of BioSciences, Rice Univ. Houston, TX 77005, USA
- Department of Chemistry, Rice Univ. Houston, TX 77005, USA
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Allen M. Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
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46
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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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47
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Isobe H. Functional significance of the “distorted chair” topology of the Mn cluster for oxygen evolution in photosynthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.4019/bjscc.70.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University
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48
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Sequential and Coupled Proton and Electron Transfer Events in the S2 → S3 Transition of Photosynthetic Water Oxidation Revealed by Time-Resolved X-ray Absorption Spectroscopy. Biochemistry 2016; 55:6996-7004. [DOI: 10.1021/acs.biochem.6b01078] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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49
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Kositzki R, Mebs S, Marx J, Griese JJ, Schuth N, Högbom M, Schünemann V, Haumann M. Protonation State of MnFe and FeFe Cofactors in a Ligand-Binding Oxidase Revealed by X-ray Absorption, Emission, and Vibrational Spectroscopy and QM/MM Calculations. Inorg Chem 2016; 55:9869-9885. [PMID: 27610479 DOI: 10.1021/acs.inorgchem.6b01752] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enzymes with a dimetal-carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O2) activation. Recently described proteins bind a manganese-iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O2 reduction and an unusual tyrosine-valine ether cross-link formation, as revealed by X-ray crystallography. Advanced X-ray absorption, emission, and vibrational spectroscopy methods and quantum chemical and molecular mechanics calculations provided relative Mn/Fe contents, X-ray photoreduction kinetics, metal-ligand bond lengths, metal-metal distances, metal oxidation states, spin configurations, valence-level degeneracy, molecular orbital composition, nuclear quadrupole splitting energies, and vibrational normal modes for both cofactors. A protonation state with an axial water (H2O) ligand at Mn or Fe in binding site 1 and a metal-bridging hydroxo group (μOH) in a hydrogen-bonded network is assigned. Our comprehensive picture of the molecular, electronic, and dynamic properties of the cofactors highlights reorientation of the unique axis along the Mn-OH2 bond for the Mn1(III) Jahn-Teller ion but along the Fe-μOH bond for the octahedral Fe1(III). This likely corresponds to a more positive redox potential of the Mn(III)Fe(III) cofactor and higher proton affinity of its μOH group. Refined model structures for the Mn(III)Fe(III) and Fe(III)Fe(III) cofactors are presented. Implications of our findings for the site-specific metalation of R2lox and performance of the O2 reduction and cross-link formation reactions are discussed.
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Affiliation(s)
- Ramona Kositzki
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Jennifer Marx
- Fachbereich Physik, Technische Universität Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
| | - Nils Schuth
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden.,Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
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50
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Chatterjee R, Han G, Kern J, Gul S, Fuller FD, Garachtchenko A, Young ID, Weng TC, Nordlund D, Alonso-Mori R, Bergmann U, Sokaras D, Hatakeyama M, Yachandra VK, Yano J. Structural Changes Correlated with Magnetic Spin State Isomorphism in the S 2 State of the Mn 4CaO 5 Cluster in the Oxygen-Evolving Complex of Photosystem II. Chem Sci 2016; 7:5236-5248. [PMID: 28044099 PMCID: PMC5201215 DOI: 10.1039/c6sc00512h] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022] Open
Abstract
The Mn4CaO5 cluster in Photosystem II catalyzes the four-electron redox reaction of water oxidation in natural photosynthesis. This catalytic reaction cycles through four intermediate states (Si, i = 0 to 4), involving changes in the redox state of the four Mn atoms in the cluster. Recent studies suggest the presence and importance of isomorphous structures within the same redox/intermediate S-state. It is highly likely that geometric and electronic structural flexibility play a role in the catalytic mechanism. Among the catalytic intermediates that have been identified experimentally thus far, there is clear evidence of such isomorphism in the S2 state, with a high-spin (5/2) (HS) and a low spin (1/2) (LS) form, identified and characterized by their distinct electron paramagnetic resonance (EPR spectroscopy) signals. We studied these two S2 isomers with Mn extended X-ray absorption fine structure (EXAFS) and absorption and emission spectroscopy (XANES/XES) to characterize the structural and electronic structural properties. The geometric and electronic structure of the HS and LS S2 states are different as determined using Mn EXAFS and XANES/XES, respectively. The Mn K-edge XANES and XES for the HS form are different from the LS and indicate a slightly lower positive charge on the Mn atoms compared to the LS form. Based on the EXAFS results which are clearly different, we propose possible structural differences between the two spin states. Such structural and magnetic redox-isomers if present at room temperature, will likely play a role in the mechanism for water-exchange/oxidation in photosynthesis.
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Affiliation(s)
- Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Guangye Han
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
- LCLS
, SLAC National Accelerator Laboratory
,
Menlo Park
, CA
, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Anna Garachtchenko
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Tsu-Chien Weng
- Center for High Pressure Science &Technology Advanced Research
,
Shanghai
, China
| | - Dennis Nordlund
- SSRL
, SLAC National Accelerator Laboratory
,
Menlo Park
, CA
, USA
| | | | - Uwe Bergmann
- PULSE
, SLAC National Accelerator Laboratory
,
Menlo Park
, CA
, USA
| | | | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| |
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