1
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Liu J, Yang KR, Long Z, Armstrong WH, Brudvig GW, Batista VS. Water Ligands Regulate the Redox Leveling Mechanism of the Oxygen-Evolving Complex of the Photosystem II. J Am Chem Soc 2024; 146:15986-15999. [PMID: 38833517 DOI: 10.1021/jacs.4c02926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Understanding how water ligands regulate the conformational changes and functionality of the oxygen-evolving complex (OEC) in photosystem II (PSII) throughout the catalytic cycle of oxygen evolution remains a highly intriguing and unresolved challenge. In this study, we investigate the effect of water insertion (WI) on the redox state of the OEC by using the molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) hybrid methods. We find that water binding significantly reduces the free energy change for proton-coupled electron transfer (PCET) from Mn to YZ•, underscoring the important regulatory role of water binding, which is essential for enabling the OEC redox-leveling mechanism along the catalytic cycle. We propose a water binding mechanism in which WI is thermodynamically favored by the closed-cubane form of the OEC, with water delivery mediated by Ca2+ ligand exchange. Isomerization from the closed- to open-cubane conformation at three post-WI states highlights the importance of the location of the MnIII center in the OEC and the orientation of its Jahn-Teller axis to conformational changes of the OEC, which might be critical for the formation of the O-O bond. These findings reveal a complex interplay between conformational changes in the OEC and the ligand environment during the activation of the OEC by YZ•. Analogous regulatory effects due to water ligand binding are expected to be important for a wide range of catalysts activated by redox state transitions in aqueous environments.
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Affiliation(s)
- Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ke R Yang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhuoran Long
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - William H Armstrong
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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2
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Pavlou A, Styring S, Mamedov F. The S 1 to S 2 and S 2 to S 3 state transitions in plant photosystem II: relevance to the functional and structural heterogeneity of the water oxidizing complex. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01096-4. [PMID: 38662327 DOI: 10.1007/s11120-024-01096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
In Photosystem II, light-induced water splitting occurs via the S state cycle of the CaMn4O5-cluster. To understand the role of various possible conformations of the CaMn4O5-cluster in this process, the temperature dependence of the S1 → S2 and S2 → S3 state transitions, induced by saturating laser flashes, was studied in spinach photosystem II membrane preparations under different conditions. The S1 → S2 transition temperature dependence was shown to be much dependent on the type of the cryoprotectant and presence of 3.5% methanol, resulting in the variation of transition half-inhibition temperature by 50 K. No similar effect was observed for the S2 → S3 state transition, for which we also show that both the low spin g = 2.0 multiline and high spin g = 4.1 EPR configurations of the S2 state advance with similar efficiency to the S3 state, both showing a transition half-inhibition temperature of 240 K. This was further confirmed by following the appearance of the Split S3 EPR signal. The results are discussed in relevance to the functional and structural heterogeneity of the water oxidizing complex intermediates in photosystem II.
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Affiliation(s)
- Andrea Pavlou
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden
| | - Stenbjörn Styring
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden.
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3
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Debus RJ, Oyala PH. Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O 2-Evolving Mn 4CaO 5 Cluster in Photosystem II. J Phys Chem B 2024; 128:3870-3884. [PMID: 38602496 DOI: 10.1021/acs.jpcb.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The O2-evolving Mn4CaO5 cluster in photosystem II is ligated by six carboxylate residues. One of these is D170 of the D1 subunit. This carboxylate bridges between one Mn ion (Mn4) and the Ca ion. A second carboxylate ligand is D342 of the D1 subunit. This carboxylate bridges between two Mn ions (Mn1 and Mn2). D170 and D342 are located on opposite sides of the Mn4CaO5 cluster. Recently, it was shown that the D170E mutation perturbs both the intricate networks of H-bonds that surround the Mn4CaO5 cluster and the equilibrium between different conformers of the cluster in two of its lower oxidation states, S1 and S2, while still supporting O2 evolution at approximately 50% the rate of the wild type. In this study, we show that the D342E mutation produces much the same alterations to the cluster's FTIR and EPR spectra as D170E, while still supporting O2 evolution at approximately 20% the rate of the wild type. Furthermore, the double mutation, D170E + D342E, behaves similarly to the two single mutations. We conclude that D342E alters the equilibrium between different conformers of the cluster in its S1 and S2 states in the same manner as D170E and perturbs the H-bond networks in a similar fashion. This is the second identification of a Mn4CaO5 metal ligand whose mutation influences the equilibrium between the different conformers of the S1 and S2 states without eliminating O2 evolution. This finding has implications for our understanding of the mechanism of O2 formation in terms of catalytically active/inactive conformations of the Mn4CaO5 cluster in its lower oxidation states.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106, United States
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4
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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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5
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Saito M, Saito K, Ishikita H. Structural and energetic insights into Mn-to-Fe substitution in the oxygen-evolving complex. iScience 2023; 26:107352. [PMID: 37520740 PMCID: PMC10382916 DOI: 10.1016/j.isci.2023.107352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Manganese (Mn) serves as the catalytic center for water splitting in photosystem II (PSII), despite the abundance of iron (Fe) on earth. As a first step toward why Mn and not Fe is employed by Nature in the water oxidation catalyst, we investigated the Fe4CaO5 cluster in the PSII protein environment using a quantum mechanical/molecular mechanical (QM/MM) approach, assuming an equivalence between Mn(III/IV) and Fe(II/III). Substituting Mn with Fe resulted in the protonation of μ-oxo bridges at sites O2 and O3 by Arg357 and D1-His337, respectively. While the Mn4CaO5 cluster exhibits distinct open- and closed-cubane S2 conformations, the Fe4CaO5 cluster lacks this variability due to an equal spin distribution over sites Fe1 and Fe4. The absence of a low-barrier H-bond between a ligand water molecule (W1) and D1-Asp61 in the Fe4CaO5 cluster may underlie its incapability for ligand water deprotonation, highlighting the relevance of Mn in natural water splitting.
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Affiliation(s)
- Masahiro Saito
- 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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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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Greife P, Schönborn M, Capone M, Assunção R, Narzi D, Guidoni L, Dau H. The electron-proton bottleneck of photosynthetic oxygen evolution. Nature 2023; 617:623-628. [PMID: 37138082 DOI: 10.1038/s41586-023-06008-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today's oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S4 state-which was postulated half a century ago1 and remains largely uncharacterized. Here we resolve this key stage of photosynthetic O2 formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combining these results with computational chemistry reveals that a crucial proton vacancy is initally created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in a single-electron, multi-proton transfer event. This is the slowest step in photosynthetic O2 formation, with a moderate energetic barrier and marked entropic slowdown. We identify the S4 state as the oxygen-radical state; its formation is followed by fast O-O bonding and O2 release. In conjunction with previous breakthroughs in experimental and computational investigations, a compelling atomistic picture of photosynthetic O2 formation emerges. Our results provide insights into a biological process that is likely to have occurred unchanged for the past three billion years, which we expect to support the knowledge-based design of artificial water-splitting systems.
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Affiliation(s)
- Paul Greife
- Department of Physics, Freie Universität, Berlin, Germany
| | | | - Matteo Capone
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, L'Aquila, Italy
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Daniele Narzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Holger Dau
- Department of Physics, Freie Universität, Berlin, Germany.
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8
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Guo Y, Messinger J, Kloo L, Sun L. Alternative Mechanism for O 2 Formation in Natural Photosynthesis via Nucleophilic Oxo-Oxo Coupling. J Am Chem Soc 2023; 145:4129-4141. [PMID: 36763485 DOI: 10.1021/jacs.2c12174] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
O2 formation in photosystem II (PSII) is a vital event on Earth, but the exact mechanism remains unclear. The presently prevailing theoretical model is "radical coupling" (RC) involving a Mn(IV)-oxyl unit in an "open-cubane" Mn4CaO6 cluster, which is supported experimentally by the S3 state of cyanobacterial PSII featuring an additional Mn-bound oxygenic ligand. However, it was recently proposed that the major structural form of the S3 state of higher plants lacks this extra ligand, and that the resulting S4 state would feature instead a penta-coordinate dangler Mn(V)=oxo, covalently linked to a "closed-cubane" Mn3CaO4 cluster. For this proposal, we explore here a large number of possible pathways of O-O bond formation and demonstrate that the "nucleophilic oxo-oxo coupling" (NOOC) between Mn(V)=oxo and μ3-oxo is the only eligible mechanism in such a system. The reaction is facilitated by a specific conformation of the cluster and concomitant water binding, which is delayed compared to the RC mechanism. An energetically feasible process is described starting from the valid S4 state through the sequential formation of peroxide and superoxide, followed by O2 release and a second water insertion. The newly found mechanism is consistent with available experimental thermodynamic and kinetic data and thus a viable alternative pathway for O2 formation in natural photosynthesis, in particular for higher plants.
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Affiliation(s)
- Yu Guo
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), Umeå SE-90187, Sweden
- Molecular Biomimetics, Department of Chemistry─Ångström Laboratory, Uppsala University, Uppsala SE-75120, Sweden
| | - Lars Kloo
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm SE-10044, Sweden
| | - Licheng Sun
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
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9
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Shimada Y, Sugiyama A, Nagao R, Noguchi T. Role of D1-Glu65 in Proton Transfer during Photosynthetic Water Oxidation in Photosystem II. J Phys Chem B 2022; 126:8202-8213. [PMID: 36199221 DOI: 10.1021/acs.jpcb.2c05869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Photosynthetic water oxidation takes place at the Mn4CaO5 cluster in photosystem II (PSII) through a light-driven cycle of five intermediates called S states (S0-S4). Although the PSII structures have shown the presence of several channels around the Mn4CaO5 cluster leading to the lumen, the pathways for proton release in the individual S-state transitions remain unidentified. Here, we studied the involvement of the so-called Cl channel in proton transfer during water oxidation by examining the effect of the mutation of D1-Glu65, a key residue in this channel, to Ala using Fourier transform infrared difference and time-resolved infrared spectroscopies together with thermoluminescence and delayed luminescence measurements. It was shown that the structure and the redox property of the catalytic site were little affected by the D1-Glu65Ala mutation. In the S2 → S3 transition, the efficiency was still high and the transition rate was only moderately retarded in the D1-Glu65Ala mutant. In contrast, the S3 → S0 transition was significantly inhibited by this mutation. These results suggest that proton transfer in the S2 → S3 transition occurs through multiple pathways including the Cl channel, whereas this channel likely serves as a single pathway for proton exit in the S3 → S0 transition.
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Affiliation(s)
- Yuichiro Shimada
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
| | - Ayane Sugiyama
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
| | - Ryo Nagao
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan.,Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Okayama700-8530, Japan
| | - Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
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10
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Auman D, Ecker F, Mader SL, Dorst KM, Bräuer A, Widmalm G, Groll M, Kaila VRI. Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ. J Am Chem Soc 2022; 144:15622-15632. [PMID: 35980821 DOI: 10.1021/jacs.2c05650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dioxygenases catalyze stereoselective oxygen atom transfer in metabolic pathways of biological, industrial, and pharmaceutical importance, but their precise chemical principles remain controversial. The α-ketoglutarate (αKG)-dependent dioxygenase AsqJ synthesizes biomedically active quinolone alkaloids via desaturation and subsequent epoxidation of a carbon-carbon bond in the cyclopeptin substrate. Here, we combine high-resolution X-ray crystallography with enzyme engineering, quantum-classical (QM/MM) simulations, and biochemical assays to describe a peroxidic intermediate that bridges the substrate and active site metal ion in AsqJ. Homolytic cleavage of this moiety during substrate epoxidation generates an activated high-valent ferryl (FeIV = O) species that mediates the next catalytic cycle, possibly without the consumption of the metabolically valuable αKG cosubstrate. Our combined findings provide an important understanding of chemical bond activation principles in complex enzymatic reaction networks and molecular mechanisms of dioxygenases.
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Affiliation(s)
- Dirk Auman
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Felix Ecker
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Kevin M Dorst
- Department of Organic Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Alois Bräuer
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Michael Groll
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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11
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Guo Y, Messinger J, Kloo L, Sun L. Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation. J Am Chem Soc 2022; 144:11736-11747. [PMID: 35748306 PMCID: PMC9264352 DOI: 10.1021/jacs.2c03528] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Photosynthetic water
oxidation is catalyzed by a manganese–calcium
oxide cluster, which experiences five “S-states” during
a light-driven reaction cycle. The unique “distorted chair”-like
geometry of the Mn4CaO5(6) cluster shows structural
flexibility that has been frequently proposed to involve “open”
and “closed”-cubane forms from the S1 to
S3 states. The isomers are interconvertible in the S1 and S2 states, while in the S3 state,
the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples.
In this work, using density functional theory calculations, we go
beyond the S3+Yz state to the S3nYz• → S4+Yz step, and report for the first time
that the reversible isomerism, which is suppressed in the S3+Yz state, is fully recovered
in the ensuing S3nYz• state due to the proton release
from a manganese-bound water ligand. The altered coordination strength
of the manganese–ligand facilitates formation of the closed-cubane
form, in a dynamic equilibrium with the open-cubane form. This tautomerism
immediately preceding dioxygen formation may constitute the rate limiting
step for O2 formation, and exert a significant influence
on the water oxidation mechanism in photosystem II.
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Affiliation(s)
- Yu Guo
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou 310024, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), SE-90187 Umeå, Sweden.,Molecular Biomimetics, Department of Chemistry─Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | - Lars Kloo
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Licheng Sun
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou 310024, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
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12
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Allgöwer F, Gamiz-Hernandez AP, Rutherford AW, Kaila VRI. Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II. J Am Chem Soc 2022; 144:7171-7180. [PMID: 35421304 PMCID: PMC9052759 DOI: 10.1021/jacs.1c13041] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O2 into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn4O5Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyrz (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca2+-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624-12,635]. Further oxidation of the Mn4O5Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn4O5Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O2 formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.
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Affiliation(s)
- Friederike Allgöwer
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - A William Rutherford
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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13
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Bicarbonate-controlled reduction of oxygen by the Q A semiquinone in Photosystem II in membranes. Proc Natl Acad Sci U S A 2022; 119:2116063119. [PMID: 35115403 PMCID: PMC8833163 DOI: 10.1073/pnas.2116063119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
In Photosystem II (PSII), O2 reduction by QA•− is often discussed but has not been demonstrated. Here, we show in PSII membranes that QA•− can reduce O2 to superoxide, but only when bicarbonate is absent from its binding site on the nonheme Fe2+. Bicarbonate’s role in PSII was recently shown to involve a regulatory/protective redox-tuning mechanism linking PSII function to CO2 concentration. A key aspect is the presence of stable QA•− causing release of bicarbonate from its site on Fe2+. Here, we show that under these conditions, O2 binds to the empty site on the Fe2+ and is reduced by QA•−. This unexpected reaction may be a further indication of cross-talk between the regulation of PSII and CO2 fixation. Photosystem II (PSII), the water/plastoquinone photo-oxidoreductase, plays a key energy input role in the biosphere. QA•−, the reduced semiquinone form of the nonexchangeable quinone, is often considered capable of a side reaction with O2, forming superoxide, but this reaction has not yet been demonstrated experimentally. Here, using chlorophyll fluorescence in plant PSII membranes, we show that O2 does oxidize QA•− at physiological O2 concentrations with a t1/2 of 10 s. Superoxide is formed stoichiometrically, and the reaction kinetics are controlled by the accessibility of O2 to a binding site near QA•−, with an apparent dissociation constant of 70 ± 20 µM. Unexpectedly, QA•− could only reduce O2 when bicarbonate was absent from its binding site on the nonheme iron (Fe2+) and the addition of bicarbonate or formate blocked the O2-dependant decay of QA•−. These results, together with molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations, indicate that electron transfer from QA•− to O2 occurs when the O2 is bound to the empty bicarbonate site on Fe2+. A protective role for bicarbonate in PSII was recently reported, involving long-lived QA•− triggering bicarbonate dissociation from Fe2+ [Brinkert et al., Proc. Natl. Acad. Sci. U.S.A. 113, 12144–12149 (2016)]. The present findings extend this mechanism by showing that bicarbonate release allows O2 to bind to Fe2+ and to oxidize QA•−. This could be beneficial by oxidizing QA•− and by producing superoxide, a chemical signal for the overreduced state of the electron transfer chain.
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14
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Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proc Natl Acad Sci U S A 2022; 119:e2116765118. [PMID: 34937700 PMCID: PMC8740770 DOI: 10.1073/pnas.2116765118] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.
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Affiliation(s)
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Ke R Yang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | | | - M R Gunner
- Department of Physics, City College of New York, New York, NY 100031
| | | | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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15
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Debus RJ. Alteration of the O 2-Producing Mn 4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand. Biochemistry 2021; 60:3841-3855. [PMID: 34898175 DOI: 10.1021/acs.biochem.1c00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The O2-evolving Mn4Ca cluster in photosystem II (PSII) is arranged as a distorted Mn3Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn4Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn4Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn4Ca cluster in the dark-stable S1 state so that a high-spin form of the S2 state is produced during the S1-to-S2 transition instead of the low-spin form that gives rise to the S2 state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn4Ca cluster without substantially eliminating O2 evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn4Ca cluster in the mechanism of O2 formation.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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16
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Kaila VRI. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Acc Chem Res 2021; 54:4462-4473. [PMID: 34894649 PMCID: PMC8697550 DOI: 10.1021/acs.accounts.1c00524] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
Biological energy conversion is catalyzed by membrane-bound proteins
that transduce chemical or light energy into energy forms that power
endergonic processes in the cell. At a molecular level, these catalytic
processes involve elementary electron-, proton-, charge-, and energy-transfer
reactions that take place in the intricate molecular machineries of
cell respiration and photosynthesis. Recent developments in structural
biology, particularly cryo-electron microscopy (cryoEM), have resolved
the molecular architecture of several energy transducing proteins,
but detailed mechanistic principles of their charge transfer reactions
still remain poorly understood and a major challenge for modern biochemical
research. To this end, multiscale molecular simulations provide a
powerful approach to probe mechanistic principles on a broad range
of time scales (femtoseconds to milliseconds) and spatial resolutions
(101–106 atoms), although technical challenges
also require balancing between the computational accuracy, cost, and
approximations introduced within the model. Here we discuss how the
combination of atomistic (aMD) and hybrid quantum/classical molecular
dynamics (QM/MM MD) simulations with free energy (FE) sampling methods
can be used to probe mechanistic principles of enzymes responsible
for biological energy conversion. We present mechanistic explorations
of long-range proton-coupled electron transfer (PCET) dynamics in
the highly intricate respiratory chain enzyme Complex I, which functions
as a redox-driven proton pump in bacterial and mitochondrial respiratory
chains by catalyzing a 300 Å fully reversible PCET process. This
process is initiated by a hydride (H–) transfer
between NADH and FMN, followed by long-range (>100 Å) electron
transfer along a wire of 8 FeS centers leading to a quinone biding
site. The reduction of the quinone to quinol initiates dissociation
of the latter to a second membrane-bound binding site, and triggers
proton pumping across the membrane domain of complex I, in subunits
up to 200 Å away from the active site. Our simulations across
different size and time scales suggest that transient charge transfer
reactions lead to changes in the internal hydration state of key regions,
local electric fields, and the conformation of conserved ion pairs,
which in turn modulate the dynamics of functional steps along the
reaction cycle. Similar functional principles, which operate on much
shorter length scales, are also found in some unrelated proteins,
suggesting that enzymes may employ conserved principles in the catalysis
of biological energy transduction processes.
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Affiliation(s)
- Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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17
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Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J. Structural dynamics in the water and proton channels of photosystem II during the S 2 to S 3 transition. Nat Commun 2021; 12:6531. [PMID: 34764256 PMCID: PMC8585918 DOI: 10.1038/s41467-021-26781-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022] Open
Abstract
Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.
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Affiliation(s)
- Rana Hussein
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mohamed Ibrahim
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Asmit Bhowmick
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Philipp S. Simon
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Ruchira Chatterjee
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Louise Lassalle
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Margaret Doyle
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Isabel Bogacz
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - In-Sik Kim
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Mun Hon Cheah
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Sheraz Gul
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Casper de Lichtenberg
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden ,grid.12650.300000 0001 1034 3451Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - Petko Chernev
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Cindy C. Pham
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Iris D. Young
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sergio Carbajo
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Franklin D. Fuller
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Roberto Alonso-Mori
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Alex Batyuk
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Kyle D. Sutherlin
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aaron S. Brewster
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Robert Bolotovsky
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Derek Mendez
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - James M. Holton
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Nigel W. Moriarty
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Uwe Bergmann
- grid.14003.360000 0001 2167 3675Department of Physics, University of Wisconsin–Madison, Madison, WI 53706 USA
| | - Nicholas K. Sauter
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Holger Dobbek
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120, Uppsala, Sweden. .,Department of Chemistry, Umeå University, SE 90187, Umeå, Sweden.
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Vittal K. Yachandra
- grid.184769.50000 0001 2231 4551Molecular 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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18
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Amin M, Kaur D, Gunner M, Brudvig G. Toward understanding the S2-S3 transition in the Kok cycle of Photosystem II: Lessons from Sr-substituted structure. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2021.108890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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de Lichtenberg C, Kim CJ, Chernev P, Debus RJ, Messinger J. The exchange of the fast substrate water in the S 2 state of photosystem II is limited by diffusion of bulk water through channels - implications for the water oxidation mechanism. Chem Sci 2021; 12:12763-12775. [PMID: 34703563 PMCID: PMC8494045 DOI: 10.1039/d1sc02265b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/31/2021] [Indexed: 12/02/2022] Open
Abstract
The molecular oxygen we breathe is produced from water-derived oxygen species bound to the Mn4CaO5 cluster in photosystem II (PSII). Present research points to the central oxo-bridge O5 as the 'slow exchanging substrate water (Ws)', while, in the S2 state, the terminal water ligands W2 and W3 are both discussed as the 'fast exchanging substrate water (Wf)'. A critical point for the assignment of Wf is whether or not its exchange with bulk water is limited by barriers in the channels leading to the Mn4CaO5 cluster. In this study, we measured the rates of H2 16O/H2 18O substrate water exchange in the S2 and S3 states of PSII core complexes from wild-type (WT) Synechocystis sp. PCC 6803, and from two mutants, D1-D61A and D1-E189Q, that are expected to alter water access via the Cl1/O4 channels and the O1 channel, respectively. We found that the exchange rates of Wf and Ws were unaffected by the E189Q mutation (O1 channel), but strongly perturbed by the D61A mutation (Cl1/O4 channel). It is concluded that all channels have restrictions limiting the isotopic equilibration of the inner water pool near the Mn4CaO5 cluster, and that D61 participates in one such barrier. In the D61A mutant this barrier is lowered so that Wf exchange occurs more rapidly. This finding removes the main argument against Ca-bound W3 as fast substrate water in the S2 state, namely the indifference of the rate of Wf exchange towards Ca/Sr substitution.
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Affiliation(s)
- Casper de Lichtenberg
- Department of Chemistry, Umeå University Linnaeus väg 6 (KBC huset), SE-901 87 Umeå Sweden
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University POB 523 SE-75120 Uppsala Sweden
| | - Christopher J Kim
- Department of Biochemistry, University of California Riverside California 92521 USA
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University POB 523 SE-75120 Uppsala Sweden
| | - Richard J Debus
- Department of Biochemistry, University of California Riverside California 92521 USA
| | - Johannes Messinger
- Department of Chemistry, Umeå University Linnaeus väg 6 (KBC huset), SE-901 87 Umeå Sweden
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University POB 523 SE-75120 Uppsala Sweden
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20
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Okamoto Y, Shimada Y, Nagao R, Noguchi T. Proton and Water Transfer Pathways in the S 2 → S 3 Transition of the Water-Oxidizing Complex in Photosystem II: Time-Resolved Infrared Analysis of the Effects of D1-N298A Mutation and NO 3- Substitution. J Phys Chem B 2021; 125:6864-6873. [PMID: 34152151 DOI: 10.1021/acs.jpcb.1c03386] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Photosynthetic water oxidation is performed through a light-driven cycle of five intermediates (S0-S4 states) in photosystem II (PSII). The S2 → S3 transition, which involves concerted water and proton transfer, is a key process for understanding the water oxidation mechanism. Here, to identify the water and proton transfer pathways during the S2 → S3 transition, we examined the effects of D1-N298A mutation and NO3- substitution for Cl-, which perturbed the O1 and Cl channels, respectively, on the S2 → S3 kinetics using time-resolved infrared spectroscopy. The S2 → S3 transition was retarded both upon NO3- substitution and upon D1-N298A mutation, whereas it was unaffected by further NO3- substitution in N298A PSII. The H/D kinetic isotope effect in N298A PSII was relatively small, revealing that water transfer is a rate-limiting step in this mutant. From these results, it was suggested that during the S2 → S3 transition, water delivery and proton release occur through the O1 and Cl channels, respectively.
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Affiliation(s)
- Yasutada Okamoto
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuichiro Shimada
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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21
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Kaur D, Khaniya U, Zhang Y, Gunner MR. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Front Chem 2021; 9:660954. [PMID: 34211960 PMCID: PMC8239185 DOI: 10.3389/fchem.2021.660954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
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22
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Kaur D, Zhang Y, Reiss KM, Mandal M, Brudvig GW, Batista VS, Gunner MR. Proton exit pathways surrounding the oxygen evolving complex of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148446. [PMID: 33964279 DOI: 10.1016/j.bbabio.2021.148446] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022]
Abstract
Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, extend from the OEC towards the aqueous surface more than 15 Å away. However, the role of each pathway in the transport in and out of the OEC is yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths. Hydrogen bond network analysis shows that near the OEC the waters are highly interconnected with similar free energy for hydronium at all locations. The paths diverge as they move towards the lumen. The water chain in the broad channel is better connected than in the narrow and large channels, where disruptions in the network are observed approximately 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel. Thus, a proton released from any location on the OEC can access all paths, but the likely exit to the lumen passes through PsbO via the broad channel.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Manoj Mandal
- Department of Physics, City College of New York, NY 10031, United States
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States.
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23
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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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24
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Zahariou G, Ioannidis N, Sanakis Y, Pantazis DA. Arrested Substrate Binding Resolves Catalytic Intermediates in Higher-Plant Water Oxidation. Angew Chem Int Ed Engl 2021; 60:3156-3162. [PMID: 33030775 PMCID: PMC7898718 DOI: 10.1002/anie.202012304] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/05/2022]
Abstract
Among the intermediate catalytic steps of the water-oxidizing Mn4 CaO5 cluster of photosystem II (PSII), the final metastable S3 state is critically important because it binds one substrate and precedes O2 evolution. Herein, we combine X- and Q-band EPR experiments on native and methanol-treated PSII of Spinacia oleracea and show that methanol-treated PSII preparations of the S3 state correspond to a previously uncharacterized high-spin (S=6) species. This is confirmed as a major component also in intact photosynthetic membranes, coexisting with the previously known intermediate-spin conformation (S=3). The high-spin intermediate is assigned to a water-unbound form, with a MnIV3 subunit interacting ferromagnetically via anisotropic exchange with a coordinatively unsaturated MnIV ion. These results resolve and define the structural heterogeneity of the S3 state, providing constraints on the S3 to S4 transition, on substrate identity and delivery pathways, and on the mechanism of O-O bond formation.
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Affiliation(s)
- Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos”Athens15310Greece
| | - Nikolaos Ioannidis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos”Athens15310Greece
| | - Yiannis Sanakis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos”Athens15310Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
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25
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Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S3 state of the oxygen evolving complex of photosystem II. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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26
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Johansson MP, Niederegger L, Rauhalahti M, Hess CR, Kaila VRI. Dispersion forces drive water oxidation in molecular ruthenium catalysts. RSC Adv 2020; 11:425-432. [PMID: 35423068 PMCID: PMC8691110 DOI: 10.1039/d0ra09004b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Rational design of artificial water-splitting catalysts is central for developing new sustainable energy technology. However, the catalytic efficiency of the natural light-driven water-splitting enzyme, photosystem II, has been remarkably difficult to achieve artificially. Here we study the molecular mechanism of ruthenium-based molecular catalysts by integrating quantum chemical calculations with inorganic synthesis and functional studies. By employing correlated ab initio calculations, we show that the thermodynamic driving force for the catalysis is obtained by modulation of π-stacking dispersion interactions within the catalytically active dimer core, supporting recently suggested mechanistic principles of Ru-based water-splitting catalysts. The dioxygen bond forms in a semi-concerted radical coupling mechanism, similar to the suggested water-splitting mechanism in photosystem II. By rationally tuning the dispersion effects, we design a new catalyst with a low activation barrier for the water-splitting. The catalytic principles are probed by synthesis, structural, and electrochemical characterization of the new catalyst, supporting enhanced water-splitting activity under the examined conditions. Our combined findings show that modulation of dispersive interactions provides a rational catalyst design principle for controlling challenging chemistries.
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Affiliation(s)
- Mikael P Johansson
- Department of Chemistry, University of Helsinki P.O. Box 55 FI-00014 Helsinki Finland.,Department of Chemistry, Technical University of Munich (TUM) Lichtenbergstraße 4 Garching D-85747 Germany .,Helsinki Institute of Sustainability Science (Helsus) FI-00014 Helsinki Finland.,CSC-IT Center for Science P.O. Box 405 FI-02101 Espoo Finland
| | - Lukas Niederegger
- Department of Chemistry, Technical University of Munich (TUM) Lichtenbergstraße 4 Garching D-85747 Germany
| | - Markus Rauhalahti
- Department of Chemistry, University of Helsinki P.O. Box 55 FI-00014 Helsinki Finland
| | - Corinna R Hess
- Department of Chemistry, Technical University of Munich (TUM) Lichtenbergstraße 4 Garching D-85747 Germany
| | - Ville R I Kaila
- Department of Chemistry, Technical University of Munich (TUM) Lichtenbergstraße 4 Garching D-85747 Germany .,Department of Biochemistry and Biophysics, Stockholm University Stockholm Sweden
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27
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Zahariou G, Ioannidis N, Sanakis Y, Pantazis DA. Arrested Substrate Binding Resolves Catalytic Intermediates in Higher‐Plant Water Oxidation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Georgia Zahariou
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos” Athens 15310 Greece
| | - Nikolaos Ioannidis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos” Athens 15310 Greece
| | - Yiannis Sanakis
- Institute of Nanoscience & Nanotechnology, NCSR “Demokritos” Athens 15310 Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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28
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de Lichtenberg C, Avramov AP, Zhang M, Mamedov F, Burnap RL, Messinger J. The D1-V185N mutation alters substrate water exchange by stabilizing alternative structures of the Mn 4Ca-cluster in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148319. [PMID: 32979346 DOI: 10.1016/j.bbabio.2020.148319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 11/30/2022]
Abstract
In photosynthesis, the oxygen-evolving complex (OEC) of the pigment-protein complex photosystem II (PSII) orchestrates the oxidation of water. Introduction of the V185N mutation into the D1 protein was previously reported to drastically slow O2-release and strongly perturb the water network surrounding the Mn4Ca cluster. Employing time-resolved membrane inlet mass spectrometry, we measured here the H218O/H216O-exchange kinetics of the fast (Wf) and slow (Ws) exchanging substrate waters bound in the S1, S2 and S3 states to the Mn4Ca cluster of PSII core complexes isolated from wild type and D1-V185N strains of Synechocystis sp. PCC 6803. We found that the rate of exchange for Ws was increased in the S1 and S2 states, while both Wf and Ws exchange rates were decreased in the S3 state. Additionally, we used EPR spectroscopy to characterize the Mn4Ca cluster and its interaction with the redox active D1-Tyr161 (YZ). In the S2 state, we observed a greatly diminished multiline signal in the V185N-PSII that could be recovered by addition of ammonia. The split signal in the S1 state was not affected, while the split signal in the S3 state was absent in the D1-V185N mutant. These findings are rationalized by the proposal that the N185 residue stabilizes the binding of an additional water-derived ligand at the Mn1 site of the Mn4Ca cluster via hydrogen bonding. Implications for the sites of substrate water binding are discussed.
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Affiliation(s)
- Casper de Lichtenberg
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), SE-901 87 Umeå, Sweden; Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, POB 523, SE-75120 Uppsala, Sweden
| | - Anton P Avramov
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States
| | - Minquan Zhang
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, POB 523, SE-75120 Uppsala, Sweden
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), SE-901 87 Umeå, Sweden; Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, POB 523, SE-75120 Uppsala, Sweden.
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29
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Kim CJ, Debus RJ. Roles of D1-Glu189 and D1-Glu329 in O2 Formation by the Water-Splitting Mn4Ca Cluster in Photosystem II. Biochemistry 2020; 59:3902-3917. [DOI: 10.1021/acs.biochem.0c00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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30
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Mühlbauer ME, Saura P, Nuber F, Di Luca A, Friedrich T, Kaila VRI. Water-Gated Proton Transfer Dynamics in Respiratory Complex I. J Am Chem Soc 2020; 142:13718-13728. [PMID: 32643371 PMCID: PMC7659035 DOI: 10.1021/jacs.0c02789] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The respiratory complex I transduces
redox energy into an electrochemical
proton gradient in aerobic respiratory chains, powering energy-requiring
processes in the cell. However, despite recently resolved molecular
structures, the mechanism of this gigantic enzyme remains poorly understood.
By combining large-scale quantum and classical simulations with site-directed
mutagenesis and biophysical experiments, we show here how the conformational
state of buried ion-pairs and water molecules control the protonation
dynamics in the membrane domain of complex I and establish evolutionary
conserved long-range coupling elements. We suggest that an electrostatic
wave propagates in forward and reverse directions across the 200 Å
long membrane domain during enzyme turnover, without significant dissipation
of energy. Our findings demonstrate molecular principles that enable
efficient long-range proton–electron coupling (PCET) and how
perturbation of this PCET machinery may lead to development of mitochondrial
disease.
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Affiliation(s)
- Max E Mühlbauer
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Franziska Nuber
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
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31
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Saito K, Nakagawa M, Ishikita H. pK a of the ligand water molecules in the oxygen-evolving Mn 4CaO 5 cluster in photosystem II. Commun Chem 2020; 3:89. [PMID: 36703312 PMCID: PMC9814768 DOI: 10.1038/s42004-020-00336-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/30/2020] [Indexed: 01/29/2023] Open
Abstract
Release of the protons from the substrate water molecules is prerequisite for O2 evolution in photosystem II (PSII). Proton-releasing water molecules with low pKa values at the catalytic moiety can be the substrate water molecules. In some studies, one of the ligand water molecules, W2, is regarded as OH-. However, the PSII crystal structure shows neither proton acceptor nor proton-transfer pathway for W2, which is not consistent with the assumption of W2 = OH-. Here we report the pKa values of the four ligand water molecules, W1 and W2 at Mn4 and W3 and W4 at Ca2+, of the Mn4CaO5 cluster. pKa(W1) ≈ pKa(W2) << pKa(W3) ≈ pKa(W4) in the Mn4CaO5 cluster in water. However, pKa(W1) ≈ pKa(D1-Asp61) << pKa(W2) in the PSII protein environment. These results suggest that in PSII, deprotonation of W2 is energetically disfavored as far as W1 exists.
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Affiliation(s)
- Keisuke Saito
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
| | - Minesato Nakagawa
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
| | - Hiroshi Ishikita
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
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32
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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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33
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Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A 2020; 117:12624-12635. [PMID: 32434915 PMCID: PMC7293653 DOI: 10.1073/pnas.2000529117] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
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Affiliation(s)
- Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Casper de Lichtenberg
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Petko Chernev
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, OX11 0FA Didcot, United Kingdom
| | - Nicholas Saichek
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Trent Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
| | - Shigeki Owada
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bolotovsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany;
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden;
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
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34
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Saura P, Röpke M, Gamiz-Hernandez AP, Kaila VRI. Quantum Chemical and QM/MM Models in Biochemistry. Methods Mol Biol 2020; 2022:75-104. [PMID: 31396900 DOI: 10.1007/978-1-4939-9608-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe how QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field representation of the biochemical surroundings. We also discuss the QM cluster model approach, as well as embedding theories, that provide complementary methodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.
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Affiliation(s)
- Patricia Saura
- Department Chemie, Technische Universität München, Garching, Germany
| | - Michael Röpke
- Department Chemie, Technische Universität München, Garching, Germany
| | | | - Ville R I Kaila
- Department Chemie, Technische Universität München, Garching, Germany.
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35
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Petrie S, Terrett R, Stranger R, Pace RJ. Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution, Nominal S 3 State Crystal Structures of Photosystem II. Chemphyschem 2020; 21:785-801. [PMID: 32133758 DOI: 10.1002/cphc.201901106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/14/2020] [Indexed: 11/06/2022]
Abstract
Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S3 structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S1 structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5-O6 separation of ∼1.5 Å. In the latest S3 variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S3 , closely ligating one Mn, with O5-Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed 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). In 2018 we showed (Chem. Phys. Chem., 2018) this oxidation state assumption predicted two energetically close S3 structural forms, one with the metal centres and O5 (as OH- ) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H2 O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S3 structure is also a likely superposition of forms, but with O5 (as OH- ) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural 'lability' of the WOC centre in the S3 state, which is likely catalytically relevant to its water splitting function.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Richard Terrett
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
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Shimada Y, Kitajima-Ihara T, Nagao R, Noguchi T. Role of the O4 Channel in Photosynthetic Water Oxidation as Revealed by Fourier Transform Infrared Difference and Time-Resolved Infrared Analysis of the D1-S169A Mutant. J Phys Chem B 2020; 124:1470-1480. [DOI: 10.1021/acs.jpcb.9b11946] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yuichiro Shimada
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomomi Kitajima-Ihara
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Mandal M, Kawashima K, Saito K, Ishikita H. Redox Potential of the Oxygen-Evolving Complex in the Electron Transfer Cascade of Photosystem II. J Phys Chem Lett 2020; 11:249-255. [PMID: 31729876 DOI: 10.1021/acs.jpclett.9b02831] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In photosystem II (PSII), water oxidation occurs in the Mn4CaO5 cluster with the release of electrons via the redox-active tyrosine (TyrZ) to the reaction-center chlorophylls (PD1/PD2). Using a quantum mechanical/molecular mechanical approach, we report the redox potentials (Em) of these cofactors in the PSII protein environment. The Em values suggest that the Mn4CaO5 cluster, TyrZ, and PD1/PD2 form a downhill electron transfer pathway. Em for the first oxidation step, Em(S0/S1), is uniquely low (730 mV) and is ∼100 mV lower than that for the second oxidation step, Em(S1/S2) (830 mV) only when the O4 site of the Mn4CaO5 cluster is protonated in S0. The O4-water chain, which directly forms a low-barrier H-bond with the Mn4CaO5 cluster and mediates proton-coupled electron transfer in the S0 to S1 transition, explains why the second lowest oxidation state, S1, is the most stable and S0 is converted to S1 even in the dark.
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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 Kawashima
- Department of Applied Chemistry , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8654 , 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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de Lichtenberg C, Messinger J. Substrate water exchange in the S2 state of photosystem II is dependent on the conformation of the Mn4Ca cluster. Phys Chem Chem Phys 2020; 22:12894-12908. [DOI: 10.1039/d0cp01380c] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural flexibility of the Mn4Ca cluster in photosystem II supports the exchange of the central O5 bridge.
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39
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Fourier transform infrared and mass spectrometry analyses of a site-directed mutant of D1-Asp170 as a ligand to the water-oxidizing Mn4CaO5 cluster in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148086. [DOI: 10.1016/j.bbabio.2019.148086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/09/2019] [Accepted: 09/15/2019] [Indexed: 01/02/2023]
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40
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Nakamura S, Capone M, Narzi D, Guidoni L. Pivotal role of the redox-active tyrosine in driving the water splitting catalyzed by photosystem II. Phys Chem Chem Phys 2020; 22:273-285. [DOI: 10.1039/c9cp04605d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
TyrZ oxidation state triggers hydrogen bond modification in the water oxidation catalysis.
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Affiliation(s)
- Shin Nakamura
- Department of Biochemical Sciences “A. Rossi Fanelli”
- University of Rome “Sapienza”
- Rome
- Italy
| | - Matteo Capone
- Department of Information Engineering, Computational Science, and Mathematics
- Università dell’Aquila
- L’Aquila
- Italy
| | - Daniele Narzi
- Institute of Chemical Sciences and Engineering Ecole Polytechnique Federale de Lausanne Av. F.-A. Forel 2
- 1015 Lausanne
- Switzerland
| | - Leonardo Guidoni
- Department of Physical and Chemical Science
- Università dell’Aquila
- L’Aquila
- Italy
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41
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Ugur I, Chandrasekhar P. Proton relay network in P450cam formed upon docking of putidaredoxin. Proteins 2019; 88:558-572. [PMID: 31597203 DOI: 10.1002/prot.25835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/13/2019] [Accepted: 09/28/2019] [Indexed: 11/08/2022]
Abstract
Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O─O cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular mechanics computations, both on the well-studied FeOO state and on Cpd(0) (compound 0). Our simulations include (all camphor-bound): (a) WT (wild type), FeOO state. (b) WT, Cpd(0). (c) Pdx (Putidaredoxin, redox partner of P450)-docked-WT, FeOO state. (d) Pdx-docked WT, Cpd(0). (e) Pdx-docked T252A mutant, Cpd(0). Among our key findings: (a) Effect of Pdx docking appears to go far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (b) Specific proton relay networks we identify are: FeOO(H)⋯T252⋯nH 2 O⋯D251 in WT; FeOO(H)⋯nH 2 O⋯D251 in T252A mutant; both occur with Pdx docking. (c) Direct interaction of D251 with -FeOOH is, respectively, rare/frequent in WT/T252A mutant. (d) In WT, T252 is in the proton relay network. (e) Positioning of camphor appears significant: when camphor is part of H-bonding network, second protonation appears to be facilitated.
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Affiliation(s)
- Ilke Ugur
- Research Division, Ashwin-Ushas Corporation, Marlboro, New Jersey
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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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Mechanism of protonation of the over-reduced Mn4CaO5 cluster in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148059. [DOI: 10.1016/j.bbabio.2019.148059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/18/2019] [Accepted: 08/02/2019] [Indexed: 01/12/2023]
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44
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Takemoto H, Sugiura M, Noguchi T. Proton Release Process during the S2-to-S3 Transition of Photosynthetic Water Oxidation As Revealed by the pH Dependence of Kinetics Monitored by Time-Resolved Infrared Spectroscopy. Biochemistry 2019; 58:4276-4283. [DOI: 10.1021/acs.biochem.9b00680] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroshi Takemoto
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Miwa Sugiura
- Proteo-Science Research Center, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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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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Five-coordinate Mn IV intermediate in the activation of nature's water splitting cofactor. Proc Natl Acad Sci U S A 2019; 116:16841-16846. [PMID: 31391299 DOI: 10.1073/pnas.1817526116] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature's water splitting cofactor passes through a series of catalytic intermediates (S0-S4) before O-O bond formation and O2 release. In the second last transition (S2 to S3) cofactor oxidation is coupled to water molecule binding to Mn1. It is this activated, water-enriched all MnIV form of the cofactor that goes on to form the O-O bond, after the next light-induced oxidation to S4 How cofactor activation proceeds remains an open question. Here, we report a so far not described intermediate (S3') in which cofactor oxidation has occurred without water insertion. This intermediate can be trapped in a significant fraction of centers (>50%) in (i) chemical-modified cofactors in which Ca2+ is exchanged with Sr2+; the Mn4O5Sr cofactor remains active, but the S2-S3 and S3-S0 transitions are slower than for the Mn4O5Ca cofactor; and (ii) upon addition of 3% vol/vol methanol; methanol is thought to act as a substrate water analog. The S3' electron paramagnetic resonance (EPR) signal is significantly broader than the untreated S3 signal (2.5 T vs. 1.5 T), indicating the cofactor still contains a 5-coordinate Mn ion, as seen in the preceding S2 state. Magnetic double resonance data extend these findings revealing the electronic connectivity of the S3' cofactor is similar to the high spin form of the preceding S2 state, which contains a cuboidal Mn3O4Ca unit tethered to an external, 5-coordinate Mn ion (Mn4). These results demonstrate that cofactor oxidation regulates water molecule insertion via binding to Mn4. The interaction of ammonia with the cofactor is also discussed.
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Krewald V, Neese F, Pantazis DA. Implications of structural heterogeneity for the electronic structure of the final oxygen-evolving intermediate in photosystem II. J Inorg Biochem 2019; 199:110797. [PMID: 31404888 DOI: 10.1016/j.jinorgbio.2019.110797] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Heterogeneity in intermediate catalytic states of the oxygen-evolving complex (OEC) of Photosystem II is known from a wide range of experimental and theoretical data, but its potential implications for the mechanism of water oxidation remain unexplored. We delineate the consequences of structural heterogeneity for the final step of the catalytic cycle by tracing the evolution of three spectroscopically relevant and structurally distinct components of the last metastable S3 state to the transient O2-evolving S4 state of the OEC. Using quantum chemical calculations, we show that each S3 isomer leads to a different electronic structure formulation for the active S4 state. Crucially, in addition to previously hypothesized Mn(IV)-oxyl species, we establish for the first time, how a genuine Mn(V)-oxo can be obtained in the catalytically active S4 state: this takes the form of a five-coordinate and locally high-spin (SMn = 1) Mn(V) site. This formulation for the S4 state evolves naturally from a preceding S3-state structural intermediate that contains a quasi-trigonal-bipyramidal Mn(IV) ion. The results strongly suggest that water binding in the S3 state is not prerequisite for reaching the oxygen-evolving S4 state of the complex, supporting the notion that both substrates are preloaded at the beginning of the catalytic cycle. This scenario allows true four-electron metal-centered hole accumulation to precede OO bond formation and hence the latter can proceed via a genuine even-electron mechanism. This can occur as intramolecular nucleophilic coupling of two oxo units synchronously with the binding of a water substrate for the next catalytic cycle.
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Affiliation(s)
- Vera Krewald
- Theoretische Chemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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48
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Kim CJ, Debus RJ. One of the Substrate Waters for O2 Formation in Photosystem II Is Provided by the Water-Splitting Mn4CaO5 Cluster’s Ca2+ Ion. Biochemistry 2019; 58:3185-3192. [DOI: 10.1021/acs.biochem.9b00418] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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49
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Ogata K, Hatakeyama M, Sakamoto Y, Nakamura S. Investigation of a Pathway for Water Delivery in Photosystem II Protein by Molecular Dynamics Simulation. J Phys Chem B 2019; 123:6444-6452. [DOI: 10.1021/acs.jpcb.9b04838] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Koji Ogata
- Nakamura Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Hatakeyama
- Nakamura Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuki Sakamoto
- Nakamura Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Biological Information, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Shinichiro Nakamura
- Nakamura Laboratory, RIKEN Cluster for Science, Technology and Innovation Hub, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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50
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Boussac A. Temperature dependence of the high-spin S2 to S3 transition in Photosystem II: Mechanistic consequences. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:508-518. [DOI: 10.1016/j.bbabio.2019.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 02/08/2023]
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