1
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Malcomson T, Rummel F, Barchenko M, O'Malley P. Hey ho, where'd the proton go? Final deprotonation of O6 within the S 3 state of photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 257:112946. [PMID: 38843709 DOI: 10.1016/j.jphotobiol.2024.112946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/04/2024] [Accepted: 05/25/2024] [Indexed: 07/16/2024]
Abstract
The deprotonation of O6 within the S3 state marks the final deprotonation event before the formation of oxygen‑oxygen bond interactions and eventual production and release of dioxygen. Gaining a thorough understanding of this event, from the proton acceptors involved, to the exfiltration pathways available, is key in determining the nature of the resulting oxygen species, influencing the mechanism through which the first oxygen‑oxygen bond forms. Computational analysis, using BS-DFT methodologies, showed that proton abstraction by the local Glu189 residue provides consistent evidence against this being a viable mechanistic pathway due to the lack of a stable product structure. In contrast, abstraction via W3 shows an increasingly stable oxo-oxo product state between r[O5O6] = 2.1 Å & 1.9 Å. The resulting oxo-oxo state is stabilised through donation of β electron character from O6 to Mn1 and α electron character from O6 to O5. This donation from the O6 lone pair is shown to be a key factor in stabilising the oxo-oxo state, in addition to showing the initiation of first O5-O6 bond.
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Affiliation(s)
- Thomas Malcomson
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK.
| | - Felix Rummel
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Maxim Barchenko
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Patrick O'Malley
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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2
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Krysiak S, Burda K. The Effect of Removal of External Proteins PsbO, PsbP and PsbQ on Flash-Induced Molecular Oxygen Evolution and Its Biphasicity in Tobacco PSII. Curr Issues Mol Biol 2024; 46:7187-7218. [PMID: 39057069 PMCID: PMC11276211 DOI: 10.3390/cimb46070428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The oxygen evolution within photosystem II (PSII) is one of the most enigmatic processes occurring in nature. It is suggested that external proteins surrounding the oxygen-evolving complex (OEC) not only stabilize it and provide an appropriate ionic environment but also create water channels, which could be involved in triggering the ingress of water and the removal of O2 and protons outside the system. To investigate the influence of these proteins on the rate of oxygen release and the efficiency of OEC function, we developed a measurement protocol for the direct measurement of the kinetics of oxygen release from PSII using a Joliot-type electrode. PSII-enriched tobacco thylakoids were used in the experiments. The results revealed the existence of slow and fast modes of oxygen evolution. This observation is model-independent and requires no specific assumptions about the initial distribution of the OEC states. The gradual removal of exogenous proteins resulted in a slowdown of the rapid phase (~ms) of O2 release and its gradual disappearance while the slow phase (~tens of ms) accelerated. The role of external proteins in regulating the biphasicity and efficiency of oxygen release is discussed based on observed phenomena and current knowledge.
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Affiliation(s)
| | - Kvetoslava Burda
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, al. Mickiewicza 30, 30-059 Krakow, Poland;
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3
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Flesher DA, Liu J, Wang J, Gisriel CJ, Yang KR, Batista VS, Debus RJ, Brudvig GW. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. J Biol Chem 2024; 300:107475. [PMID: 38879008 DOI: 10.1016/j.jbc.2024.107475] [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] [Received: 03/27/2024] [Revised: 06/02/2024] [Accepted: 06/09/2024] [Indexed: 07/11/2024] Open
Abstract
Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a Mn4CaO5 cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the Mn4CaO5 cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.
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Affiliation(s)
- David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | | | - Ke R Yang
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, California, USA.
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
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4
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Yano J, Kern J, Yachandra VK. Structure Function Studies of Photosystem II Using X-Ray Free Electron Lasers. Annu Rev Biophys 2024; 53:343-365. [PMID: 39013027 DOI: 10.1146/annurev-biophys-071723-102519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The structure and mechanism of the water-oxidation chemistry that occurs in photosystem II have been subjects of great interest. The advent of X-ray free electron lasers allowed the determination of structures of the stable intermediate states and of steps in the transitions between these intermediate states, bringing a new perspective to this field. The room-temperature structures collected as the photosynthetic water oxidation reaction proceeds in real time have provided important novel insights into the structural changes and the mechanism of the water oxidation reaction. The time-resolved measurements have also given us a view of how this reaction-which involves multielectron, multiproton processes-is facilitated by the interaction of the ligands and the protein residues in the oxygen-evolving complex. These structures have also provided a picture of the dynamics occurring in the channels within photosystem II that are involved in the transport of the substrate water to the catalytic center and protons to the bulk.
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Affiliation(s)
- Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; , ,
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; , ,
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; , ,
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5
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Noji T, Chiba Y, Saito K, Ishikita H. Energetics of the H-Bond Network in Exiguobacterium sibiricum Rhodopsin. Biochemistry 2024; 63:1505-1512. [PMID: 38745402 PMCID: PMC11155677 DOI: 10.1021/acs.biochem.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Exiguobacterium sibiricum rhodopsin (ESR) functions as a light-driven proton pump utilizing Lys96 for proton uptake and maintaining its activity over a wide pH range. Using a combination of methodologies including the linear Poisson-Boltzmann equation and a quantum mechanical/molecular mechanical approach with a polarizable continuum model, we explore the microscopic mechanisms underlying its pumping activity. Lys96, the primary proton uptake site, remains deprotonated owing to the loss of solvation in the ESR protein environment. Asp85, serving as a proton acceptor group for Lys96, does not form a low-barrier H-bond with His57. Instead, deprotonated Asp85 forms a salt-bridge with protonated His57, and the proton is predominantly located at the His57 moiety. Glu214, the only acidic residue at the end of the H-bond network exhibits a pKa value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···H2O···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.
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Affiliation(s)
- Tomoyasu Noji
- 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
| | - Yoshihiro Chiba
- 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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Noguchi T. Mechanism of Proton Transfer through the D1-E65/D2-E312 Gate during Photosynthetic Water Oxidation. J Phys Chem B 2024; 128:1866-1875. [PMID: 38364371 DOI: 10.1021/acs.jpcb.3c07787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
In photosystem II, the D1-E65/D2-E312 dyad in the Cl-1 channel has been proposed to play a pivotal role in proton transfer during water oxidation. However, the precise mechanism remains elusive. Here, the proton transfer mechanism within the Cl-1 channel was investigated using quantum mechanics/molecular mechanics calculations. The molecular vibration of the E65/E312 dyad and its deuteration effect revealed that the recently suggested stepwise proton transfer, i.e., initial proton release from the dyad followed by slow reprotonation, does not occur in the Cl-1 channel. Instead, proton transfer is proposed to take place via a conformational change at the E65/E312 dyad, acting as a gate. In its closed form, a proton is trapped within the dyad, preventing forward proton transfer. This closed form converts into the open form, where protonated D1-E65 provides a hydrogen bond to the water network, thereby facilitating fast Grotthuss-type proton transfer.
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Affiliation(s)
- Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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7
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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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8
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Li H, Nakajima Y, Nango E, Owada S, Yamada D, Hashimoto K, Luo F, Tanaka R, Akita F, Kato K, Kang J, Saitoh Y, Kishi S, Yu H, Matsubara N, Fujii H, Sugahara M, Suzuki M, Masuda T, Kimura T, Thao TN, Yonekura S, Yu LJ, Tosha T, Tono K, Joti Y, Hatsui T, Yabashi M, Kubo M, Iwata S, Isobe H, Yamaguchi K, Suga M, Shen JR. Oxygen-evolving photosystem II structures during S 1-S 2-S 3 transitions. Nature 2024; 626:670-677. [PMID: 38297122 PMCID: PMC10866707 DOI: 10.1038/s41586-023-06987-5] [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] [Received: 06/29/2023] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0-4) at the Mn4CaO5 cluster1-3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4-7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.
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Affiliation(s)
- Hongjie Li
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Sayo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Daichi Yamada
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Kobe, Japan
| | - Kana Hashimoto
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Sayo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Koji Kato
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Yasunori Saitoh
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shunpei Kishi
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Huaxin Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Naoki Matsubara
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hajime Fujii
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food and Nutrition, Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Tran Nguyen Thao
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Shinichiro Yonekura
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Long-Jiang Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Takaki Hatsui
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Minoru Kubo
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Kobe, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Sayo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Osaka, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
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9
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Russell BP, Vinyard DJ. Conformational changes in a Photosystem II hydrogen bond network stabilize the oxygen-evolving complex. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149020. [PMID: 37956939 DOI: 10.1016/j.bbabio.2023.149020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
The Mn4CaO5 oxygen-evolving complex (OEC) in Photosystem II (PSII) is assembled in situ and catalyzes water oxidation. After OEC assembly, the PsbO extrinsic subunit docks to the lumenal face of PSII and both stabilizes the OEC and facilitates efficient proton transfer to the lumen. D1 residue R334 is part of a hydrogen bond network involved in proton release during catalysis and interacts directly with PsbO. D1-R334 has recently been observed in different conformations in apo- and holo-OEC PSII structures. We generated a D1-R334G point mutant in Synechocystis sp. PCC 6803 to better understand this residue's function. D1-R334G PSII is active under continuous light, but the OEC is unstable in darkness. Isolated D1-R334G core complexes have little bound PsbO and less manganese as the wild type control. The S2 intermediate is stabilized in D1-R334G indicating that the local environment around the OEC has been altered. These results suggest that the hydrogen bond network that includes D1-R334 exists in a different functional conformation during PSII biogenesis in the absence of PsbO.
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Affiliation(s)
- Brandon P Russell
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, United States of America
| | - David J Vinyard
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, United States of America.
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10
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Saito K, Nishio S, Ishikita H. Interplay of two low-barrier hydrogen bonds in long-distance proton-coupled electron transfer for water oxidation. PNAS NEXUS 2023; 2:pgad423. [PMID: 38130665 PMCID: PMC10733176 DOI: 10.1093/pnasnexus/pgad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
D1-Tyr161 (TyrZ) forms a low-barrier H-bond with D1-His190 and functions as a redox-active group in photosystem II. When oxidized to the radical form (TyrZ-O•), it accepts an electron from the oxygen-evolving Mn4CaO5 cluster, facilitating an increase in the oxidation state (Sn; n = 0-3). In this study, we investigated the mechanism of how TyrZ-O• drives proton-coupled electron transfer during the S2 to S3 transition using a quantum mechanical/molecular mechanical approach. In response to TyrZ-O• formation and subsequent loss of the low-barrier H-bond, the ligand water molecule at the Ca2+ site (W4) reorients away from TyrZ and donates an H-bond to D1-Glu189 at Mn4 of Mn4CaO5 together with an adjacent water molecule. The H-bond donation to the Mn4CaO5 cluster triggers the release of the proton from the lowest pKa site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca2+ interface and forming the extended Grotthuss-like network [TyrZ…D1-His190]-[Mn4CaO5]-[W1…D1-Asp61], rather than the direct electrostatic interaction, is likely a basis of the apparent long-distance interaction (11.4 Å) between TyrZ-O• formation and D1-Asp61 protonation.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Shunya Nishio
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
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11
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Kato Y, Kuroda H, Ozawa SI, Saito K, Dogra V, Scholz M, Zhang G, de Vitry C, Ishikita H, Kim C, Hippler M, Takahashi Y, Sakamoto W. Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts. eLife 2023; 12:RP88822. [PMID: 37986577 PMCID: PMC10665015 DOI: 10.7554/elife.88822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.
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Affiliation(s)
- Yusuke Kato
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Faculty of Agriculture, Setsunan UniversityOsakaJapan
| | - Hiroshi Kuroda
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Shin-Ichiro Ozawa
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesShanghaiChina
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampurIndia
| | - Martin Scholz
- Institute of Plant Biology and Biotechnology, University of MünsterMünsterGermany
| | - Guoxian Zhang
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
| | - Catherine de Vitry
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université Pierre et Marie CurieParisFrance
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesShanghaiChina
| | - Michael Hippler
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Institute of Plant Biology and Biotechnology, University of MünsterMünsterGermany
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
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12
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Gates C, Williams JM, Ananyev G, Dismukes GC. How chloride functions to enable proton conduction in photosynthetic water oxidation: Time-resolved kinetics of intermediates (S-states) in vivo and bromide substitution. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148998. [PMID: 37499962 DOI: 10.1016/j.bbabio.2023.148998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Chloride (Cl-) is essential for O2 evolution during photosynthetic water oxidation. Two chlorides near the water-oxidizing complex (WOC) in Photosystem II (PSII) structures from Thermosynechococcus elongatus (and T. vulcanus) have been postulated to transfer protons generated from water oxidation. We monitored four criteria: primary charge separation flash yield (P* → P+QA-), rates of water oxidation steps (S-states), rate of proton evolution, and flash O2 yield oscillations by measuring chlorophyll variable fluorescence (P* quenching), pH-sensitive dye changes, and oximetry. Br-substitution slows and destabilizes cellular growth, resulting from lower light-saturated O2 evolution rate (-20 %) and proton release (-36 % ΔpH gradient). The latter implies less ATP production. In Br- cultures, protonogenic S-state transitions (S2 → S3 → S0') slow with increasing light intensity and during O2/water exchange (S0' → S0 → S1), while the non-protonogenic S1 → S2 transition is kinetically unaffected. As flash rate increases in Cl- cultures, both rate and extent of acidification of the lumen increase, while charge recombination is suppressed relative to Br-. The Cl- advantage in rapid proton escape from the WOC to lumen is attributed to correlated ion-pair movement of H3O+Cl- in dry water channels vs. separated Br- and H+ ion movement through different regions (>200-fold difference in Bronsted acidities). By contrast, at low flash rates a previously unreported reversal occurs that favors Br- cultures for both proton evolution and less PSII charge recombination. In Br- cultures, slower proton transfer rate is attributed to stronger ion-pairing of Br- with AA residues lining the water channels. Both anions charge-neutralize protons and shepherd them to the lumen using dry aqueous channels.
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Affiliation(s)
- Colin Gates
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Computational Biology and Molecular Biophysics, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Biochemistry, Loyola University Chicago, IL 60660, USA
| | - Jonah M Williams
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Gennady Ananyev
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - G Charles Dismukes
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA.
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13
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Bhowmick A, Simon PS, Bogacz I, Hussein R, Zhang M, Makita H, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Chernev P, Fuller FD, Fransson T, Alonso-Mori R, Brewster AS, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography. IUCRJ 2023; 10:642-655. [PMID: 37870936 PMCID: PMC10619448 DOI: 10.1107/s2052252523008928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O-O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.
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Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rana Hussein
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Margaret D. Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala SE 75120, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala SE 75120, Sweden
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas Fransson
- Department of Physics, AlbaNova University Center, Stockholm University, Stockholm SE-10691, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Holger Dobbek
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Athina Zouni
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala SE 75120, Sweden
- Department of Chemistry, Umeå University, Umeå SE 90187, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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14
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Hussein R, Ibrahim M, Bhowmick A, Simon PS, Bogacz I, Doyle MD, Dobbek H, Zouni A, Messinger J, Yachandra VK, Kern JF, Yano J. Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function. PHOTOSYNTHESIS RESEARCH 2023; 158:91-107. [PMID: 37266800 PMCID: PMC10684718 DOI: 10.1007/s11120-023-01018-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 06/03/2023]
Abstract
One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. This process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn4CaO5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the 'water wheel' to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn4CaO5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S0 → S1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421-425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831-15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).
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Affiliation(s)
- Rana Hussein
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany.
| | - Mohamed Ibrahim
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Holger Dobbek
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Athina Zouni
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, SE 75120, Uppsala, Sweden
- Department of Chemistry, Umeå University, SE 90187, Umeå, Sweden
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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15
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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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16
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Saito K, Nishio S, Asada M, Mino H, Ishikita H. Insights into the protonation state and spin structure for the g = 2 multiline electron paramagnetic resonance signal of the oxygen-evolving complex. PNAS NEXUS 2023; 2:pgad244. [PMID: 37564363 PMCID: PMC10411963 DOI: 10.1093/pnasnexus/pgad244] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/08/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
In photosystem II (PSII), one-electron oxidation of the most stable oxidation state of the Mn4CaO5 cluster (S1) leads to formation of two distinct states, the open-cubane S2 conformation [Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV)] with low spin and the closed-cubane S2 conformation [Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III)] with high spin. In electron paramagnetic resonance (EPR) spectroscopy, the open-cubane S2 conformation exhibits a g = 2 multiline signal. However, its protonation state remains unclear. Here, we investigated the protonation state of the open-cubane S2 conformation by calculating exchange couplings in the presence of the PSII protein environment and simulating the pulsed electron-electron double resonance (PELDOR). When a ligand water molecule, which forms an H-bond with D1-Asp61 (W1), is deprotonated at dangling Mn4(IV), the first-exited energy (34 cm-1) in manifold spin excited states aligns with the observed value in temperature-dependent pulsed EPR analyses, and the PELDOR signal is best reproduced. Consequently, the g = 2 multiline signal observed in EPR corresponds to the open-cubane S2 conformation with the deprotonated W1 (OH-).
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shunya Nishio
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Mizue Asada
- Instrument Center, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Hiroyuki Mino
- Division of Material Science, Graduate School of Science, Nagoya University,Furo-cho, Chikusa-ku, 464-8602 Nagoya, Aichi, 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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17
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Greife P, Schönborn M, Capone M, Assunção R, Narzi D, Guidoni L, Dau H. The electron-proton bottleneck of photosynthetic oxygen evolution. Nature 2023; 617:623-628. [PMID: 37138082 DOI: 10.1038/s41586-023-06008-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today's oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S4 state-which was postulated half a century ago1 and remains largely uncharacterized. Here we resolve this key stage of photosynthetic O2 formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combining these results with computational chemistry reveals that a crucial proton vacancy is initally created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in a single-electron, multi-proton transfer event. This is the slowest step in photosynthetic O2 formation, with a moderate energetic barrier and marked entropic slowdown. We identify the S4 state as the oxygen-radical state; its formation is followed by fast O-O bonding and O2 release. In conjunction with previous breakthroughs in experimental and computational investigations, a compelling atomistic picture of photosynthetic O2 formation emerges. Our results provide insights into a biological process that is likely to have occurred unchanged for the past three billion years, which we expect to support the knowledge-based design of artificial water-splitting systems.
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Affiliation(s)
- Paul Greife
- Department of Physics, Freie Universität, Berlin, Germany
| | | | - Matteo Capone
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, L'Aquila, Italy
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Daniele Narzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Holger Dau
- Department of Physics, Freie Universität, Berlin, Germany.
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18
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Mandal M, Saito K, Ishikita H. Substitution of Ca 2+ and changes in the H-bond network near the oxygen-evolving complex of photosystem II. Phys Chem Chem Phys 2023; 25:6473-6480. [PMID: 36785919 DOI: 10.1039/d2cp05036f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Ca2+, which provides binding sites for ligand water molecules W3 and W4 in the Mn4CaO5 cluster, is a prerequisite for O2 evolution in photosystem II (PSII). We report structural changes in the H-bond network and the catalytic cluster itself upon the replacement of Ca2+ with other alkaline earth metals, using a quantum mechanical/molecular mechanical approach. The small radius of Mg2+ makes W3 donate an H-bond to D1-Glu189 in Mg2+-PSII. If an additional water molecule binds at the large surface of Ba2+, it donates H-bonds to D1-Glu189 and the ligand water molecule at the dangling Mn, altering the H-bond network. The potential energy profiles of the H-bond between D1-Tyr161 (TyrZ) and D1-His190 and the interconversion between the open- and closed-cubane S2 conformations remain substantially unaltered upon the replacement of Ca2+. Remarkably, the O5⋯Ca2+ distance is shortest among all O5⋯metal distances irrespective of the radius being larger than that of Mg2+. Furthermore, Ca2+ is the only alkaline earth metal that equalizes the O5⋯metal and O2⋯metal distances and facilitates the formation of the symmetric cubane structure.
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Affiliation(s)
- Manoj Mandal
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India.
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. .,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. .,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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19
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Sirohiwal A, Pantazis DA. Functional Water Networks in Fully Hydrated Photosystem II. J Am Chem Soc 2022; 144:22035-22050. [PMID: 36413491 PMCID: PMC9732884 DOI: 10.1021/jacs.2c09121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone QB. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.
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20
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Yamaguchi K, Shoji M, Isobe H, Kawakami T, Miyagawa K, Suga M, Akita F, Shen JR. Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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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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22
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Saito K, Mino H, Nishio S, Ishikita H. Protonation structure of the closed-cubane conformation of the O 2-evolving complex in photosystem II. PNAS NEXUS 2022; 1:pgac221. [PMID: 36712340 PMCID: PMC9802176 DOI: 10.1093/pnasnexus/pgac221] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022]
Abstract
In photosystem II (PSII), one-electron oxidation of the most stable state of the oxygen-evolving Mn4CaO5 cluster (S1) leads to the S2 state formation, Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (open-cubane S2) or Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (closed-cubane S2). In electron paramagnetic resonance (EPR) spectroscopy, the g = 4.1 signal is not observed in cyanobacterial PSII but in plant PSII, whereas the g = 4.8 signal is observed in cyanobacterial PSII and extrinsic-subunit-depleted plant PSII. Here, we investigated the closed-cubane S2 conformation, a candidate for a higher spin configuration that accounts for g > 4.1 EPR signal, considering all pairwise exchange couplings in the PSII protein environment (i.e. instead of considering only a single exchange coupling between the [Mn3(CaO4)] cubane region and the dangling Mn4 site). Only when a ligand water molecule that forms an H-bond with D1-Asp61 (W1) is deprotonated at dangling Mn4(IV), the g = 4.1 EPR spectra can be reproduced using the cyanobacterial PSII crystal structure. The closed-cubane S2 is less stable than the open-cubane S2 in cyanobacterial PSII, which may explain why the g = 4.1 EPR signal is absent in cyanobacterial PSII.
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Affiliation(s)
| | - Hiroyuki Mino
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shunya Nishio
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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23
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Imaizumi K, Ifuku K. Binding and functions of the two chloride ions in the oxygen-evolving center of photosystem II. PHOTOSYNTHESIS RESEARCH 2022; 153:135-156. [PMID: 35698013 DOI: 10.1007/s11120-022-00921-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Light-driven water oxidation in photosynthesis occurs at the oxygen-evolving center (OEC) of photosystem II (PSII). Chloride ions (Cl-) are essential for oxygen evolution by PSII, and two Cl- ions have been found to specifically bind near the Mn4CaO5 cluster in the OEC. The retention of these Cl- ions within the OEC is critically supported by some of the membrane-extrinsic subunits of PSII. The functions of these two Cl- ions and the mechanisms of their retention both remain to be fully elucidated. However, intensive studies performed recently have advanced our understanding of the functions of these Cl- ions, and PSII structures from various species have been reported, aiding the interpretation of previous findings regarding Cl- retention by extrinsic subunits. In this review, we summarize the findings to date on the roles of the two Cl- ions bound within the OEC. Additionally, together with a short summary of the functions of PSII membrane-extrinsic subunits, we discuss the mechanisms of Cl- retention by these extrinsic subunits.
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Affiliation(s)
- Ko Imaizumi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Kentaro Ifuku
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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24
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Imaizumi K, Nishimura T, Nagao R, Saito K, Nakano T, Ishikita H, Noguchi T, Ifuku K. D139N mutation of PsbP enhances the oxygen-evolving activity of photosystem II through stabilized binding of a chloride ion. PNAS NEXUS 2022; 1:pgac136. [PMID: 36741451 PMCID: PMC9896922 DOI: 10.1093/pnasnexus/pgac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 07/19/2022] [Indexed: 02/07/2023]
Abstract
Photosystem II (PSII) is a multisubunit membrane protein complex that catalyzes light-driven oxidation of water to molecular oxygen. The chloride ion (Cl-) has long been known as an essential cofactor for oxygen evolution by PSII, and two Cl- ions (Cl-1 and Cl-2) have been found to specifically bind near the Mn4CaO5 cluster within the oxygen-evolving center (OEC). However, despite intensive studies on these Cl- ions, little is known about the function of Cl-2, the Cl- ion that is associated with the backbone nitrogens of D1-Asn338, D1-Phe339, and CP43-Glu354. In green plant PSII, the membrane extrinsic subunits-PsbP and PsbQ-are responsible for Cl- retention within the OEC. The Loop 4 region of PsbP, consisting of highly conserved residues Thr135-Gly142, is inserted close to Cl-2, but its importance has not been examined to date. Here, we investigated the importance of PsbP-Loop 4 using spinach PSII membranes reconstituted with spinach PsbP proteins harboring mutations in this region. Mutations in PsbP-Loop 4 had remarkable effects on the rate of oxygen evolution by PSII. Moreover, we found that a specific mutation, PsbP-D139N, significantly enhances the oxygen-evolving activity in the absence of PsbQ, but not significantly in its presence. The D139N mutation increased the Cl- retention ability of PsbP and induced a unique structural change in the OEC, as indicated by light-induced Fourier transform infrared (FTIR) difference spectroscopy and theoretical calculations. Our findings provide insight into the functional significance of Cl-2 in the water-oxidizing reaction of PSII.
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Affiliation(s)
- Ko Imaizumi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Taishi Nishimura
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan,Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan,Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8654 , Japan
| | - Takeshi Nakano
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan,Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8654 , Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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25
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Saito K, Xu T, Ishikita H. Correlation between C═O Stretching Vibrational Frequency and p Ka Shift of Carboxylic Acids. J Phys Chem B 2022; 126:4999-5006. [PMID: 35763701 PMCID: PMC9289881 DOI: 10.1021/acs.jpcb.2c02193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Identifying the pKa values of aspartic
acid (Asp) and glutamic acid (Glu) in active sites is essential for
understanding enzyme reaction mechanisms. In this study, we investigated
the correlation between the C=O stretching vibrational frequency
(νC=O) of protonated carboxylic acids and
the pKa values using density functional
theory calculations. In unsaturated carboxylic acids (e.g., benzoic
acid analogues), νC=O decreases as the pKa increases (the negative correlation), whereas
in saturated carboxylic acids (e.g., acetic acid analogues, Asp, and
Glu), νC=O increases as the pKa increases (the positive correlation) as long as the
structure of the H-bond network around the acid is identical. The
negative/positive correlation between νC=O and pKa can be rationalized by the presence
or absence of the C=C double bond. The pKa shift was estimated from the νC=O shift of Asp and Glu in proteins on the basis of the negative correlation
derived from benzoic acids. The previous estimations should be revisited
by using the positive correlation derived in this study, as demonstrated
by quantum mechanical/molecular mechanical calculations of νC=O and electrostatic calculations of pKa on a key Asp85 in the proton-transfer pathway of bacteriorhodopsin.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Tianyang Xu
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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26
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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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27
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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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28
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Mandal M, Saito K, Ishikita H. Requirement of Chloride for the Downhill Electron Transfer Pathway from the Water-Splitting Center in Natural Photosynthesis. J Phys Chem B 2021; 126:123-131. [PMID: 34955014 DOI: 10.1021/acs.jpcb.1c09176] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In photosystem II (PSII), Cl- is a prerequisite for the second flash-induced oxidation of the Mn4CaO5 cluster (the S2 to S3 transition). We report proton transfer from the substrate water molecule via D1-Asp61 and electron transfer via redox-active D1-Tyr161 (TyrZ) to the chlorophyll pair in Cl--depleted PSII using a quantum mechanical/molecular mechanical approach. The low-barrier H-bond formation between the substrate water molecule and D1-Asp61 remained unaffected upon the depletion of Cl-. However, the binding site, D2-Lys317, formed a salt bridge with D1-Asp61, leading to the inhibition of the subsequent proton transfer. Remarkably, the redox potential (Em) of S2/S3 increased significantly, making electron transfer from S2 to TyrZ energetically uphill, as observed in Ca2+-depleted PSII. The uphill electron transfer pathway was induced by the significant increase in Em(S2/S3) caused by the loss of charge compensation for D2-Lys317 upon the depletion of Cl-, whereas it was induced by the significant decrease in Em(TyrZ) caused by the rearrangement of the water molecules at the Ca2+ binding moiety upon the depletion of Ca2+.
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Affiliation(s)
- Manoj Mandal
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, West Bengal 700106, India
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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29
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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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30
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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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31
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Mechanism of the formation of proton transfer pathways in photosynthetic reaction centers. Proc Natl Acad Sci U S A 2021; 118:2103203118. [PMID: 34301911 PMCID: PMC8325351 DOI: 10.1073/pnas.2103203118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structures of photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II show large structural similarity. However, the proposed mechanisms of proton transfer toward the terminal electron acceptor quinone (QB) are not consistent. In particular, not His-L190, which is an H-bond partner of QB, but rather Glu-L212, which is ∼6 Å away from QB, was assumed to be the direct proton donor for QB. We demonstrate that the H-bond between His-L190 and QB is a low-barrier H-bond, which facilitates proton transfer from singly protonated His-L190 to QB. Furthermore, Glu-L212 is not a direct H-bond donor for QB. However, it facilitates proton transfer toward deprotonated His-L190 via water molecules after QBH2 forms and leaves the PbRC. In photosynthetic reaction centers from purple bacteria (PbRCs) from Rhodobacter sphaeroides, the secondary quinone QB accepts two electrons and two protons via electron-coupled proton transfer (PT). Here, we identify PT pathways that proceed toward the QB binding site, using a quantum mechanical/molecular mechanical approach. As the first electron is transferred to QB, the formation of the Grotthuss-like pre-PT H-bond network is observed along Asp-L213, Ser-L223, and the distal QB carbonyl O site. As the second electron is transferred, the formation of a low-barrier H-bond is observed between His-L190 at Fe and the proximal QB carbonyl O site, which facilitates the second PT. As QBH2 leaves PbRC, a chain of water molecules connects protonated Glu-L212 and deprotonated His-L190 forms, which serves as a pathway for the His-L190 reprotonation. The findings of the second pathway, which does not involve Glu-L212, and the third pathway, which proceeds from Glu-L212 to His-L190, provide a mechanism for PT commonly used among PbRCs.
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32
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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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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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