1
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Yokoyama T, Takayama Y, Mizuguchi M, Nabeshima Y, Kusaka K. SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD +-binding pocket. FEBS Lett 2024; 598:2269-2280. [PMID: 39031546 DOI: 10.1002/1873-3468.14961] [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] [Received: 05/06/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 07/22/2024]
Abstract
SIRT5, one of the mammalian sirtuins, specifically recognizes succinyl-lysine residues on proteins and catalyzes the desuccinylation reaction. In this study, we characterized SIRT5 mutants with hydrophobic amino acid substitutions at Q140 and N141, in addition to the catalytic residue H158, known as an active site residue, by the Michaelis-Menten analysis and X-ray crystallography. Kinetic analysis showed that the catalytic efficiency (kcat/Km) of the Q140L and N141V mutants decreased to 0.02 times and 0.0038 times that of the wild-type SIRT5, respectively, with the activity of the N141V mutant becoming comparable to that of the H158M mutant. Our findings indicate that N141 contributes significantly to the desuccinylation reaction.
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Affiliation(s)
| | - Yuki Takayama
- Faculty of Pharmaceutical Sciences, University of Toyama, Japan
| | | | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Japan
| | - Katsuhiro Kusaka
- Comprehensive Research Organization for Science and Society (CROSS), Neutron Industrial Application Promotion Center, Tokai, Japan
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2
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Kaur D, Reiss K, Wang J, Batista VS, Brudvig GW, Gunner MR. Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations. J Phys Chem B 2024; 128:2236-2248. [PMID: 38377592 DOI: 10.1021/acs.jpcb.3c05367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
At room temperature and neutral pH, the oxygen-evolving center (OEC) of photosystem II (PSII) catalyzes water oxidation. During this process, oxygen is released from the OEC, while substrate waters are delivered to the OEC and protons are passed from the OEC to the lumen through water channels known as the narrow or the O4 channel, broad or the Cl1 channel, and large or the O1 channel. Protein residues lining the surfaces of these channels play a critical role in stabilizing the hydrogen-bonding networks that assist in the process. We carried out an occupancy analysis to better understand the structural and possible substrate water dynamics in full PSII monomer molecular dynamics (MD) trajectories in both the S1 and S2 states. We find that the equilibrated positions of water molecules derived from MD-derived electron density maps largely match the experimentally observed positions in crystallography. Furthermore, the occupancy reduction in MD simulations of some water molecules inside the single-filed narrow channel also correlates well with the crystallographic data during a structural transition when the S1 state of the OEC advances to the S2 state. The overall reduced occupancies of water molecules are the source of their "vacancy-hopping" dynamic nature inside these channels, unlike water molecules inside an ice lattice where all water molecules have a fixed unit occupancy. We propose on the basis of findings in our structural and molecular dynamics analysis that the water molecule occupying a pocket formed by D1-D61, D1-S169, and O4 of the OEC could be the last steppingstone to enter into the OEC and that the broad channel may be favored for proton transfer.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, Brock University, 500 Glenridge Avenue, St. Catharines L2S 3A1, Ontario, Canada
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - M R Gunner
- Department of Physics, City College of New York New York, New York 10031, United States
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3
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Drosou M, Comas-Vilà G, Neese F, Salvador P, Pantazis DA. Does Serial Femtosecond Crystallography Depict State-Specific Catalytic Intermediates of the Oxygen-Evolving Complex? J Am Chem Soc 2023; 145:10604-10621. [PMID: 37137865 DOI: 10.1021/jacs.3c00489] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent advances in serial femtosecond crystallography (SFX) of photosystem II (PSII), enabled by X-ray free electron lasers (XFEL), provided the first geometric models of distinct intermediates in the catalytic S-state cycle of the oxygen-evolving complex (OEC). These models are obtained by flash-advancing the OEC from the dark-stable state (S1) to more oxidized intermediates (S2 and S3), eventually cycling back to the most reduced S0. However, the interpretation of these models is controversial because geometric parameters within the Mn4CaO5 cluster of the OEC do not exactly match those expected from coordination chemistry for the spectroscopically verified manganese oxidation states of the distinct S-state intermediates. Here we focus on the first catalytic transition, S1 → S2, which represents a one-electron oxidation of the OEC. Combining geometric and electronic structure criteria, including a novel effective oxidation state approach, we analyze existing 1-flash (1F) SFX-XFEL crystallographic models that should depict the S2 state of the OEC. We show that the 1F/S2 equivalence is not obvious, because the Mn oxidation states and total unpaired electron counts encoded in these models are not fully consistent with those of a pure S2 state and with the nature of the S1 → S2 transition. Furthermore, the oxidation state definition in two-flashed (2F) structural models is practically impossible to elucidate. Our results advise caution in the extraction of electronic structure information solely from the literal interpretation of crystallographic models and call for re-evaluation of structural and mechanistic interpretations that presume exact correspondence of such models to specific catalytic intermediates of the OEC.
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Affiliation(s)
- Maria Drosou
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Gerard Comas-Vilà
- Institute of Computational Chemistry and Catalysis, Chemistry Department, University of Girona, Montilivi Campus, Girona, Catalonia 17003, Spain
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Pedro Salvador
- Institute of Computational Chemistry and Catalysis, Chemistry Department, University of Girona, Montilivi Campus, Girona, Catalonia 17003, Spain
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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4
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Boussac A, Sellés J, Sugiura M. Energetics and proton release in photosystem II from Thermosynechococcus elongatus with a D1 protein encoded by either the psbA 2 or psbA 3 gene. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148979. [PMID: 37080330 DOI: 10.1016/j.bbabio.2023.148979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023]
Abstract
In the cyanobacterium Thermosynechococcus elongatus, there are three psbA genes coding for the Photosystem II (PSII) D1 subunit that interacts with most of the main cofactors involved in the electron transfers. Recently, the 3D crystal structures of both PsbA2-PSII and PsbA3-PSII have been solved [Nakajima et al., J. Biol. Chem. 298 (2022) 102668.]. It was proposed that the loss of one hydrogen bond of PheD1 due to the D1-Y147F exchange in PsbA2-PSII resulted in a more negative Em of PheD1 in PsbA2-PSII when compared to PsbA3-PSII. In addition, the loss of two water molecules in the Cl-1 channel was attributed to the D1-P173M substitution in PsbA2-PSII. This exchange, by narrowing the Cl-1 proton channel, could be at the origin of a slowing down of the proton release. Here, we have continued the characterization of PsbA2-PSII by measuring the thermoluminescence from the S2QA-/DCMU charge recombination and by measuring proton release kinetics using time-resolved absorption changes of the dye bromocresol purple. It was found that i) the Em of PheD1-•/PheD1 was decreased by ~30 mV in PsbA2-PSII when compared to PsbA3-PSII and ii) the kinetics of the proton release into the bulk was significantly slowed down in PsbA2-PSII in the S2TyrZ• to S3TyrZ and S3TyrZ• → (S3TyrZ•)' transitions. This slowing down was partially reversed by the PsbA2/M173P mutation and induced by the PsbA3/P173M mutation thus confirming a role of the D1-173 residue in the egress of protons trough the Cl-1 channel.
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Affiliation(s)
- Alain Boussac
- I2BC, UMR CNRS 9198, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | - Julien Sellés
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 and Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Miwa Sugiura
- Proteo-Science Research Center, and Department of Chemistry, Graduate School of Science and Technology, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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5
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Lubitz W, Pantazis DA, Cox N. Water oxidation in oxygenic photosynthesis studied by magnetic resonance techniques. FEBS Lett 2023; 597:6-29. [PMID: 36409002 DOI: 10.1002/1873-3468.14543] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
The understanding of light-induced biological water oxidation in oxygenic photosynthesis is of great importance both for biology and (bio)technological applications. The chemically difficult multistep reaction takes place at a unique protein-bound tetra-manganese/calcium cluster in photosystem II whose structure has been elucidated by X-ray crystallography (Umena et al. Nature 2011, 473, 55). The cluster moves through several intermediate states in the catalytic cycle. A detailed understanding of these intermediates requires information about the spatial and electronic structure of the Mn4 Ca complex; the latter is only available from spectroscopic techniques. Here, the important role of Electron Paramagnetic Resonance (EPR) and related double resonance techniques (ENDOR, EDNMR), complemented by quantum chemical calculations, is described. This has led to the elucidation of the cluster's redox and protonation states, the valence and spin states of the manganese ions and the interactions between them, and contributed substantially to the understanding of the role of the protein surrounding, as well as the binding and processing of the substrate water molecules, the O-O bond formation and dioxygen release. Based on these data, models for the water oxidation cycle are developed.
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Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim/Ruhr, Germany
| | | | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
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6
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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: 16] [Impact Index Per Article: 5.3] [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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7
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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: 7] [Impact Index Per Article: 2.3] [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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8
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Isobe H, Shoji M, Suzuki T, Shen JR, Yamaguchi K. Roles of the Flexible Primary Coordination Sphere of the Mn 4CaO x Cluster: What Are the Immediate Decay Products of the S3 State? J Phys Chem B 2022; 126:7212-7228. [DOI: 10.1021/acs.jpcb.2c02596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Mitsuo Shoji
- Center for Computational Science, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takayoshi Suzuki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-0043, Japan
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9
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Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proc Natl Acad Sci U S A 2022; 119:e2116765118. [PMID: 34937700 PMCID: PMC8740770 DOI: 10.1073/pnas.2116765118] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.
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Affiliation(s)
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Ke R Yang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | | | - M R Gunner
- Department of Physics, City College of New York, New York, NY 100031
| | | | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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10
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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: 78] [Impact Index Per Article: 19.5] [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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11
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Drosou M, Pantazis DA. Redox Isomerism in the S 3 State of the Oxygen-Evolving Complex Resolved by Coupled Cluster Theory. Chemistry 2021; 27:12815-12825. [PMID: 34288176 PMCID: PMC8518824 DOI: 10.1002/chem.202101567] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Indexed: 01/19/2023]
Abstract
The electronic and geometric structures of the water-oxidizing complex of photosystem II in the steps of the catalytic cycle that precede dioxygen evolution remain hotly debated. Recent structural and spectroscopic investigations support contradictory redox formulations for the active-site Mn4 CaOx cofactor in the final metastable S3 state. These range from the widely accepted MnIV 4 oxo-hydroxo model, which presumes that O-O bond formation occurs in the ultimate transient intermediate (S4 ) of the catalytic cycle, to a MnIII 2 MnIV 2 peroxo model representative of the contrasting "early-onset" O-O bond formation hypothesis. Density functional theory energetics of suggested S3 redox isomers are inconclusive because of extreme functional dependence. Here, we use the power of the domain-based local pair natural orbital approach to coupled cluster theory, DLPNO-CCSD(T), to present the first correlated wave function theory calculations of relative stabilities for distinct redox-isomeric forms of the S3 state. Our results enabled us to evaluate conflicting models for the S3 state of the oxygen-evolving complex (OEC) and to quantify the accuracy of lower-level theoretical approaches. Our assessment of the relevance of distinct redox-isomeric forms for the mechanism of biological water oxidation strongly disfavors the scenario of early-onset O-O formation advanced by literal interpretations of certain crystallographic models. This work serves as a case study in the application of modern coupled cluster implementations to redox isomerism problems in oligonuclear transition metal systems.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry LaboratoryNational and Kapodistrian University of AthensPanepistimiopolisZografou15771Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an derRuhrGermany
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12
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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: 4.0] [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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13
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Kaur D, Khaniya U, Zhang Y, Gunner MR. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Front Chem 2021; 9:660954. [PMID: 34211960 PMCID: PMC8239185 DOI: 10.3389/fchem.2021.660954] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
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14
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15
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Kaur D, Zhang Y, Reiss KM, Mandal M, Brudvig GW, Batista VS, Gunner MR. Proton exit pathways surrounding the oxygen evolving complex of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148446. [PMID: 33964279 DOI: 10.1016/j.bbabio.2021.148446] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022]
Abstract
Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, extend from the OEC towards the aqueous surface more than 15 Å away. However, the role of each pathway in the transport in and out of the OEC is yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths. Hydrogen bond network analysis shows that near the OEC the waters are highly interconnected with similar free energy for hydronium at all locations. The paths diverge as they move towards the lumen. The water chain in the broad channel is better connected than in the narrow and large channels, where disruptions in the network are observed approximately 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel. Thus, a proton released from any location on the OEC can access all paths, but the likely exit to the lumen passes through PsbO via the broad channel.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Manoj Mandal
- Department of Physics, City College of New York, NY 10031, United States
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States.
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16
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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17
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Xiao Y, Zhu Q, Yang Y, Wang W, Kuang T, Shen JR, Han G. Role of PsbV-Tyr137 in photosystem II studied by site-directed mutagenesis in the thermophilic cyanobacterium Thermosynechococcus vulcanus. PHOTOSYNTHESIS RESEARCH 2020; 146:41-54. [PMID: 32342261 DOI: 10.1007/s11120-020-00753-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/19/2020] [Indexed: 05/07/2023]
Abstract
PsbV (cytochrome c550) is one of the three extrinsic proteins of photosystem II (PSII) and functions to maintain the stability and activity of the Mn4CaO5 cluster, the catalytic center for water oxidation. PsbV-Y137 is the C-terminal residue of PsbV and is located at the exit of a hydrogen-bond network mediated by the D1-Y161-H190 residue pair. In order to examine the function of PsbV-Y137, four mutants, PsbV-Y137A, PsbV-Y137F, PsbV-Y137G, and PsbV-Y137W, were generated with Thermosynechococcus vulcanus (T. vulcanus). These mutants showed growth rates similar to that of the wild-type strain (WT); however, their oxygen-evolving activities were different. At pH 6.5, the oxygen evolution rates of Y137F and Y137W were almost identical to that of WT, whereas the oxygen evolution rates of the Y137A, Y137G mutants were 64% and 61% of WT, respectively. However, the oxygen evolution in the latter two mutants decreased less at higher pHs, suggesting that higher pHs facilitated oxygen evolution probably by facilitating proton egress in these two mutants. Furthermore, thylakoid membranes isolated from the PsbV-Y137A, PsbV-Y137G mutants exhibited much lower levels of oxygen-evolving activity than that of WT, which was found to be caused by the release of PsbV. In addition, PSII complexes purified from the PsbV-Y137A and PsbV-Y137G mutants lost all of the three extrinsic proteins but instead bind Psb27, an assembly cofactor of PSII. These results demonstrate that the PsbV-Tyr137 residue is required for the stable binding of PsbV to PSII, and the hydrogen-bond network mediated by D1-Y161-H190 is likely to function in proton egress during water oxidation.
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Affiliation(s)
- Yanan Xiao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Qingjun Zhu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Yanyan Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, No. 1 Beichen West Rd., Beijing, 100101, China.
- Research Institute of Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Tsushima Naka 3-1-1, Okayama, 700-8530, Japan.
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China.
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18
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Li XC, Li J, Siegbahn PEM. A Theoretical Study of the Recently Suggested Mn VII Mechanism for O-O Bond Formation in Photosystem II. J Phys Chem A 2020; 124:8011-8018. [PMID: 32877196 PMCID: PMC7586388 DOI: 10.1021/acs.jpca.0c05135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism for water oxidation in photosystem II has been a major topic for several decades. The active catalyst has four manganese atoms connected by bridging oxo bonds, in a complex termed the oxygen-evolving complex (OEC), which also includes a calcium atom. The O-O bond of oxygen is formed after absorption of four photons in a state of the OEC termed S4. There has been essential consensus that in the S4 state, all manganese atoms are in the Mn(IV) oxidation state. However, recently there has been a suggestion that one of the atoms is in the Mn(VII) state. In the present computational study, the feasibility of that proposal has been investigated. It is here shown that the mechanism involving Mn(VII) has a much higher barrier for forming O2 than the previous proposal with four Mn(IV) atoms.
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Affiliation(s)
- Xi-Chen Li
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jing Li
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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19
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Méndez-Hernández DD, Baldansuren A, Kalendra V, Charles P, Mark B, Marshall W, Molnar B, Moore TA, Lakshmi KV, Moore AL. HYSCORE and DFT Studies of Proton-Coupled Electron Transfer in a Bioinspired Artificial Photosynthetic Reaction Center. iScience 2020; 23:101366. [PMID: 32738611 PMCID: PMC7394912 DOI: 10.1016/j.isci.2020.101366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/22/2020] [Accepted: 07/10/2020] [Indexed: 11/24/2022] Open
Abstract
The photosynthetic water-oxidation reaction is catalyzed by the oxygen-evolving complex in photosystem II (PSII) that comprises the Mn4CaO5 cluster, with participation of the redox-active tyrosine residue (YZ) and a hydrogen-bonded network of amino acids and water molecules. It has been proposed that the strong hydrogen bond between YZ and D1-His190 likely renders YZ kinetically and thermodynamically competent leading to highly efficient water oxidation. However, a detailed understanding of the proton-coupled electron transfer (PCET) at YZ remains elusive owing to the transient nature of its intermediate states involving YZ⋅. Herein, we employ a combination of high-resolution two-dimensional 14N hyperfine sublevel correlation spectroscopy and density functional theory methods to investigate a bioinspired artificial photosynthetic reaction center that mimics the PCET process involving the YZ residue of PSII. Our results underscore the importance of proximal water molecules and charge delocalization on the electronic structure of the artificial reaction center. Structural factors are critical in the design of artificial photosynthetic systems Correlation between hyperfine couplings of the N atoms and electron spin density Spin density distribution affected by charge delocalization and explicit waters Spin density modulation by electronic coupling as observed with P680 and YZ in PSII
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Affiliation(s)
| | - Amgalanbaatar Baldansuren
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Vidmantas Kalendra
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Philip Charles
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Brian Mark
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - William Marshall
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Brian Molnar
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Thomas A Moore
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Ana L Moore
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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20
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Evaluation of new low-valent computational models for the oxygen-evolving complex of photosystem II. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Cox N, Pantazis DA, Lubitz W. Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data. Annu Rev Biochem 2020; 89:795-820. [DOI: 10.1146/annurev-biochem-011520-104801] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOxcomplex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.
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Affiliation(s)
- Nicholas Cox
- Research School of Chemistry, The Australian National University, Canberra ACT 2601, Australia
| | | | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim an der Ruhr, Germany
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22
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Shimada Y, Kitajima-Ihara T, Nagao R, Noguchi T. Role of the O4 Channel in Photosynthetic Water Oxidation as Revealed by Fourier Transform Infrared Difference and Time-Resolved Infrared Analysis of the D1-S169A Mutant. J Phys Chem B 2020; 124:1470-1480. [DOI: 10.1021/acs.jpcb.9b11946] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yuichiro Shimada
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomomi Kitajima-Ihara
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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23
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Takemoto H, Sugiura M, Noguchi T. Proton Release Process during the S2-to-S3 Transition of Photosynthetic Water Oxidation As Revealed by the pH Dependence of Kinetics Monitored by Time-Resolved Infrared Spectroscopy. Biochemistry 2019; 58:4276-4283. [DOI: 10.1021/acs.biochem.9b00680] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroshi Takemoto
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Miwa Sugiura
- Proteo-Science Research Center, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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24
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Ghosh I, Khan S, Banerjee G, Dziarski A, Vinyard DJ, Debus RJ, Brudvig GW. Insights into Proton-Transfer Pathways during Water Oxidation in Photosystem II. J Phys Chem B 2019; 123:8195-8202. [DOI: 10.1021/acs.jpcb.9b06244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Sahr Khan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alisha Dziarski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - David J. Vinyard
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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25
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Odella E, Wadsworth BL, Mora SJ, Goings JJ, Huynh MT, Gust D, Moore TA, Moore GF, Hammes-Schiffer S, Moore AL. Proton-Coupled Electron Transfer Drives Long-Range Proton Translocation in Bioinspired Systems. J Am Chem Soc 2019; 141:14057-14061. [DOI: 10.1021/jacs.9b06978] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Emmanuel Odella
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Brian L. Wadsworth
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - S. Jimena Mora
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Joshua J. Goings
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Mioy T. Huynh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Devens Gust
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas A. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Gary F. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana L. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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26
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Krewald V, Neese F, Pantazis DA. Implications of structural heterogeneity for the electronic structure of the final oxygen-evolving intermediate in photosystem II. J Inorg Biochem 2019; 199:110797. [PMID: 31404888 DOI: 10.1016/j.jinorgbio.2019.110797] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Heterogeneity in intermediate catalytic states of the oxygen-evolving complex (OEC) of Photosystem II is known from a wide range of experimental and theoretical data, but its potential implications for the mechanism of water oxidation remain unexplored. We delineate the consequences of structural heterogeneity for the final step of the catalytic cycle by tracing the evolution of three spectroscopically relevant and structurally distinct components of the last metastable S3 state to the transient O2-evolving S4 state of the OEC. Using quantum chemical calculations, we show that each S3 isomer leads to a different electronic structure formulation for the active S4 state. Crucially, in addition to previously hypothesized Mn(IV)-oxyl species, we establish for the first time, how a genuine Mn(V)-oxo can be obtained in the catalytically active S4 state: this takes the form of a five-coordinate and locally high-spin (SMn = 1) Mn(V) site. This formulation for the S4 state evolves naturally from a preceding S3-state structural intermediate that contains a quasi-trigonal-bipyramidal Mn(IV) ion. The results strongly suggest that water binding in the S3 state is not prerequisite for reaching the oxygen-evolving S4 state of the complex, supporting the notion that both substrates are preloaded at the beginning of the catalytic cycle. This scenario allows true four-electron metal-centered hole accumulation to precede OO bond formation and hence the latter can proceed via a genuine even-electron mechanism. This can occur as intramolecular nucleophilic coupling of two oxo units synchronously with the binding of a water substrate for the next catalytic cycle.
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Affiliation(s)
- Vera Krewald
- Theoretische Chemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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