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Liu J, Yang KR, Long Z, Armstrong WH, Brudvig GW, Batista VS. Water Ligands Regulate the Redox Leveling Mechanism of the Oxygen-Evolving Complex of the Photosystem II. J Am Chem Soc 2024; 146:15986-15999. [PMID: 38833517 DOI: 10.1021/jacs.4c02926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Understanding how water ligands regulate the conformational changes and functionality of the oxygen-evolving complex (OEC) in photosystem II (PSII) throughout the catalytic cycle of oxygen evolution remains a highly intriguing and unresolved challenge. In this study, we investigate the effect of water insertion (WI) on the redox state of the OEC by using the molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) hybrid methods. We find that water binding significantly reduces the free energy change for proton-coupled electron transfer (PCET) from Mn to YZ•, underscoring the important regulatory role of water binding, which is essential for enabling the OEC redox-leveling mechanism along the catalytic cycle. We propose a water binding mechanism in which WI is thermodynamically favored by the closed-cubane form of the OEC, with water delivery mediated by Ca2+ ligand exchange. Isomerization from the closed- to open-cubane conformation at three post-WI states highlights the importance of the location of the MnIII center in the OEC and the orientation of its Jahn-Teller axis to conformational changes of the OEC, which might be critical for the formation of the O-O bond. These findings reveal a complex interplay between conformational changes in the OEC and the ligand environment during the activation of the OEC by YZ•. Analogous regulatory effects due to water ligand binding are expected to be important for a wide range of catalysts activated by redox state transitions in aqueous environments.
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Affiliation(s)
- Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ke R Yang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhuoran Long
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - William H Armstrong
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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2
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Zhu Q, Yang Y, Xiao Y, Han W, Li X, Wang W, Kuang T, Shen JR, Han G. Effects of mutations of D1-R323, D1-N322, D1-D319, D1-H304 on the functioning of photosystem II in Thermosynechococcus vulcanus. PHOTOSYNTHESIS RESEARCH 2022; 152:193-206. [PMID: 35503495 DOI: 10.1007/s11120-022-00920-z] [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: 01/07/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Photosystem II (PSII) has a number of hydrogen-bonding networks connecting the manganese cluster with the lumenal bulk solution. The structure of PSII from Thermosynechococcus vulcanus (T. vulcanus) showed that D1-R323, D1-N322, D1-D319 and D1-H304 are involved in one of these hydrogen-bonding networks located in the interfaces between the D1, CP43 and PsbV subunits. In order to investigate the functions of these residues in PSII, we generated seven site-directed mutants D1-R323A, D1-R323E, D1-N322R, D1-D319L, D1-D319R, D1-D319Y and D1-H304D of T. vulcanus and examined the effects of these mutations on the growth and functions of the oxygen-evolving complex. The photoautotrophic growth rates of these mutants were similar to that of the wild type, whereas the oxygen-evolving activities of the mutant cells were decreased differently to 63-91% of that of the wild type at pH 6.5. The mutant cells showed a higher relative activity at higher pH region than the wild type cells, suggesting that higher pH facilitated proton egress in the mutants. In addition, oxygen evolution of thylakoid membranes isolated from these mutants showed an apparent decrease compared to that of the cells. This is due to the loss of PsbU during purification of the thylakoid membranes. Moreover, PsbV was also lost in the PSII core complexes purified from the mutants. Taken together, D1-R323, D1-N322, D1-D319 and D1-H304 are vital for the optimal function of oxygen evolution and functional binding of extrinsic proteins to PSII core, and may be involved in the proton egress pathway mediated by YZ.
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Affiliation(s)
- 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
| | - 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
| | - Wenhui Han
- 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
| | - Xingyue Li
- 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
| | - 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.
- Institute for 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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3
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Kalendra V, Reiss KM, Banerjee G, Ghosh I, Baldansuren A, Batista VS, Brudvig GW, Lakshmi KV. Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria. Faraday Discuss 2022; 234:195-213. [PMID: 35147155 DOI: 10.1039/d1fd00094b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn4Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S0-S4). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this study, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S2 state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the "narrow" channel is altered in D1-N87A PSII, allowing for the binding of deprotonated 13C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S2 state. This has important implications on the mechanistic models for water oxidation in PSII.
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Affiliation(s)
- Vidmantas Kalendra
- Department of Chemistry and Chemical Biology, The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA.
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA.
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA.
| | - Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA.
| | - Amgalanbaatar Baldansuren
- Department of Chemistry and Chemical Biology, The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA.
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA.
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520, USA.
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology, The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA.
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4
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Debus RJ. Alteration of the O 2-Producing Mn 4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand. Biochemistry 2021; 60:3841-3855. [PMID: 34898175 DOI: 10.1021/acs.biochem.1c00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The O2-evolving Mn4Ca cluster in photosystem II (PSII) is arranged as a distorted Mn3Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn4Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn4Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn4Ca cluster in the dark-stable S1 state so that a high-spin form of the S2 state is produced during the S1-to-S2 transition instead of the low-spin form that gives rise to the S2 state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn4Ca cluster without substantially eliminating O2 evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn4Ca cluster in the mechanism of O2 formation.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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5
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Kaur D, Zhang Y, Reiss KM, Mandal M, Brudvig GW, Batista VS, Gunner MR. Proton exit pathways surrounding the oxygen evolving complex of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148446. [PMID: 33964279 DOI: 10.1016/j.bbabio.2021.148446] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022]
Abstract
Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, extend from the OEC towards the aqueous surface more than 15 Å away. However, the role of each pathway in the transport in and out of the OEC is yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths. Hydrogen bond network analysis shows that near the OEC the waters are highly interconnected with similar free energy for hydronium at all locations. The paths diverge as they move towards the lumen. The water chain in the broad channel is better connected than in the narrow and large channels, where disruptions in the network are observed approximately 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel. Thus, a proton released from any location on the OEC can access all paths, but the likely exit to the lumen passes through PsbO via the broad channel.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Manoj Mandal
- Department of Physics, City College of New York, NY 10031, United States
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States.
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6
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Li H, Nakajima Y, Nomura T, Sugahara M, Yonekura S, Chan SK, Nakane T, Yamane T, Umena Y, Suzuki M, Masuda T, Motomura T, Naitow H, Matsuura Y, Kimura T, Tono K, Owada S, Joti Y, Tanaka R, Nango E, Akita F, Kubo M, Iwata S, Shen JR, Suga M. Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography. IUCRJ 2021; 8:431-443. [PMID: 33953929 PMCID: PMC8086164 DOI: 10.1107/s2052252521002177] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/24/2021] [Indexed: 05/21/2023]
Abstract
Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.
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Affiliation(s)
- Hongjie Li
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shinichiro Yonekura
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Siu Kit Chan
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Yamane
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Yasufumi Umena
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Taiki Motomura
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, -1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
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7
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Wang L, Wan B, Lai S, Weng L, Liu H, Wang H. Light‐Induced Electron Transfer in Manganese(V)–Oxo Corroles. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202000272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Li‐Li Wang
- School of Physics Sun Yat-Sen University 510275 Guangzhou P. R. China
| | - Bei Wan
- Department of Chemistry South China University of Technology 510641 Guangzhou P. R. China
| | - Shu‐Hui Lai
- Department of Chemistry South China University of Technology 510641 Guangzhou P. R. China
| | - Lin‐Fang Weng
- School of Physics Sun Yat-Sen University 510275 Guangzhou P. R. China
| | - Hai‐Yang Liu
- Department of Chemistry South China University of Technology 510641 Guangzhou P. R. China
| | - Hui Wang
- School of Physics Sun Yat-Sen University 510275 Guangzhou P. R. China
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8
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Sugiura M, Taniguchi T, Tango N, Nakamura M, Sellés J, Boussac A. Probing the role of arginine 323 of the D1 protein in photosystem II function. PHYSIOLOGIA PLANTARUM 2021; 171:183-199. [PMID: 32359083 DOI: 10.1111/ppl.13115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
The Mn4 CaO5 cluster of photosystem II (PSII) advances sequentially through five oxidation states (S0 to S4 ). Under the enzyme cycle, two water molecules are oxidized, O2 is generated and four protons are released into the lumen. Umena et al. (2011) have proposed that, with other charged amino acids, the R323 residue of the D1 protein could contribute to regulate a proton egress pathway from the Mn4 CaO5 cluster and TyrZ via a proton channel identified from the 3D structure. To test this suggestion, a PsbA3/R323E site-directed mutant has been constructed and the properties of its PSII have been compared to those of the PsbA3-PSII by using EPR spectroscopy, polarography, thermoluminescence and time-resolved UV-visible absorption spectroscopy. Neither the oscillations with a period four nor the kinetics and S-state-dependent stoichiometry of the proton release were affected. However, several differences have been found: (1) the P680 + decay in the hundreds of ns time domain was much slower in the mutant, (2) the S2 QA - /DCMU and S3 QA - /DCMU radiative charge recombination occurred at higher temperatures and (3) the S0 TyrZ • , S1 TyrZ • , S2 TyrZ • split EPR signals induced at 4.2 K by visible light from the S0 TyrZ , S1 TyrZ , S2 TyrZ , respectively, and the (S2 TyrZ • )' induced by NIR illumination at 4.2 K of the S3 TyrZ state differed. It is proposed that the R323 residue of the D1 protein interacts with TyrZ likely via the H-bond network previously proposed to be a proton channel. Therefore, rather than participating in the egress of protons to the lumen, this channel could be involved in the relaxations of the H-bonds around TyrZ by interacting with the bulk, thus tuning the driving force required for TyrZ oxidation.
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Affiliation(s)
- Miwa Sugiura
- Proteo-Science Research Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Tomonori Taniguchi
- Department of Chemistry, Graduate School of Science and Technology, Ehime University, Matsuyama, 790-8577, Japan
| | - Nanami Tango
- Department of Chemistry, Graduate School of Science and Technology, Ehime University, Matsuyama, 790-8577, Japan
| | - Makoto Nakamura
- Department of Chemistry, Graduate School of Science and Technology, Ehime University, Matsuyama, 790-8577, Japan
| | - Julien Sellés
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 and Sorbonne Université, Paris, 75005, France
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9
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Ghosh I, Banerjee G, Reiss K, Kim CJ, Debus RJ, Batista VS, Brudvig GW. D1-S169A substitution of photosystem II reveals a novel S 2-state structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148301. [PMID: 32860756 DOI: 10.1016/j.bbabio.2020.148301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 10/23/2022]
Abstract
In photosystem II (PSII), photosynthetic water oxidation occurs at the O2-evolving complex (OEC), a tetramanganese-calcium cluster that cycles through light-induced redox intermediates (S0-S4) to produce oxygen from two substrate water molecules. The OEC is surrounded by a hydrogen-bonded network of amino-acid residues that plays a crucial role in proton transfer and substrate water delivery. Previously, we found that D1-S169 was crucial for water oxidation and its mutation to alanine perturbed the hydrogen-bonding network. In this study, we demonstrate that the activation energy for the S2 to S1 transition of D1-S169A PSII is higher than wild-type PSII with a ~1.7-2.7× slower rate of charge recombination with QA- relative to wild-type PSII. Arrhenius analysis of the decay kinetics shows an Ea of 5.87 ± 1.15 kcal mol-1 for decay back to the S1 state, compared to 0.80 ± 0.13 kcal mol-1 for the wild-type S2 state. In addition, we find that ammonia does not affect the S2-state EPR signal, indicating that ammonia does not bind to the Mn cluster in D1-S169A PSII. Finally, a QM/MM analysis indicates that an additional water molecule binds to the Mn4 ion in place of an oxo ligand O5 in the S2 state of D1-S169A PSII. The altered S2 state of D1-S169A PSII provides insight into the S2➔S3 state transition.
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Affiliation(s)
- Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Christopher J Kim
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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10
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Kim CJ, Debus RJ. Roles of D1-Glu189 and D1-Glu329 in O2 Formation by the Water-Splitting Mn4Ca Cluster in Photosystem II. Biochemistry 2020; 59:3902-3917. [DOI: 10.1021/acs.biochem.0c00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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11
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Shimada Y, Kitajima-Ihara T, Nagao R, Noguchi T. Role of the O4 Channel in Photosynthetic Water Oxidation as Revealed by Fourier Transform Infrared Difference and Time-Resolved Infrared Analysis of the D1-S169A Mutant. J Phys Chem B 2020; 124:1470-1480. [DOI: 10.1021/acs.jpcb.9b11946] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yuichiro Shimada
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomomi Kitajima-Ihara
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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12
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Fourier transform infrared and mass spectrometry analyses of a site-directed mutant of D1-Asp170 as a ligand to the water-oxidizing Mn4CaO5 cluster in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148086. [DOI: 10.1016/j.bbabio.2019.148086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/09/2019] [Accepted: 09/15/2019] [Indexed: 01/02/2023]
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13
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Study of the role of Mg 2+ in dsRNA processing mechanism by bacterial RNase III through QM/MM simulations. J Biol Inorg Chem 2019; 25:89-98. [PMID: 31754801 DOI: 10.1007/s00775-019-01741-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
The ribonuclease III (RNase III) cleaves dsRNA in specific positions generating mature RNAs. RNase III enzymes play important roles in RNA processing, post-transcriptional gene expression, and defense against viral infection. The enzyme's active site contains Mg2+ ions bound by a network of acidic residues and water molecules, but there is a lack of information about their specific roles. In this work, multiple steered molecular dynamics simulations at QM/MM level were performed to explore the hydrolysis reaction carried out by the enzyme. Free energy profiles modifying the features of the active site are obtained and the role of Mg2+ ions, the solvent molecules and the residues of the active site are discussed in detail. Our results show that Mg2+ ions carry out different roles in the hydrolysis process positioning the substrate for the attack from a coordinated nucleophile and activating it to perform hydrolysis reaction, cleaving the dsRNA backbone in a SN2 substitution. In addition, water molecules present in the active site lower the energy barrier of the process. RNase III hydrolyzes dsRNA to generate mature RNAs. For this purpose, its active site contains Mg2+ which has an important role during the reaction. Results show that the Mg2+ activates the solvent molecule that produces the nucleophilic attack and the surrounding waters contribute significantly to the hydrolysis process.
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14
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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: 3.0] [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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15
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Banerjee G, Ghosh I, Kim CJ, Debus RJ, Brudvig GW. Bicarbonate rescues damaged proton-transfer pathway in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:611-617. [DOI: 10.1016/j.bbabio.2019.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 01/04/2023]
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16
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Kim CJ, Debus RJ. One of the Substrate Waters for O2 Formation in Photosystem II Is Provided by the Water-Splitting Mn4CaO5 Cluster’s Ca2+ Ion. Biochemistry 2019; 58:3185-3192. [DOI: 10.1021/acs.biochem.9b00418] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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