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Kamada S, Nakajima Y, Shen JR. Structural insights into the action mechanisms of artificial electron acceptors in photosystem II. J Biol Chem 2023:104839. [PMID: 37209822 PMCID: PMC10300377 DOI: 10.1016/j.jbc.2023.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to QB, a plastoquinone (PQ) molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with similar molecular structures to PQ can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95-2.10 Å resolution. Our results show that all AEAs substitute for QB and are bound to the QB-binding site (QB site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the QB site, and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone binding site, designated the QD site, was discovered, which is located in the vicinity of QB site and close to QC site, a binding site reported previously. This QD site is expected to play a role as a channel or a storage site for quinones to be transported to the QB site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of QB in PSII, and also provide information for the design of more efficient electron acceptors.
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Affiliation(s)
- Shinji Kamada
- Faculty of Science, Okayama University, Okayama 700-8503, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8503, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8503, Japan.
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Sugo Y, Ishikita H. Proton-mediated photoprotection mechanism in photosystem II. FRONTIERS IN PLANT SCIENCE 2022; 13:934736. [PMID: 36161009 PMCID: PMC9490181 DOI: 10.3389/fpls.2022.934736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Photo-induced charge separation, which is terminated by electron transfer from the primary quinone QA to the secondary quinone QB, provides the driving force for O2 evolution in photosystem II (PSII). However, the backward charge recombination using the same electron-transfer pathway leads to the triplet chlorophyll formation, generating harmful singlet-oxygen species. Here, we investigated the molecular mechanism of proton-mediated QA ⋅- stabilization. Quantum mechanical/molecular mechanical (QM/MM) calculations show that in response to the loss of the bicarbonate ligand, a low-barrier H-bond forms between D2-His214 and QA ⋅-. The migration of the proton from D2-His214 toward QA ⋅- stabilizes QA ⋅-. The release of the bicarbonate ligand from the binding Fe2+ site is an energetically uphill process, whereas the bidentate-to-monodentate reorientation is almost isoenergetic. These suggest that the bicarbonate protonation and decomposition may be a basis of the mechanism of photoprotection via QA ⋅-/QAH⋅ stabilization, increasing the QA redox potential and activating a charge-recombination pathway that does not generate the harmful singlet oxygen.
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Affiliation(s)
- Yu Sugo
- Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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Kobayashi T, Shimada Y, Nagao R, Noguchi T. pH-Dependent Regulation of Electron Flow in Photosystem II by a Histidine Residue at the Stromal Surface. Biochemistry 2022; 61:1351-1362. [PMID: 35686693 DOI: 10.1021/acs.biochem.2c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In photosystem II (PSII), the secondary plastoquinone electron acceptor QB functions as a substrate that converts into plastoquinol upon its double reduction by electrons abstracted from water. It has been suggested that a histidine residue, D1-H252, which is located at the stromal surface near QB, is involved in the pH-dependent regulation of electron flow and proton transfer to QB. However, definitive evidence for the involvement of D1-H252 in the QB reactions has not been obtained yet. Here, we studied the roles of D1-H252 in PSII using a cyanobacterial mutant, in which D1-H252 was replaced with Ala. Delayed luminescence (DL) measurement upon a single flash showed a faster QB- decay at higher pH in the thylakoids from the wild-type strain due to the downshift of the redox potential of QB [Em(QB-/QB)]. This pH dependence of the QB- decay was lost in the D1-H252A mutant. The experimental Em(QB-/QB) changes were well reproduced by the density functional theory calculations for models with different protonation states of D1-H252 and with Ala replaced for H252. It was further shown that the period-four oscillation of the DL intensity by successive flashes was significantly diminished in the D1-H252A mutant, suggesting the inhibition of plastoquinone exchange at the QB pocket in this mutant. It is thus concluded that D1-H252 is a key amino acid residue that regulates electron flow in PSII by sensing pH in the stroma and stabilizes the QB binding site to facilitate the quinone exchange reaction.
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Affiliation(s)
- Tomoyuki Kobayashi
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuichiro Shimada
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Ryo Nagao
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Okayama 700-8530, Japan
| | - Takumi Noguchi
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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Boussac A, Sugiura M, Sellés J. Probing the proton release by Photosystem II in the S 1 to S 2 high-spin transition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148546. [PMID: 35337840 DOI: 10.1016/j.bbabio.2022.148546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The stoichiometry and kinetics of the proton release were investigated during each transition of the S-state cycle in Photosystem II (PSII) from Thermosynechococcus elongatus containing either a Mn4CaO5 (PSII/Ca) or a Mn4SrO5 (PSII/Sr) cluster. The measurements were done at pH 6.0 and pH 7.0 knowing that, in PSII/Ca at pH 6.0 and pH 7.0 and in PSII/Sr at pH 6.0, the flash-induced S2-state is in a low-spin configuration (S2LS) whereas in PSII/Sr at pH 7.0, the S2-state is in a high-spin configuration (S2HS) in half of the centers. Two measurements were done; the time-resolved flash dependent i) absorption of either bromocresol purple at pH 6.0 or neutral red at pH 7.0 and ii) electrochromism in the Soret band of PD1 at 440 nm. The fittings of the oscillations with a period of four indicate that one proton is released in the S1 to S2HS transition in PSII/Sr at pH 7.0. It has previously been suggested that the proton released in the S2LS to S3 transition would be released in a S2LSTyrZ• → S2HSTyrZ• transition before the electron transfer from the cluster to TyrZ• occurs. The release of a proton in the S1TyrZ• → S2HSTyrZ transition would logically imply that this proton release is missing in the S2HSTyrZ• to S3TyrZ transition. Instead, the proton release in the S1 to S2HS transition in PSII/Sr at pH 7.0 was mainly done at the expense of the proton release in the S3 to S0 and S0 to S1 transitions. However, at pH 7.0, the electrochromism of PD1 seems larger in PSII/Sr when compared to PSII/Ca in the S3 state. This points to the complex link between proton movements in and immediately around the Mn4 cluster and the mechanism leading to the release of protons into the bulk.
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Affiliation(s)
- Alain Boussac
- I(2)BC, UMR CNRS 9198, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | - Miwa Sugiura
- Proteo-Science Research Center, Department of Chemistry, Graduate School of Science and Technology, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Julien Sellés
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 and Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France
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Kato Y, Noguchi T. Redox properties and regulatory mechanism of the iron-quinone electron acceptor in photosystem II as revealed by FTIR spectroelectrochemistry. PHOTOSYNTHESIS RESEARCH 2022; 152:135-151. [PMID: 34985636 DOI: 10.1007/s11120-021-00894-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/24/2021] [Indexed: 05/09/2023]
Abstract
Photosystem II (PSII) performs oxidation of water and reduction of plastoquinone through light-induced electron transfer. Electron transfer reactions at individual redox cofactors are controlled by their redox potentials, and the forward and backward electron flows in PSII are regulated by tuning them. It is, thus, crucial to accurately estimate the redox potentials of the cofactors and their shifts by environmental changes to understand the regulatory mechanisms in PSII. Fourier-transform infrared (FTIR) spectroelectrochemistry combined with a light-induced difference technique is a powerful method to investigate the mechanisms of the redox reactions in PSII. In this review, we introduce the methodology and the application of this method in the studies of the iron-quinone complex, which consists of two plastoquinone molecules, QA and QB, and the non-heme iron, on the electron-acceptor side of PSII. It is shown that FTIR spectroelectrochemistry is a useful method not only for estimating the redox potentials but also for detecting the reactions of nearby amino-acid residues coupled with the redox reactions.
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Affiliation(s)
- Yuki Kato
- 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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Mechanism of the formation of proton transfer pathways in photosynthetic reaction centers. Proc Natl Acad Sci U S A 2021; 118:2103203118. [PMID: 34301911 PMCID: PMC8325351 DOI: 10.1073/pnas.2103203118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structures of photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II show large structural similarity. However, the proposed mechanisms of proton transfer toward the terminal electron acceptor quinone (QB) are not consistent. In particular, not His-L190, which is an H-bond partner of QB, but rather Glu-L212, which is ∼6 Å away from QB, was assumed to be the direct proton donor for QB. We demonstrate that the H-bond between His-L190 and QB is a low-barrier H-bond, which facilitates proton transfer from singly protonated His-L190 to QB. Furthermore, Glu-L212 is not a direct H-bond donor for QB. However, it facilitates proton transfer toward deprotonated His-L190 via water molecules after QBH2 forms and leaves the PbRC. In photosynthetic reaction centers from purple bacteria (PbRCs) from Rhodobacter sphaeroides, the secondary quinone QB accepts two electrons and two protons via electron-coupled proton transfer (PT). Here, we identify PT pathways that proceed toward the QB binding site, using a quantum mechanical/molecular mechanical approach. As the first electron is transferred to QB, the formation of the Grotthuss-like pre-PT H-bond network is observed along Asp-L213, Ser-L223, and the distal QB carbonyl O site. As the second electron is transferred, the formation of a low-barrier H-bond is observed between His-L190 at Fe and the proximal QB carbonyl O site, which facilitates the second PT. As QBH2 leaves PbRC, a chain of water molecules connects protonated Glu-L212 and deprotonated His-L190 forms, which serves as a pathway for the His-L190 reprotonation. The findings of the second pathway, which does not involve Glu-L212, and the third pathway, which proceeds from Glu-L212 to His-L190, provide a mechanism for PT commonly used among PbRCs.
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Kato Y, Watanabe H, Noguchi T. ATR-FTIR Spectroelectrochemical Study on the Mechanism of the pH Dependence of the Redox Potential of the Non-Heme Iron in Photosystem II. Biochemistry 2021; 60:2170-2178. [PMID: 34181388 DOI: 10.1021/acs.biochem.1c00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The non-heme iron that bridges the two plastoquinone electron acceptors, QA and QB, in photosystem II (PSII) is known to have a redox potential (Em) of ∼+400 mV with a pH dependence of ∼-60 mV/pH. However, titratable amino acid residues that are coupled to the redox reaction of the non-heme ion and responsible for its pH dependence remain unidentified. In this study, to clarify the mechanism of the pH dependent change of Em(Fe2+/Fe3+), we investigated the protonation structures of amino acid residues correlated with the pH-induced Em(Fe2+/Fe3+) changes using Fourier transform infrared (FTIR) spectroelectrochemistry combined with the attenuated total reflection (ATR) and light-induced difference techniques. Flash-induced Fe2+/Fe3+ ATR-FTIR difference spectra obtained at different electrode potentials in the pH range of 5.0-8.5 showed a linear pH dependence of Em(Fe2+/Fe3+) with a slope of -52 mV/pH close to the theoretical value at 10 °C, the measurement temperature. The spectral features revealed that D1-H215, a ligand to the non-heme iron interacting with QB, was deprotonated to an imidazolate anion at higher pH with a pKa of ∼5.6 in the Fe3+ state, while carboxylate groups from Glu/Asp residues present on the stromal side of PSII were protonated at lower pH with a pKa of ∼5.7 in the Fe2+ state. It is thus concluded that the deprotonation/protonation reactions of D1-H215 and Glu/Asp residues located near the non-heme iron cause the pH-dependent changes in Em(Fe2+/Fe3+) at higher and lower pH regions, respectively, realizing a linear pH dependence over a wide pH range.
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Affiliation(s)
- Yuki Kato
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroki Watanabe
- 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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Sato A, Nakano Y, Nakamura S, Noguchi T. Rapid-Scan Time-Resolved ATR-FTIR Study on the Photoassembly of the Water-Oxidizing Mn4CaO5 Cluster in Photosystem II. J Phys Chem B 2021; 125:4031-4045. [DOI: 10.1021/acs.jpcb.1c01624] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Akihiko Sato
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuki Nakano
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shin Nakamura
- 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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