1
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Hussein R, Graça A, Forsman J, Aydin AO, Hall M, Gaetcke J, Chernev P, Wendler P, Dobbek H, Messinger J, Zouni A, Schröder WP. Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II. Science 2024; 384:1349-1355. [PMID: 38900892 DOI: 10.1126/science.adn6541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.
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Affiliation(s)
- Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - André Graça
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Jack Forsman
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Michael Hall
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - Julia Gaetcke
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, D 14476, Potsdam-Golm, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden
| | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Wolfgang P Schröder
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden
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2
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Nishikawa G, Saito K, Ishikita H. Modulation of Electron Transfer Branches by Atrazine and Triazine Herbicides in Photosynthetic Reaction Centers. Biochemistry 2024; 63:1206-1213. [PMID: 38587893 PMCID: PMC11080998 DOI: 10.1021/acs.biochem.4c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/15/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024]
Abstract
Quinone analogue molecules, functioning as herbicides, bind to the secondary quinone site, QB, in type-II photosynthetic reaction centers, including those from purple bacteria (PbRC). Here, we investigated the impact of herbicide binding on electron transfer branches, using herbicide-bound PbRC crystal structures and employing the linear Poisson-Boltzmann equation. In contrast to urea and phenolic herbicides [Fufezan, C. Biochemistry 2005, 44, 12780-12789], binding of atrazine and triazine did not cause significant changes in the redox-potential (Em) values of the primary quinone (QA) in these crystal structures. However, a slight Em difference at the bacteriopheophytin in the electron transfer inactive branch (HM) was observed between the S(-)- and R(+)-triazine-bound PbRC structures. This discrepancy is linked to variations in the protonation pattern of the tightly coupled Glu-L212 and Glu-H177 pairs, crucial components of the proton uptake pathway in native PbRC. These findings suggest the existence of a QB-mediated link between the electron transfer inactive HM and the proton uptake pathway in PbRCs.
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Affiliation(s)
- Gai Nishikawa
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguru-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguru-ku, Tokyo 153-8904, Japan
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3
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Sheridan KJ, Eaton-Rye JJ, Summerfield TC. Mutagenesis of Ile184 in the cd-loop of the photosystem II D1 protein modifies acceptor-side function via spontaneous mutation of D1-His252 in Synechocystis sp. PCC 6803. Biochem Biophys Res Commun 2024; 702:149595. [PMID: 38340653 DOI: 10.1016/j.bbrc.2024.149595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
The Photosystem II water-plastoquinone oxidoreductase is a multi-subunit complex which catalyses the light-driven oxidation of water to molecular oxygen in oxygenic photosynthesis. The D1 reaction centre protein exists in multiple forms in cyanobacteria, including D1FR which is expressed under far-red light. We investigated the role of Phe184 that is found in the lumenal cd-loop of D1FR but is typically an isoleucine in other D1 isoforms. The I184F mutant in Synechocystis sp. PCC 6803 was similar to the control strain but accumulated a spontaneous mutation that introduced a Gln residue in place of His252 located on the opposite side of the thylakoid membrane. His252 participates in the protonation of the secondary plastoquinone electron acceptor QB. The I184F:H252Q double mutant exhibited reduced high-light-induced photodamage and an altered QB-binding site that impaired herbicide binding. Additionally, the H252Q mutant had a large increase in the variable fluorescence yield although the number of photochemically active PS II centres was unchanged. In the I184F:H252Q mutant the extent of the increased fluorescence yield decreased. Our data indicates substitution of Ile184 to Phe modulates PS II-specific variable fluorescence in cells with the His252 to Gln substitution by modifying the QB-binding site.
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Affiliation(s)
- Kevin J Sheridan
- Department of Botany, University of Otago, Dunedin, 9016, New Zealand; Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Julian J Eaton-Rye
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
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4
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Gates C, Williams JM, Ananyev G, Dismukes GC. How chloride functions to enable proton conduction in photosynthetic water oxidation: Time-resolved kinetics of intermediates (S-states) in vivo and bromide substitution. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148998. [PMID: 37499962 DOI: 10.1016/j.bbabio.2023.148998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Chloride (Cl-) is essential for O2 evolution during photosynthetic water oxidation. Two chlorides near the water-oxidizing complex (WOC) in Photosystem II (PSII) structures from Thermosynechococcus elongatus (and T. vulcanus) have been postulated to transfer protons generated from water oxidation. We monitored four criteria: primary charge separation flash yield (P* → P+QA-), rates of water oxidation steps (S-states), rate of proton evolution, and flash O2 yield oscillations by measuring chlorophyll variable fluorescence (P* quenching), pH-sensitive dye changes, and oximetry. Br-substitution slows and destabilizes cellular growth, resulting from lower light-saturated O2 evolution rate (-20 %) and proton release (-36 % ΔpH gradient). The latter implies less ATP production. In Br- cultures, protonogenic S-state transitions (S2 → S3 → S0') slow with increasing light intensity and during O2/water exchange (S0' → S0 → S1), while the non-protonogenic S1 → S2 transition is kinetically unaffected. As flash rate increases in Cl- cultures, both rate and extent of acidification of the lumen increase, while charge recombination is suppressed relative to Br-. The Cl- advantage in rapid proton escape from the WOC to lumen is attributed to correlated ion-pair movement of H3O+Cl- in dry water channels vs. separated Br- and H+ ion movement through different regions (>200-fold difference in Bronsted acidities). By contrast, at low flash rates a previously unreported reversal occurs that favors Br- cultures for both proton evolution and less PSII charge recombination. In Br- cultures, slower proton transfer rate is attributed to stronger ion-pairing of Br- with AA residues lining the water channels. Both anions charge-neutralize protons and shepherd them to the lumen using dry aqueous channels.
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Affiliation(s)
- Colin Gates
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Computational Biology and Molecular Biophysics, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Biochemistry, Loyola University Chicago, IL 60660, USA
| | - Jonah M Williams
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Gennady Ananyev
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - G Charles Dismukes
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, NJ 08854, USA.
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5
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Manoj KM, Gideon DA, Parashar A, Nirusimhan V, Annadurai P, Jacob VD, Manekkathodi A. Validating the predictions of murburn model for oxygenic photosynthesis: Analyses of ligand-binding to protein complexes and cross-system comparisons. J Biomol Struct Dyn 2022; 40:11024-11056. [PMID: 34328391 DOI: 10.1080/07391102.2021.1953607] [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] [Indexed: 12/23/2022]
Abstract
In this second half of our treatise on oxygenic photosynthesis, we provide support for the murburn model of the light reaction of photosynthesis and ratify key predictions made in the first part. Molecular docking and visualization of various ligands of quinones/quinols (and their derivatives) with PS II/Cytochrome b6f complexes did not support chartered 2e-transport role of quinols. A broad variety of herbicides did not show any affinity/binding-based rationales for inhibition of photosynthesis. We substantiate the proposal that disubstituted phenolics (perceived as protonophores/uncouplers or affinity-based inhibitors in the classical purview) serve as interfacial modulators of diffusible reactive (oxygen) species or DR(O)S. The DRS-based murburn model is evidenced by the identification of multiple ADP-binding sites on the extra-membraneous projection of protein complexes and structure/distribution of the photo/redox catalysts. With a panoramic comparison of the redox metabolic machinery across diverse organellar/cellular systems, we highlight the ubiquitous one-electron murburn facets (cofactors of porphyrin, flavin, FeS, other metal centers and photo/redox active pigments) that enable a facile harnessing of the utility of DRS. In the summative analyses, it is demonstrated that the murburn model of light reaction explains the structures of membrane supercomplexes recently observed in thylakoids and also accounts for several photodynamic experimental observations and evolutionary considerations. In toto, the work provides a new orientation and impetus to photosynthesis research. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Daniel Andrew Gideon
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Abhinav Parashar
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vijay Nirusimhan
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Pushparaj Annadurai
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vivian David Jacob
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Afsal Manekkathodi
- RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India
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6
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Sugo Y, Tamura H, Ishikita H. Electron Transfer Route between Quinones in Type-II Reaction Centers. J Phys Chem B 2022; 126:9549-9558. [PMID: 36374126 PMCID: PMC9707520 DOI: 10.1021/acs.jpcb.2c05713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/28/2022] [Indexed: 11/16/2022]
Abstract
In photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II (PSII), the photoinduced charge separation is terminated by an electron transfer between the primary (QA) and secondary (QB) quinones. Here, we investigate the electron transfer route, calculating the superexchange coupling (HQA-QB) for electron transfer from QA to QB in the protein environment. HQA-QB is significantly larger in PbRC than in PSII. In superexchange electron tunneling, the electron transfer via unoccupied molecular orbitals of the nonheme Fe complex (QA → Fe → QB) is pronounced in PbRC, whereas the electron transfer via occupied molecular orbitals (Fe → QB followed by QA → Fe) is pronounced in PSII. The significantly large HQA-QB is caused by a water molecule that donates the H-bond to the ligand Glu-M234 in PbRC. The corresponding water molecule is absent in PSII due to the existence of D1-Tyr246. HQA-QB increases in response to the Ser-L223···QB H-bond formation caused by an extension of the H-bond network, which facilitates charge delocalization over the QB site. This explains the observed discrepancy in the QA-to-QB electron transfer between PbRC and PSII, despite their structural similarity.
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Affiliation(s)
- Yu Sugo
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
| | - Hiroyuki Tamura
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
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7
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Nakajima Y, Ugai-Amo N, Tone N, Nakagawa A, Iwai M, Ikeuchi M, Sugiura M, Suga M, Shen JR. Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit. J Biol Chem 2022; 298:102668. [PMID: 36334624 PMCID: PMC9709244 DOI: 10.1016/j.jbc.2022.102668] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/07/2022] Open
Abstract
Three psbA genes (psbA1, psbA2, and psbA3) encoding the D1 subunit of photosystem II (PSII) are present in the thermophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA2 or psbA3), were crystallized, and we analyzed their structures at resolutions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (PheoD1) and D1-130 became stronger in PsbA2- and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of PheoD1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in PheoD1 due to the change of D1-Y147F, which may explain the decrease in stability of PheoD1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S2 in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near QB disappeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound QB with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high QB exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.
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Affiliation(s)
- Yoshiki Nakajima
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
| | - Natsumi Ugai-Amo
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Naoki Tone
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Akiko Nakagawa
- Proteo-Science Research Center, Ehime University, Matsuyama, Japan
| | - Masako Iwai
- Graduate School and College of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Masahiko Ikeuchi
- Graduate School and College of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Miwa Sugiura
- Proteo-Science Research Center, Ehime University, Matsuyama, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan,Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan,For correspondence: Michihiro Suga; Jian-Ren Shen
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan,Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan,For correspondence: Michihiro Suga; Jian-Ren Shen
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8
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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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9
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Sugo Y, Saito K, Ishikita H. Conformational Changes and H-Bond Rearrangements during Quinone Release in Photosystem II. Biochemistry 2022; 61:1836-1843. [PMID: 35914244 PMCID: PMC9454826 DOI: 10.1021/acs.biochem.2c00324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In photosystem II (PSII) and photosynthetic reaction centers from purple bacteria (PbRC), the electron released from the electronically excited chlorophyll is transferred to the terminal electron acceptor quinone, QB. QB accepts two electrons and two protons before leaving the protein. We investigated the molecular mechanism of quinone exchange in PSII, conducting molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations. MD simulations suggest that the release of QB leads to the transformation of the short helix (D1-Phe260 to D1-Ser264), which is adjacent to the stromal helix de (D1-Asn247 to D1-Ile259), into a loop and to the formation of a water-intake channel. Water molecules enter the QB binding pocket via the channel and form an H-bond network. QM/MM calculations indicate that the H-bond network serves as a proton-transfer pathway for the reprotonation of D1-His215, the proton donor during QBH-/QBH2 conversion. Together with the absence of the corresponding short helix but the presence of Glu-L212 in PbRC, it seems likely that the two type-II reaction centers undergo quinone exchange via different mechanisms.
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Affiliation(s)
- Yu Sugo
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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10
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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: 2] [Impact Index Per Article: 1.0] [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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11
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Tamura H, Saito K, Ishikita H. Long-Range Electron Tunneling from the Primary to Secondary Quinones in Photosystem II Enhanced by Hydrogen Bonds with a Nonheme Fe Complex. J Phys Chem B 2021; 125:13460-13466. [PMID: 34875835 DOI: 10.1021/acs.jpcb.1c09538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms governing the long-range electron tunneling from the primary (QA) to secondary (QB) quinones in photosystem II are clarified by analyzing superexchange pathways through a nonheme Fe complex, using a quantum mechanics/molecular mechanics/polarizable continuum model approach. The electron tunneling rate is evaluated using the Marcus-Levich-Jortner theory considering electronic coupling, energy difference, and Franck-Condon factor. The superexchange QA → QB electron tunneling is enhanced by hybridized σ/σ* orbitals of histidines (D2-His214 and D1-His215) via penetration of the wave function into hydrogen bonds with both QA and QB. Despite a large energy gap to the intermediate states, the contributions of the histidine σ/σ* orbitals to the superexchange coupling are larger than those of π/π* orbitals. Fe2+ is not an essential component for the QA → QB electron tunneling because hybridized histidine molecular orbitals can be coupled with both QA and QB simultaneously in the absence of Fe d orbitals.
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Affiliation(s)
- Hiroyuki Tamura
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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12
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Wang D, Tan J, Zhu H, Mei Y, Liu X. Biomedical Implants with Charge-Transfer Monitoring and Regulating Abilities. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004393. [PMID: 34166584 PMCID: PMC8373130 DOI: 10.1002/advs.202004393] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/12/2021] [Indexed: 05/06/2023]
Abstract
Transmembrane charge (ion/electron) transfer is essential for maintaining cellular homeostasis and is involved in many biological processes, from protein synthesis to embryonic development in organisms. Designing implant devices that can detect or regulate cellular transmembrane charge transfer is expected to sense and modulate the behaviors of host cells and tissues. Thus, charge transfer can be regarded as a bridge connecting living systems and human-made implantable devices. This review describes the mode and mechanism of charge transfer between organisms and nonliving materials, and summarizes the strategies to endow implants with charge-transfer regulating or monitoring abilities. Furthermore, three major charge-transfer controlling systems, including wired, self-activated, and stimuli-responsive biomedical implants, as well as the design principles and pivotal materials are systematically elaborated. The clinical challenges and the prospects for future development of these implant devices are also discussed.
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Affiliation(s)
- Donghui Wang
- State Key Laboratory of High Performance Ceramics and Superfine MicrostructureShanghai Institutes of CeramicsChinese Academy of SciencesShanghai200050China
- School of Materials Science and EngineeringHebei University of TechnologyTianjin300130China
| | - Ji Tan
- State Key Laboratory of High Performance Ceramics and Superfine MicrostructureShanghai Institutes of CeramicsChinese Academy of SciencesShanghai200050China
| | - Hongqin Zhu
- State Key Laboratory of High Performance Ceramics and Superfine MicrostructureShanghai Institutes of CeramicsChinese Academy of SciencesShanghai200050China
- Department of Materials ScienceFudan UniversityShanghai200433China
| | - Yongfeng Mei
- Department of Materials ScienceFudan UniversityShanghai200433China
| | - Xuanyong Liu
- State Key Laboratory of High Performance Ceramics and Superfine MicrostructureShanghai Institutes of CeramicsChinese Academy of SciencesShanghai200050China
- School of Chemistry and Materials ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
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13
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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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14
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Kimura M, Kato Y, Noguchi T. Protonation State of a Key Histidine Ligand in the Iron–Quinone Complex of Photosystem II as Revealed by Light-Induced ATR-FTIR Spectroscopy. Biochemistry 2020; 59:4336-4343. [DOI: 10.1021/acs.biochem.0c00810] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masakazu Kimura
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - 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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15
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Kuroda H, Kawashima K, Ueda K, Ikeda T, Saito K, Ninomiya R, Hida C, Takahashi Y, Ishikita H. Proton transfer pathway from the oxygen-evolving complex in photosystem II substantiated by extensive mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148329. [PMID: 33069681 DOI: 10.1016/j.bbabio.2020.148329] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
We report a structure-based biological approach to identify the proton-transfer pathway in photosystem II. First, molecular dynamics (MD) simulations were conducted to analyze the H-bond network that may serve as a Grotthuss-like proton conduit. MD simulations show that D1-Asp61, the H-bond acceptor of H2O at the Mn4CaO5 cluster (W1), forms an H-bond via one water molecule with D1-Glu65 but not with D2-Glu312. Then, D1-Asp61, D1-Glu65, D2-Glu312, and the adjacent residues, D1-Arg334, D2-Glu302, and D2-Glu323, were thoroughly mutated to the other 19 residues, i.e., 114 Chlamydomonas chloroplast mutant cells were generated. Mutation of D1-Asp61 was most crucial. Only the D61E and D61C cells grew photoautotrophically and exhibit O2-evolving activity. Mutations of D2-Glu312 were less crucial to photosynthetic growth than mutations of D1-Glu65. Quantum mechanical/molecular mechanical calculations indicated that in the PSII crystal structure, the proton is predominantly localized at D1-Glu65 along the H-bond with D2-Glu312, i.e., pKa(D1-Glu65) > pKa(D2-Glu312). The potential-energy profile shows that the release of the proton from D1-Glu65 leads to the formation of the two short H-bonds between D1-Asp61 and D1-Glu65, which facilitates downhill proton transfer along the Grotthuss-like proton conduit in the S2 to S3 transition. It seems possible that D1-Glu65 is involved in the dominant pathway that proceeds from W1 via D1-Asp61 toward the thylakoid lumen, whereas D2-Glu312 and D1-Arg334 may be involved in alternative pathways in some mutants.
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Affiliation(s)
- Hiroshi Kuroda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Keisuke Kawashima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8654, Japan
| | - Kazuyo Ueda
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Takuya Ikeda
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8654, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Ryo Ninomiya
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Chisato Hida
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
| | - Hiroshi Ishikita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8654, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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16
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Durgaryan NA, Miraqyan NA, Minasyan PG. Study of the reaction of 1,4-benzoquinone with aniline oligomers and benzidine. JOURNAL OF POLYMER RESEARCH 2020. [DOI: 10.1007/s10965-020-02243-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Gates C, Ananyev G, Dismukes GC. Realtime kinetics of the light driven steps of photosynthetic water oxidation in living organisms by "stroboscopic" fluorometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148212. [PMID: 32320684 DOI: 10.1016/j.bbabio.2020.148212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 10/24/2022]
Abstract
We develop a rapid "stroboscopic" fluorescence induction method, using the fast repetition rate fluorometry (FRRF) technique, to measure changes in the quantum yield of light emission from chlorophyll in oxygenic photosynthesis arising from competition with primary photochemical charge separation (P680* ➔ P680+QA-). This method determines the transit times of electrons that pass through PSII during the successive steps in the catalytic cycle of water oxidation/O2 formation (S states) and plastoquinone reduction in any oxygenic phototroph (in vivo or in vitro). We report the first measurements from intact living cells, illustrated by a eukaryotic alga (Nannochloropsis oceanica). We demonstrate that S state transition times depend strongly on the redox state of the PSII acceptor side, at both QB and the plastoquinone pool which serve as the major locus of regulation of PSII electron flux. We provide evidence for a kinetic intermediate S3' state (lifetime 220 μs) following formation of S3 and prior to the release of O2. We compare the FRRF-detected kinetics to other previous spectroscopic methods (optical absorbance, EPR, and XES) that are applicable only to in vitro samples.
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Affiliation(s)
- Colin Gates
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, United States of America; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States of America; Department of Computational Biology and Molecular Biophysics, Rutgers University, Piscataway, NJ 08854, United States of America
| | - Gennady Ananyev
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, United States of America; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States of America
| | - G Charles Dismukes
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, United States of America; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States of America.
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18
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The study of conformational changes in photosystem II during a charge separation. J Mol Model 2020; 26:75. [PMID: 32152736 DOI: 10.1007/s00894-020-4332-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/23/2020] [Indexed: 12/14/2022]
Abstract
Photosystem II (PSII) is a multi-subunit pigment-protein complex and is one of several protein assemblies that function cooperatively in photosynthesis in plants and cyanobacteria. As more structural data on PSII become available, new questions arise concerning the nature of the charge separation in PSII reaction center (RC). The crystal structure of PSII RC from cyanobacteria Thermosynechococcus vulcanus was selected for the computational study of conformational changes in photosystem II associated to the charge separation process. The parameterization of cofactors and lipids for classical MD simulation with Amber force field was performed. The parametrized complex of PSII was embedded in the lipid membrane for MD simulation with Amber in Gromacs. The conformational behavior of protein and the cofactors directly involved in the charge separation were studied by MD simulations and QM/MM calculations. This study identified the most likely mechanism of the proton-coupled reduction of plastoquinone QB. After the charge separation and the first electron transfer to QB, the system undergoes conformational change allowing the first proton transfer to QB- mediated via Ser264. After the second electron transfer to QBH, the system again adopts conformation allowing the second proton transfer to QBH-. The reduced QBH2 would then leave the binding pocket.
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19
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Saito K, Mandal M, Ishikita H. Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways. Phys Chem Chem Phys 2020; 22:25467-25473. [DOI: 10.1039/d0cp04265j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H+ position in low-barrier H-bonds.
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Affiliation(s)
- Keisuke Saito
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
| | - Manoj Mandal
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
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20
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Cardona T, Rutherford AW. Evolution of Photochemical Reaction Centres: More Twists? TRENDS IN PLANT SCIENCE 2019; 24:1008-1021. [PMID: 31351761 DOI: 10.1016/j.tplants.2019.06.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 05/27/2023]
Abstract
One of the earliest events in the molecular evolution of photosynthesis is the structural and functional specialisation of type I (ferredoxin-reducing) and type II (quinone-reducing) reaction centres. In this opinion article we point out that the homodimeric type I reaction centre of heliobacteria has a calcium-binding site with striking structural similarities to the Mn4CaO5 cluster of photosystem II. These similarities indicate that most of the structural elements required to evolve water oxidation chemistry were present in the earliest reaction centres. We suggest that the divergence of type I and type II reaction centres was made possible by a drastic structural shift linked to a change in redox properties that coincided with or facilitated the origin of photosynthetic water oxidation.
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Affiliation(s)
- Tanai Cardona
- Imperial College London, Department of Life Sciences, London, UK. @imperial.ac.uk
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21
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Koua FHM. Structural Changes in the Acceptor Site of Photosystem II upon Ca 2+/Sr 2+ Exchange in the Mn 4CaO 5 Cluster Site and the Possible Long-Range Interactions. Biomolecules 2019; 9:biom9080371. [PMID: 31416291 PMCID: PMC6722538 DOI: 10.3390/biom9080371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/12/2019] [Indexed: 01/15/2023] Open
Abstract
The Mn4CaO5 cluster site in the oxygen-evolving complex (OEC) of photosystem II (PSII) undergoes structural perturbations, such as those induced by Ca2+/Sr2+ exchanges or Ca/Mn removal. These changes have been known to induce long-range positive shifts (between +30 and +150 mV) in the redox potential of the primary quinone electron acceptor plastoquinone A (QA), which is located 40 Å from the OEC. To further investigate these effects, we reanalyzed the crystal structure of Sr-PSII resolved at 2.1 Å and compared it with the native Ca-PSII resolved at 1.9 Å. Here, we focus on the acceptor site and report the possible long-range interactions between the donor, Mn4Ca(Sr)O5 cluster, and acceptor sites.
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Affiliation(s)
- Faisal Hammad Mekky Koua
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.
- National University Biomedical Research Institute, National University-Sudan, Air St. PO Box 3783, Khartoum, Sudan.
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22
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Chen J, Chen J, Liu Y, Zheng Y, Zhu Q, Han G, Shen JR. Proton-Coupled Electron Transfer of Plastoquinone Redox Reactions in Photosystem II: A Pump-Probe Ultraviolet Resonance Raman Study. J Phys Chem Lett 2019; 10:3240-3247. [PMID: 31117681 DOI: 10.1021/acs.jpclett.9b00959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plastoquinones (PQs) act as electron and proton mediators in photosystem II (PSII) for solar-to-chemical energy conversion. It is known that the redox potential of PQ varies in a wide range spanning hundreds of millivolts; however, its structural origin is not known yet. Here, by developing a pump-probe ultraviolet resonance Raman technique, we measured the vibrational structures of PQs including QA and QB in cyanobacterial PSII directly. The conversion of QA to QA•- in the Mn-depleted PSII is verified by direct observation of the distinct QA•- vibrational bands. A frequency upshift of the ring C=O/C=C stretch band at 1565 cm-1 for QA•- was observed, which suggests a π-π interaction between the quinone ring and Trp253. In contrast, proton-coupled reduction of QA to QAH upon light-driven electron transfer is demonstrated in PSII without QB bound. The H-bond between QA and His214 is likely the proton origin of this proton-coupled electron transfer.
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Affiliation(s)
- Jun Chen
- Science and Technology on Surface Physics and Chemistry Laboratory , Jiangyou 621908 , China
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Jinfan Chen
- Science and Technology on Surface Physics and Chemistry Laboratory , Jiangyou 621908 , China
| | - Ying Liu
- Institute of Materials , China Academy of Engineering Physics , Mianyang 621907 , China
| | - Yang Zheng
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Qingjun Zhu
- Photosynthesis Research Center, Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , No. 20, Nanxincun , Xiangshan, Beijing , 100093 , China
| | - Guangye Han
- 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
- Research Institute of Interdisciplinary Science, Graduate School of Natural Science and Technology , Okayama University , Tsushima Naka 3-1-1 , Okayama 700-8530 , Japan
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23
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Ananyev G, Roy-Chowdhury S, Gates C, Fromme P, Dismukes GC. The Catalytic Cycle of Water Oxidation in Crystallized Photosystem II Complexes: Performance and Requirements for Formation of Intermediates. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | - Shatabdi Roy-Chowdhury
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute and School of Molecular Sciences Arizona State University, Tempe, Arizona 85287, United States
| | | | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute and School of Molecular Sciences Arizona State University, Tempe, Arizona 85287, United States
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24
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Schulz CE, Dutta AK, Izsák R, Pantazis DA. Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones. J Comput Chem 2018; 39:2439-2451. [PMID: 30281169 DOI: 10.1002/jcc.25570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/07/2022]
Abstract
Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T0 ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Christine E Schulz
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Achintya Kumar Dutta
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Róbert Izsák
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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25
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Abstract
Complex I couples the free energy released from quinone (Q) reduction to pump protons across the biological membrane in the respiratory chains of mitochondria and many bacteria. The Q reduction site is separated by a large distance from the proton-pumping membrane domain. To address the molecular mechanism of this long-range proton-electron coupling, we perform here full atomistic molecular dynamics simulations, free energy calculations, and continuum electrostatics calculations on complex I from Thermus thermophilus We show that the dynamics of Q is redox-state-dependent, and that quinol, QH2, moves out of its reduction site and into a site in the Q tunnel that is occupied by a Q analog in a crystal structure of Yarrowia lipolytica We also identify a second Q-binding site near the opening of the Q tunnel in the membrane domain, where the Q headgroup forms strong interactions with a cluster of aromatic and charged residues, while the Q tail resides in the lipid membrane. We estimate the effective diffusion coefficient of Q in the tunnel, and in turn the characteristic time for Q to reach the active site and for QH2 to escape to the membrane. Our simulations show that Q moves along the Q tunnel in a redox-state-dependent manner, with distinct binding sites formed by conserved residue clusters. The motion of Q to these binding sites is proposed to be coupled to the proton-pumping machinery in complex I.
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26
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Nozawa Y, Noguchi T. pH-Dependent Regulation of the Relaxation Rate of the Radical Anion of the Secondary Quinone Electron Acceptor QB in Photosystem II As Revealed by Fourier Transform Infrared Spectroscopy. Biochemistry 2018; 57:2828-2836. [DOI: 10.1021/acs.biochem.8b00263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yosuke Nozawa
- 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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27
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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28
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Hasegawa R, Saito K, Takaoka T, Ishikita H. pK a of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution. PHOTOSYNTHESIS RESEARCH 2017; 133:297-304. [PMID: 28405861 PMCID: PMC5500672 DOI: 10.1007/s11120-017-0382-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/03/2017] [Indexed: 05/22/2023]
Abstract
Quinones can accept two electrons and two protons, and are involved in electron transfer and proton transfer reactions in photosynthetic reaction centers. To date, the pK a of these quinones in aqueous solution have not been reported. We calculated the pK a of the initial protonation (Q·- to QH·) and the second protonation (QH- to QH2) of 1,4-quinones using a quantum chemical approach. The calculated energy differences of the protonation reactions Q·- to QH· and QH- to QH2 in the aqueous phase for nine 1,4-quinones were highly correlated with the experimentally measured pK a(Q·-/QH·) and pK a(QH-/QH2), respectively. In the present study, we report the pK a(Q·-/QH·) and pK a(QH-/QH2) of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution.
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Affiliation(s)
- Ryo Hasegawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Tomohiro Takaoka
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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Photosystem II-cyclic electron flow powers exceptional photoprotection and record growth in the microalga Chlorella ohadii. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:873-883. [PMID: 28734933 DOI: 10.1016/j.bbabio.2017.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 01/13/2023]
Abstract
The desert microalga Chlorella ohadii was reported to grow at extreme light intensities with minimal photoinhibition, tolerate frequent de/re-hydrations, yet minimally employs antenna-based non-photochemical quenching for photoprotection. Here we investigate the molecular mechanisms by measuring Photosystem II charge separation yield (chlorophyll variable fluorescence, Fv/Fm) and flash-induced O2 yield to measure the contributions from both linear (PSII-LEF) and cyclic (PSII-CEF) electron flow within PSII. Cells grow increasingly faster at higher light intensities (μE/m2/s) from low (20) to high (200) to extreme (2000) by escalating photoprotection via shifting from PSII-LEF to PSII-CEF. This shifts PSII charge separation from plastoquinone reduction (PSII-LEF) to plastoquinol oxidation (PSII-CEF), here postulated to enable proton gradient and ATP generation that powers photoprotection. Low light-grown cells have unusually small antennae (332 Chl/PSII), use mainly PSII-LEF (95%) and convert 40% of PSII charge separations into O2 (a high O2 quantum yield of 0.06mol/mol PSII/flash). High light-grown cells have smaller antenna and lower PSII-LEF (63%). Extreme light-grown cells have only 42 Chl/PSII (no LHCII antenna), minimal PSII-LEF (10%), and grow faster than any known phototroph (doubling time 1.3h). Adding a synthetic quinone in excess to supplement the PQ pool fully uncouples PSII-CEF from its natural regulation and produces maximum PSII-LEF. Upon dark adaptation PSII-LEF rapidly reverts to PSII-CEF, a transient protection mechanism to conserve water and minimize the cost of antenna biosynthesis. The capacity of the electron acceptor pool (plastoquinone pool), and the characteristic times for exchange of (PQH2)B with PQpool and reoxidation of (PQH2)pool were determined.
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Durgaryan AA, Arakelyan RA, Durgaryan NA. Synthesis of polymers containing polyaniline fragments linked by 1,4-benzoquinone groups. RUSS J GEN CHEM+ 2017. [DOI: 10.1134/s1070363217010224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Zobnina V, Lambreva MD, Rea G, Campi G, Antonacci A, Scognamiglio V, Giardi MT, Polticelli F. The plastoquinol-plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations. PHOTOSYNTHESIS RESEARCH 2017; 131:15-30. [PMID: 27376842 DOI: 10.1007/s11120-016-0292-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/22/2016] [Indexed: 05/23/2023]
Abstract
In the photosystem II (PSII) of oxygenic photosynthetic organisms, the reaction center (RC) core mediates the light-induced electron transfer leading to water splitting and production of reduced plastoquinone molecules. The reduction of plastoquinone to plastoquinol lowers PSII affinity for the latter and leads to its release. However, little is known about the role of protein dynamics in this process. Here, molecular dynamics simulations of the complete PSII complex embedded in a lipid bilayer have been used to investigate the plastoquinol release mechanism. A distinct dynamic behavior of PSII in the presence of plastoquinol is observed which, coupled to changes in charge distribution and electrostatic interactions, causes disruption of the interactions seen in the PSII-plastoquinone complex and leads to the "squeezing out" of plastoquinol from the binding pocket. Displacement of plastoquinol closes the second water channel, recently described in a 2.9 Å resolution PSII structure (Guskov et al. in Nat Struct Mol Biol 16:334-342, 2009), allowing to rule out the proposed "alternating" mechanism of plastoquinol-plastoquinone exchange, while giving support to the "single-channel" one. The performed simulations indicated a pivotal role of D1-Ser264 in modulating the dynamics of the plastoquinone binding pocket and plastoquinol-plastoquinone exchange via its interaction with D1-His252 residue. The effects of the disruption of this hydrogen bond network on the PSII redox reactions were experimentally assessed in the D1 site-directed mutant Ser264Lys.
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Affiliation(s)
- Veranika Zobnina
- Theoretical Biology and Bioinformatics Laboratory, Department of Sciences, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Maya D Lambreva
- Institute of Crystallography CNR, 00015, Monterotondo Scalo, Rome, Italy
| | - Giuseppina Rea
- Institute of Crystallography CNR, 00015, Monterotondo Scalo, Rome, Italy
| | - Gaetano Campi
- Institute of Crystallography CNR, 00015, Monterotondo Scalo, Rome, Italy
| | - Amina Antonacci
- Institute of Crystallography CNR, 00015, Monterotondo Scalo, Rome, Italy
| | | | | | - Fabio Polticelli
- Theoretical Biology and Bioinformatics Laboratory, Department of Sciences, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy.
- National Institute of Nuclear Physics, Roma Tre Section, 00146, Rome, Italy.
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32
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Kato Y, Ishii R, Noguchi T. Comparative Analysis of the Interaction of the Primary Quinone QA in Intact and Mn-Depleted Photosystem II Membranes Using Light-Induced ATR-FTIR Spectroscopy. Biochemistry 2016; 55:6355-6358. [DOI: 10.1021/acs.biochem.6b01052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Kato
- Division of Material
Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Rina Ishii
- 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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33
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Fisher N, Kramer DM. Non-photochemical reduction of thylakoid photosynthetic redox carriers in vitro: relevance to cyclic electron flow around photosystem I? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1837:1944-1954. [PMID: 25251244 DOI: 10.1016/j.bbabio.2014.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/07/2014] [Accepted: 09/14/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED Non-photochemical (dark) increases in chlorophyll a fluorescence yield associated with non-photochemical reduction of redox carriers (Fnpr) have been attributed to the reduction of plastoquinone (PQ) related to cyclic electron flow (CEF) around photosystem I. In vivo, this rise in fluorescence is associated with activity of the chloroplast plastoquinone reductase (plastid NAD(P)H plastoquinone oxidoreductase) complex. In contrast, this signal measured in isolated thylakoids has been attributed to the activity of the protein gradient regulation-5 (PGR5)/PGR5-like (PGRL1)-associated CEF pathway. Here, we report a systematic experimentation on the origin of Fnpr in isolated thylakoids. Addition of NADPH and ferredoxin to isolated spinach thylakoids resulted in the reduction of the PQ pool, but neither its kinetics nor its inhibitor sensitivities matched those of Fnpr. Notably, Fnpr was more rapid than PQ reduction, and completely insensitive to inhibitors of the PSII QB site and oxygen evolving complex as well as inhibitors of the cytochrome b6f complex. We thus conclude that Fnpr in isolated thylakoids is not a result of redox equilibrium with bulk PQ. Redox titrations and fluorescence emission spectra imply that Fnpr is dependent on the reduction of a low potential redox component (Em about − 340 mV) within photosystem II (PSII), and is likely related to earlier observations of low potential variants of QA within a subpopulation of PSII that is directly reducible by ferredoxin. The implications of these results for our understanding of CEF and other photosynthetic processes are discussed.
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Affiliation(s)
- Nicholas Fisher
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - David M Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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34
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Derks A, Schaven K, Bruce D. Diverse mechanisms for photoprotection in photosynthesis. Dynamic regulation of photosystem II excitation in response to rapid environmental change. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:468-485. [DOI: 10.1016/j.bbabio.2015.02.008] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/03/2015] [Accepted: 02/07/2015] [Indexed: 12/26/2022]
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35
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Lambreva MD, Russo D, Polticelli F, Scognamiglio V, Antonacci A, Zobnina V, Campi G, Rea G. Structure/function/dynamics of photosystem II plastoquinone binding sites. Curr Protein Pept Sci 2015; 15:285-95. [PMID: 24678671 PMCID: PMC4030317 DOI: 10.2174/1389203715666140327104802] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 11/22/2013] [Accepted: 03/16/2014] [Indexed: 11/22/2022]
Abstract
Photosystem II (PSII)
continuously attracts the attention of researchers aiming to unravel the riddle
of its functioning and efficiency fundamental for all life on Earth. Besides, an
increasing number of biotechnological applications have been envisaged
exploiting and mimicking the unique properties of this macromolecular
pigment-protein complex. The PSII organization and working principles have
inspired the design of electrochemical water splitting schemes and charge
separating triads in energy storage systems as well as biochips and sensors for
environmental, agricultural and industrial screening of toxic compounds. An
intriguing opportunity is the development of sensor devices, exploiting native
or manipulated PSII complexes or ad hoc synthesized polypeptides
mimicking the PSII reaction centre proteins as bio-sensing elements. This review
offers a concise overview of the recent improvements in the understanding of
structure and function of PSII donor side, with focus on the interactions of the
plastoquinone cofactors with the surrounding environment and operational
features. Furthermore, studies focused on photosynthetic proteins
structure/function/dynamics and computational analyses aimed at rational design
of high-quality bio-recognition elements in biosensor devices are discussed.
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Affiliation(s)
| | | | | | | | | | | | | | - Giuseppina Rea
- Institute of Crystallography, National Research Council, Monterotondo, Italy.
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36
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Cardona T, Murray JW, Rutherford AW. Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria. Mol Biol Evol 2015; 32:1310-28. [PMID: 25657330 PMCID: PMC4408414 DOI: 10.1093/molbev/msv024] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages toward the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria.
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Affiliation(s)
- Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James W Murray
- Department of Life Sciences, Imperial College London, London, United Kingdom
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37
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de Almeida WB, Taguchi A, Dikanov SA, Wraight CA, O’Malley PJ. The 2-Methoxy Group Orientation Regulates the Redox Potential Difference between the Primary (Q A) and Secondary (Q B) Quinones of Type II Bacterial Photosynthetic Reaction Centers. J Phys Chem Lett 2014; 5:2506-2509. [PMID: 25126386 PMCID: PMC4126703 DOI: 10.1021/jz500967d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/24/2014] [Indexed: 05/24/2023]
Abstract
Recent studies have shown that only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from purple bacteria such as Rb. sphaeroides. 13C HYSCORE measurements of the 2-methoxy group in the semiquinone states, SQA and SQB, were compared with DFT calculations of the 13C hyperfine couplings as a function of the 2-methoxy dihedral angle. X-ray structure comparisons support 2-methoxy dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of 175-193 mV. A model having a methyl group substituted for the 2-methoxy group exhibits no electron affinity difference. This is consistent with the failure of a 2-methyl ubiquinone analogue to function as QB in mutant reaction centers with a ΔEm of ∼160-195 mV. The conclusion reached is that the 2-methoxy group is the principal determinant of electron transfer from QA to QB in type II photosynthetic reaction centers with ubiquinone serving as both acceptor quinones.
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Affiliation(s)
- Wagner B. de Almeida
- LQC-MM, Departamento
de Química, ICEx, Universidade
Federal de Minas Gerais (UFMG), Campus
Pampulh, Belo Horizonte, MG 31.910-270, Brazil
| | - Alexander
T. Taguchi
- Center for Biophysics and Computational Biology, Department of Veterinary Clinical
Medicine, and Department of BiochemistryUniversity of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sergei A. Dikanov
- Center for Biophysics and Computational Biology, Department of Veterinary Clinical
Medicine, and Department of BiochemistryUniversity of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Colin A. Wraight
- Center for Biophysics and Computational Biology, Department of Veterinary Clinical
Medicine, and Department of BiochemistryUniversity of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Patrick J. O’Malley
- School
of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
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38
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Kato Y, Noguchi T. Long-Range Interaction between the Mn4CaO5 Cluster and the Non-heme Iron Center in Photosystem II as Revealed by FTIR Spectroelectrochemistry. Biochemistry 2014; 53:4914-23. [DOI: 10.1021/bi500549b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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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39
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Computer modeling of electron and proton transport in chloroplasts. Biosystems 2014; 121:1-21. [PMID: 24835748 DOI: 10.1016/j.biosystems.2014.04.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/21/2022]
Abstract
Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of chloroplasts and lateral heterogeneity of lamellar system of thylakoids. The lateral profiles of pH in the thylakoid lumen and in the narrow gap between grana thylakoids have been calculated under different metabolic conditions. Analyzing topological aspects of diffusion-controlled stages of electron and proton transport in chloroplasts, we conclude that along with the NPQ mechanism of attenuation of PSII activity and deceleration of PQH2 oxidation by the cytochrome b6f complex caused by the lumen acidification, the intersystem electron transport may be down-regulated due to the light-induced alkalization of the narrow partition between adjacent thylakoids of grana. The computer models of electron and proton transport described in this article may be integrated as appropriate modules into a comprehensive model of oxygenic photosynthesis.
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40
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Ashizawa R, Noguchi T. Effects of hydrogen bonding interactions on the redox potential and molecular vibrations of plastoquinone as studied using density functional theory calculations. Phys Chem Chem Phys 2014; 16:11864-76. [DOI: 10.1039/c3cp54742f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Mareeswaran PM, Rajkumar E, Sathish V, Rajagopal S. Electron transfer reactions of ruthenium(II)-bipyridine complexes carrying tyrosine moiety with quinones. LUMINESCENCE 2013; 29:754-61. [DOI: 10.1002/bio.2617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/07/2013] [Accepted: 10/27/2013] [Indexed: 11/11/2022]
Affiliation(s)
| | - Eswaran Rajkumar
- School of Chemistry; Madurai Kamaraj University; Madurai Tamil Nadu India
- Vel Tech University; Avadi Chennai Tamil Nadu India
| | - Veerasamy Sathish
- School of Chemistry; Madurai Kamaraj University; Madurai Tamil Nadu India
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Ishikita H, Saito K. Proton transfer reactions and hydrogen-bond networks in protein environments. J R Soc Interface 2013; 11:20130518. [PMID: 24284891 DOI: 10.1098/rsif.2013.0518] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKa values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pKa matching condition and allow for proton transfer reactions, proteins often adjust the pKa via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.
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Affiliation(s)
- Hiroshi Ishikita
- Department of Biological Sciences, Graduate School of Science, Osaka University, , Machikaneyama-cho 1-1, Toyonaka 560-0043, Japan
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43
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Sayil C, Kurban S, Ibis C. Synthesis and Characterization of Nitrogen and Sulfur Containing 1,4-Naphthoquinones. PHOSPHORUS SULFUR 2013. [DOI: 10.1080/10426507.2013.796475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Cigdem Sayil
- a Department of Chemistry , Faculty of Engineering, Istanbul University , Avcilar-Istanbul , Turkey
| | - Semih Kurban
- a Department of Chemistry , Faculty of Engineering, Istanbul University , Avcilar-Istanbul , Turkey
| | - Cemil Ibis
- a Department of Chemistry , Faculty of Engineering, Istanbul University , Avcilar-Istanbul , Turkey
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44
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The discovery of 3-(1-aminoethylidene)quinoline-2, 4(1H,3H)-dione derivatives as novel PSII electron transport inhibitors. Mol Divers 2013; 17:701-10. [DOI: 10.1007/s11030-013-9466-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
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45
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Polonini HC, Dias RM, Souza IO, Gonçalves KM, Gomes TB, Raposo NR, da Silva AD. Quinolines derivatives as novel sunscreening agents. Bioorg Med Chem Lett 2013; 23:4506-10. [DOI: 10.1016/j.bmcl.2013.06.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/12/2013] [Accepted: 06/17/2013] [Indexed: 01/29/2023]
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46
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Coates CS, Ziegler J, Manz K, Good J, Kang B, Milikisiyants S, Chatterjee R, Hao S, Golbeck JH, Lakshmi KV. The structure and function of quinones in biological solar energy transduction: a cyclic voltammetry, EPR, and hyperfine sub-level correlation (HYSCORE) spectroscopy study of model naphthoquinones. J Phys Chem B 2013; 117:7210-20. [PMID: 23676117 DOI: 10.1021/jp401024p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quinones function as electron transport cofactors in photosynthesis and cellular respiration. The versatility and functional diversity of quinones is primarily due to the diverse midpoint potentials that are tuned by the substituent effects and interactions with surrounding amino acid residues in the binding site in the protein. In the present study, a library of substituted 1,4-naphthoquinones are analyzed by cyclic voltammetry in both protic and aprotic solvents to determine effects of substituent groups and hydrogen bonds on the midpoint potential. We use continuous-wave electron paramagnetic resonance (EPR) spectroscopy to determine the influence of substituent groups on the electronic properties of the 1,4-naphthoquinone models in an aprotic solvent. The results establish a correlation between the presence of substituent group(s) and the modification of electronic properties and a corresponding shift in the midpoint potential of the naphthoquinone models. Further, we use pulsed EPR spectroscopy to determine the effect of substituent groups on the strength and planarity of the hydrogen bonds of naphthoquinone models in a protic solvent. This study provides support for the tuning of the electronic properties of quinone cofactors by the influence of substituent groups and hydrogen bonding interactions.
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Affiliation(s)
- Christopher S Coates
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Vinyard DJ, Ananyev GM, Charles Dismukes G. Photosystem II: The Reaction Center of Oxygenic Photosynthesis. Annu Rev Biochem 2013; 82:577-606. [DOI: 10.1146/annurev-biochem-070511-100425] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David J. Vinyard
- Department of Chemistry and Chemical Biology and the Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854; ,
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540;
| | - Gennady M. Ananyev
- Department of Chemistry and Chemical Biology and the Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854; ,
| | - G. Charles Dismukes
- Department of Chemistry and Chemical Biology and the Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854; ,
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Abstract
Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q(A) and Q(B), working in series. Q(A) is a one-electron carrier, whereas Q(B) undergoes sequential reduction and protonation to form Q(B)H(2). Q(B)H(2) exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to Q(B)(•-) occurs from the protonated, D1-His252 to Q(B)(•)(-) via D1-Ser264. The second PT is likely to occur from D1-His215 to Q(B)H(-) via an H-bond with an energy profile with a single well, resulting in the formation of Q(B)H(2) and the D1-His215 anion. The pathway for reprotonation of D1-His215(-) may involve bicarbonate, D1-Tyr246 and water in the Q(B) site. Formate ligation to Fe(2+) did not significantly affect the protonation of reduced Q(B), suggesting that formate inhibits Q(B)H(2) release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe(3+) state in the presence of Q(B)(•-), a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for Q(B) reduction is presented.
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Rutherford AW, Osyczka A, Rappaport F. Back-reactions, short-circuits, leaks and other energy wasteful reactions in biological electron transfer: redox tuning to survive life in O(2). FEBS Lett 2012; 586:603-16. [PMID: 22251618 DOI: 10.1016/j.febslet.2011.12.039] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/15/2011] [Accepted: 12/24/2011] [Indexed: 12/21/2022]
Abstract
The energy-converting redox enzymes perform productive reactions efficiently despite the involvement of high energy intermediates in their catalytic cycles. This is achieved by kinetic control: with forward reactions being faster than competing, energy-wasteful reactions. This requires appropriate cofactor spacing, driving forces and reorganizational energies. These features evolved in ancestral enzymes in a low O(2) environment. When O(2) appeared, energy-converting enzymes had to deal with its troublesome chemistry. Various protective mechanisms duly evolved that are not directly related to the enzymes' principal redox roles. These protective mechanisms involve fine-tuning of reduction potentials, switching of pathways and the use of short circuits, back-reactions and side-paths, all of which compromise efficiency. This energetic loss is worth it since it minimises damage from reactive derivatives of O(2) and thus gives the organism a better chance of survival. We examine photosynthetic reaction centres, bc(1) and b(6)f complexes from this view point. In particular, the evolution of the heterodimeric PSI from its homodimeric ancestors is explained as providing a protective back-reaction pathway. This "sacrifice-of-efficiency-for-protection" concept should be generally applicable to bioenergetic enzymes in aerobic environments.
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Chatterjee R, Coates CS, Milikisiyants S, Poluektov OG, Lakshmi KV. Structure and Function of Quinones in Biological Solar Energy Transduction: A High-Frequency D-Band EPR Spectroscopy Study of Model Benzoquinones. J Phys Chem B 2011; 116:676-82. [DOI: 10.1021/jp210156a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Ruchira Chatterjee
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Christopher S. Coates
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Sergey Milikisiyants
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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