1
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Capone M, Parisse G, Narzi D, Guidoni L. Unravelling Mn 4Ca cluster vibrations in the S 1, S 2 and S 3 states of the Kok-Joliot cycle of photosystem II. Phys Chem Chem Phys 2024; 26:20598-20609. [PMID: 39037338 PMCID: PMC11290063 DOI: 10.1039/d4cp01307g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Vibrational spectroscopy serves as a powerful tool for characterizing intermediate states within the Kok-Joliot cycle. In this study, we employ a QM/MM molecular dynamics framework to calculate the room temperature infrared absorption spectra of the S1, S2, and S3 states via the Fourier transform of the dipole time auto-correlation function. To better analyze the computational data and assign spectral peaks, we introduce an approach based on dipole-dipole correlation function of cluster moieties of the reaction center. Our analysis reveals variation in the infrared signature of the Mn4Ca cluster along the Kok-Joliot cycle, attributed to its increasing symmetry and rigidity resulting from the rising oxidation state of the Mn ions. Furthermore, we successfully assign the debated contributions in the frequency range around 600 cm-1. This computational methodology provides valuable insights for deciphering experimental infrared spectra and understanding the water oxidation process in both biological and artificial systems.
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Affiliation(s)
- Matteo Capone
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Gianluca Parisse
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Daniele Narzi
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Leonardo Guidoni
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
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2
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Ang AKR, Umena Y, Sato-Tomita A, Shibayama N, Happo N, Marumi R, Yamamoto Y, Kimura K, Kawamura N, Takano Y, Matsushita T, Sasaki YC, Shen JR, Hayashi K. Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:368-378. [PMID: 36891850 PMCID: PMC10000799 DOI: 10.1107/s1600577522011833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.
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Affiliation(s)
- Artoni Kevin R. Ang
- Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan
| | - Yasufumi Umena
- Synchrotron Radiation Research Center, Nagoya University, Furo, Chikusa, Nagoya 466-8603, Japan
| | - Ayana Sato-Tomita
- Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Naoya Shibayama
- Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Naohisa Happo
- Department of Computer and Network Engineering, Graduate School of Information Sciences, Hiroshima City University, Asa-Minami-ku, Hiroshima 731-3194, Japan
| | - Riho Marumi
- Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan
| | - Yuta Yamamoto
- Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan
| | - Koji Kimura
- Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan
| | - Naomi Kawamura
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyôgo 679-5198, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, Asa-Minami-ku, Hiroshima 731-3194, Japan
| | - Tomohiro Matsushita
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Tsushima Naka, Okayama 700-8530, Japan
| | - Kouichi Hayashi
- Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyôgo 679-5198, Japan
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3
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Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Debus RJ. Alteration of the O 2-Producing Mn 4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand. Biochemistry 2021; 60:3841-3855. [PMID: 34898175 DOI: 10.1021/acs.biochem.1c00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The O2-evolving Mn4Ca cluster in photosystem II (PSII) is arranged as a distorted Mn3Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn4Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn4Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn4Ca cluster in the dark-stable S1 state so that a high-spin form of the S2 state is produced during the S1-to-S2 transition instead of the low-spin form that gives rise to the S2 state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn4Ca cluster without substantially eliminating O2 evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn4Ca cluster in the mechanism of O2 formation.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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5
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Kim CJ, Debus RJ. Roles of D1-Glu189 and D1-Glu329 in O2 Formation by the Water-Splitting Mn4Ca Cluster in Photosystem II. Biochemistry 2020; 59:3902-3917. [DOI: 10.1021/acs.biochem.0c00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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6
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Fourier transform infrared and mass spectrometry analyses of a site-directed mutant of D1-Asp170 as a ligand to the water-oxidizing Mn4CaO5 cluster in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148086. [DOI: 10.1016/j.bbabio.2019.148086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/09/2019] [Accepted: 09/15/2019] [Indexed: 01/02/2023]
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7
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A bio-inspired coordination polymer as outstanding water oxidation catalyst via second coordination sphere engineering. Nat Commun 2019; 10:5074. [PMID: 31699987 PMCID: PMC6838099 DOI: 10.1038/s41467-019-13052-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/17/2019] [Indexed: 11/12/2022] Open
Abstract
First-row transition metal-based catalysts have been developed for the oxygen evolution reaction (OER) during the past years, however, such catalysts typically operate at overpotentials (η) significantly above thermodynamic requirements. Here, we report an iron/nickel terephthalate coordination polymer on nickel form (NiFeCP/NF) as catalyst for OER, in which both coordinated and uncoordinated carboxylates were maintained after electrolysis. NiFeCP/NF exhibits outstanding electro-catalytic OER activity with a low overpotential of 188 mV at 10 mA cm−2 in 1.0 KOH, with a small Tafel slope and excellent stability. The pH-independent OER activity of NiFeCP/NF on the reversible hydrogen electrode scale suggests that a concerted proton-coupled electron transfer (c-PET) process is the rate-determining step (RDS) during water oxidation. Deuterium kinetic isotope effects, proton inventory studies and atom-proton-transfer measurements indicate that the uncoordinated carboxylates are serving as the proton transfer relays, with a similar function as amino acid residues in photosystem II (PSII), accelerating the proton-transfer rate. Proton-coupled electron transfer (PCET) process is very important for water oxidation catalysis. Here, the authors introduced uncoordinated carboxylate in the second-coordination-sphere of Ni-Fe coordination polymer catalyst as an internal base to promote the water oxidation kinetics by such PCET process.
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8
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Tychengulova A, Capone M, Pitari F, Guidoni L. Molecular Vibrations of an Oxygen-Evolving Complex and Its Synthetic Mimic. Chemistry 2019; 25:13385-13395. [PMID: 31340068 DOI: 10.1002/chem.201902621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/18/2019] [Indexed: 11/07/2022]
Abstract
Bio-inspired catalysis for artificial photosynthesis has been widely studied for decades, in particular, with the purpose of using bio-disposable and non-toxic metals as building blocks. The characterisation of such catalysts has been achieved by using different kinds of spectroscopic methods, from X-ray crystallography to NMR spectroscopy. An artificial Mn4 CaO4 cubane cluster with dangling Mn4 was synthesised in 2015 [Zhang et al. Science 2015, 348, 690-693]; this cluster showed many structural similarities to that of the natural oxygen-evolving complex. An accurate structural and spectroscopic comparison between the natural and artificial systems is highly relevant to understand the catalytic mechanism. Among data from different techniques, the differential FTIR spectra (Sn+1 -Sn ) of photosystem II are still lacking a complete interpretation. The availability of IR data of the artificial cluster offers a unique opportunity to assign absolute absorption spectra on a well-defined and easier to interpret analogous moiety. The present work aims to investigate the novel inorganic compound as a model system for an oxygen-evolving complex through measurement of its spectroscopic properties. The experimental results are compared with calculations by using a variety of theoretical methods (normal mode analysis, effective normal mode analysis) in the S1 state. We underline the similarities and the differences in the computational spectra based on atomistic models of Mn4 CaO5 and Mn4 CaO4 complexes.
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Affiliation(s)
- Aliya Tychengulova
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via Scarpa 16, 00161, Rome, Italy
| | - Mateo Capone
- Department of Engineering, Computer Science and Mathematics, University of L'Aquila, Via Vetoio Coppito, 67100, L'Aquila, Italy
| | - Fabio Pitari
- Department of Engineering, Computer Science and Mathematics, University of L'Aquila, Via Vetoio Coppito, 67100, L'Aquila, Italy
- Current address: CINECA High Performance Computing Department, Via Magnanelli, 40033, Casalecchio di Reno, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Science, University of L'Aquila, Via Vetoio Coppito, 67100, L'Aquila, Italy
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9
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Capone M, Narzi D, Tychengulova A, Guidoni L. On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:33-43. [PMID: 30801735 DOI: 10.1111/ppl.12949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Understanding the structural modification experienced by the Mn4 CaO5 oxygen-evolving complex of photosystem II along the Kok-Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction center, to catch spectral changes between different S-states along the catalytic cycle. Because of the complexity of the signals, only a limited quantity of identified peaks have been assigned so far, also because of the difficulty of a direct comparison with theoretical calculations. In the present work, we critically reconsider the comparison between differential vibrational spectroscopy and theoretical calculations performed on the structural models of the photosystem II active site and an inorganic structural mimic. Several factors are currently limiting the reliability of a quantitative comparison, such as intrinsic errors associated to theoretical methods, and most of all, the uncertainty attributed to the lack of knowledge about the localization of the underlying structural changes. Critical points in this comparison are extensively discussed. Comparing several computational data of differential S2 /S1 infrared spectroscopy, we have identified weak and strong points in their interpretation when compared with experimental spectra.
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Affiliation(s)
- Matteo Capone
- Department of Information Engineering, Computational Science and Mathematics, Università dell'Aquila, 67100, L'Aquila, Italy
| | - Daniele Narzi
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Aliya Tychengulova
- Department of Basic Sciences Applied for Engineering, "Sapienza" Università di Roma, 00185, Rome, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Science, Università dell'Aquila, 67100, L'Aquila, Italy
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10
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Nakamura S, Noguchi T. Initial Mn2+ binding site in photoassembly of the water-oxidizing Mn4CaO5 cluster in photosystem II as studied by quantum mechanics/molecular mechanics calculations. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.02.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Kim CJ, Bao H, Burnap RL, Debus RJ. Impact of D1-V185 on the Water Molecules That Facilitate O2 Formation by the Catalytic Mn4CaO5 Cluster in Photosystem II. Biochemistry 2018; 57:4299-4311. [DOI: 10.1021/acs.biochem.8b00630] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Han Bao
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Robert L. Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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12
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Banerjee G, Ghosh I, Kim CJ, Debus RJ, Brudvig GW. Substitution of the D1-Asn 87 site in photosystem II of cyanobacteria mimics the chloride-binding characteristics of spinach photosystem II. J Biol Chem 2017; 293:2487-2497. [PMID: 29263091 DOI: 10.1074/jbc.m117.813170] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/19/2017] [Indexed: 11/06/2022] Open
Abstract
Photoinduced water oxidation at the O2-evolving complex (OEC) of photosystem II (PSII) is a complex process involving a tetramanganese-calcium cluster that is surrounded by a hydrogen-bonded network of water molecules, chloride ions, and amino acid residues. Although the structure of the OEC has remained conserved over eons of evolution, significant differences in the chloride-binding characteristics exist between cyanobacteria and higher plants. An analysis of amino acid residues in and around the OEC has identified residue 87 in the D1 subunit as the only significant difference between PSII in cyanobacteria and higher plants. We substituted the D1-Asn87 residue in the cyanobacterium Synechocystis sp. PCC 6803 (wildtype) with alanine, present in higher plants, or with aspartic acid. We studied PSII core complexes purified from D1-N87A and D1-N87D variant strains to probe the function of the D1-Asn87 residue in the water-oxidation mechanism. EPR spectra of the S2 state and flash-induced FTIR spectra of both D1-N87A and D1-N87D PSII core complexes exhibited characteristics similar to those of wildtype Synechocystis PSII core complexes. However, flash-induced O2-evolution studies revealed a decreased cycling efficiency of the D1-N87D variant, whereas the cycling efficiency of the D1-N87A PSII variant was similar to that of wildtype PSII. Steady-state O2-evolution activity assays revealed that substitution of the D1 residue at position 87 with alanine perturbs the chloride-binding site in the proton-exit channel. These findings provide new insight into the role of the D1-Asn87 site in the water-oxidation mechanism and explain the difference in the chloride-binding properties of cyanobacterial and higher-plant PSII.
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Affiliation(s)
- Gourab Banerjee
- From the Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107 and
| | - Ipsita Ghosh
- From the Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107 and
| | - Christopher J Kim
- the Department of Biochemistry, University of California, Riverside, California 92521
| | - Richard J Debus
- the Department of Biochemistry, University of California, Riverside, California 92521
| | - Gary W Brudvig
- From the Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107 and
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13
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Semin BК, Davletshina LN, Seibert M, Rubin AB. Creation of a 3Mn/1Fe cluster in the oxygen-evolving complex of photosystem II and investigation of its functional activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2017; 178:192-200. [PMID: 29156347 DOI: 10.1016/j.jphotobiol.2017.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/28/2017] [Accepted: 11/09/2017] [Indexed: 01/04/2023]
Abstract
Extraction of Mn cations from the oxygen-evolving complex (OEC) of Ca-depleted PSII membranes (PSII[-Ca,4Mn]) by reductants like hydroquinone (H2Q) occurs with lower efficiency at acidic pH (2Mn/reaction center [RC] are extracted at pH5.7) than at neutral pH (3Mn/RC are extracted at pH6.5) [Semin et al. Photosynth. Res. 125 (2015) 95]. Fe(II) also extracts Mn cations from PSII(-Ca,4Mn), but only 2Mn/RC at pH6.5, forming a heteronuclear 2Mn/2Fe cluster [Semin and Seibert, J. Bioenerg. Biomembr. 48 (2016) 227]. Here we investigated the efficiency of Mn extraction by Fe(II) at acidic pH and found that Fe(II) cations can extract only 1Mn/RC from PSII(-Ca,4Mn) membranes at pH 5.7, forming a 3Mn/1Fe cluster. Also we found that the presence of Fe cations in a heteronuclear cluster (2Mn/2Fe) increases the resistance of the remaining Mn cations to H2Q action, since H2Q can extract Mn cations from homonuclear Mn clusters of PSII(-Ca,4Mn) and PSII(-Ca,2Mn) membranes but not from the heteronuclear cluster in PSII(-Ca,2Mn,2Fe) membranes. H2Q also cannot extract Mn from PSII membranes obtained by incubation of PSII(-Ca,4Mn) membranes with Fe(II) cations at pH5.7, which suggests the formation of a heteronuclear 3Mn/1Fe cluster in the OEC. Functional activity of PSII with a 3Mn/1Fe cluster was investigated. PSII preparations with a 3Mn/1Fe cluster in the OEC are able to photoreduce the exogenous electron acceptor 2,6-dichlorophenolindophenol, possibly due to incomplete oxidation of water molecules as is the case with PSII(-Ca,2Mn,2Fe) samples. However, in the contrast to PSII(-Ca,2Mn,2Fe) samples PSII(-Ca,3Mn,1Fe) membranes can evolve O2 at a low rate in the presence of exogenous Ca2+ (at about 27% of the rate of O2 evolution in native PSII membranes). The explanation for this phenomenon (either water splitting and production of molecular O2 by the 3Mn/1Fe cluster or apparent O2 evolution due to minor contamination of PSII(3Mn,1Fe) samples with PSII(-Ca,4Mn) membranes) is discussed.
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Affiliation(s)
- B К Semin
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - L N Davletshina
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - M Seibert
- BioEnergy Sciences & Technology Directorate, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - A B Rubin
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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14
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Nakamura S, Noguchi T. Infrared Determination of the Protonation State of a Key Histidine Residue in the Photosynthetic Water Oxidizing Center. J Am Chem Soc 2017. [DOI: 10.1021/jacs.7b04924] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shin Nakamura
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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15
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Kim CJ, Debus RJ. Evidence from FTIR Difference Spectroscopy That a Substrate H2O Molecule for O2 Formation in Photosystem II Is Provided by the Ca Ion of the Catalytic Mn4CaO5 Cluster. Biochemistry 2017; 56:2558-2570. [DOI: 10.1021/acs.biochem.6b01278] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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16
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Nakamura S, Noguchi T. Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn 4CaO 5 cluster in photosystem II. Proc Natl Acad Sci U S A 2016; 113:12727-12732. [PMID: 27729534 PMCID: PMC5111704 DOI: 10.1073/pnas.1607897113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During photosynthesis, the light-driven oxidation of water performed by photosystem II (PSII) provides electrons necessary to fix CO2, in turn supporting life on Earth by liberating molecular oxygen. Recent high-resolution X-ray images of PSII show that the water-oxidizing center (WOC) is composed of an Mn4CaO5 cluster with six carboxylate, one imidazole, and four water ligands. FTIR difference spectroscopy has shown significant structural changes of the WOC during the S-state cycle of water oxidation, especially within carboxylate groups. However, the roles that these carboxylate groups play in water oxidation as well as how they should be properly assigned in spectra are unresolved. In this study, we performed a normal mode analysis of the WOC using the quantum mechanics/molecular mechanics (QM/MM) method to simulate FTIR difference spectra on the S1 to S2 transition in the carboxylate stretching region. By evaluating WOC models with different oxidation and protonation states, we determined that models of high-oxidation states, Mn(III)2Mn(IV)2, satisfactorily reproduced experimental spectra from intact and Ca-depleted PSII compared with low-oxidation models. It is further suggested that the carboxylate groups bridging Ca and Mn ions within this center tune the reactivity of water ligands bound to Ca by shifting charge via their π conjugation.
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Affiliation(s)
- Shin Nakamura
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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17
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Identifying carboxylate ligand vibrational modes in photosystem II with QM/MM methods. Proc Natl Acad Sci U S A 2016; 113:12613-12615. [PMID: 27794121 DOI: 10.1073/pnas.1615794113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Semin BK, Seibert M. Substituting Fe for two of the four Mn ions in photosystem II-effects on water-oxidation. J Bioenerg Biomembr 2016; 48:227-40. [PMID: 26847716 DOI: 10.1007/s10863-016-9651-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
Abstract
We have investigated the interaction of Fe(II) cations with Ca-depleted PSII membranes (PSII[-Ca,4Mn]) in the dark and found that Fe(II) incubation removes 2 of 4 Mn ions from the tetranuclear Mn cluster of the photosynthetic O2-evolving complex (OEC). The reduction of Mn ions in PSII(-Ca,4Mn) by Fe(II) and the concomitant release of two Mn(II) cations is accompanied by the binding of newly generated Fe(III) in at least one vacated Mn site. Flash-induced chlorophyll (Chl) fluorescence yield measurements of this new 2Mn/nFe cluster (PSII[-Ca,2Mn,nFe]) show that charge recombination in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) occurs between Qa (-) and the remaining Mn/Fe cluster (but not YZ (●)) in the OEC, and extraction of 2 Mn occurs uniformly in all PSII complexes. No O2 evolution is observed, but the heteronuclear metal cluster in PSII(-Ca,2Mn,nFe) samples is still able to supply electrons for reduction of the exogenous electron acceptor, 2,6-dichlorophrenolindophenol, by photooxidizing water and producing H2O2 in the absence of an exogenous donor as seen previously with PSII(-Ca,4Mn). Selective extraction of Mn or Fe cations from the 2Mn/nFe heteronuclear cluster demonstrates that the high-affinity Mn-binding site is occupied by one of the iron cations. It is notable that partial water-oxidation function still occurs when only two Mn cations are present in the PSII OEC.
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Affiliation(s)
- Boris K Semin
- BioEnergy Sciences & Technology Directorate, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - Michael Seibert
- BioEnergy Sciences & Technology Directorate, National Renewable Energy Laboratory, Golden, CO, 80401, USA
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19
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Chuah WY, Stranger R, Pace RJ, Krausz E, Frankcombe TJ. Deprotonation of Water/Hydroxo Ligands in Clusters Mimicking the Water Oxidizing Complex of PSII and Its Effect on the Vibrational Frequencies of Ligated Carboxylate Groups. J Phys Chem B 2016; 120:377-85. [PMID: 26727127 DOI: 10.1021/acs.jpcb.5b09987] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The IR absorptions of several first-shell carboxylate ligands of the water oxidizing complex (WOC) have been experimentally shown to be unaffected by oxidation state changes in the WOC during its catalytic cycle. Several model clusters that mimic the Mn4O5Ca core of the WOC in the S1 state, with electronic configurations that correspond to both the so-called "high" and "low" oxidation paradigms, were investigated. Deprotonation at W2, W1, or O3 sites was found to strongly reduce carboxylate ligand frequency shifts on oxidation of the metal cluster. The frequency shifts were smallest in neutrally charged clusters where the initial mean Mn oxidation state was +3, with W2 as an hydroxide and O5 a water. Deprotonation also reduced and balanced the oxidation energy of all clusters in successive oxidations.
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Affiliation(s)
- Wooi Yee Chuah
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Rob Stranger
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Elmars Krausz
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Terry J Frankcombe
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia.,School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra, Australian Capital Territory 2600, Australia
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20
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Terrett R, Frankcombe T, Pace R, Stranger R. Effect of concomitant oxidation and deprotonation of hydrated Mn centres in rationalising the FTIR difference silence of D1-Asp170 in Photosystem II. J Inorg Biochem 2015; 155:101-4. [PMID: 26684583 DOI: 10.1016/j.jinorgbio.2015.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/29/2015] [Accepted: 11/24/2015] [Indexed: 11/28/2022]
Abstract
The observation of negligible FTIR differences in carboxylate vibrational modes for the D1-Asp170 residue of Photosystem II (PSII) on successive one-electron oxidations of the Mn4CaO5 oxygen-evolving complex (OEC) is counterintuitive in light of the apparent ligation of D1-Asp170 to an oxidisable Mn ion in the X-ray crystallographic structures of PSII. Here, we show computational support for the hypothesis that suppression of the FTIR difference spectrum in the 1100cm(-1) to 1700cm(-1) region of D1-Asp170 occurs by concomitant Mn oxidation and deprotonation of water ligands bound to the ligated metal centre. Density functional theory calculations on the model species [Mn(II)Ca(COOH)(OH)2(H2O)2](+) over two successive oxidations of the Mn ion are performed, where those oxidations are accompanied by deprotonation of water and μ-hydroxo ligands coordinated to the Mn ion. In contrast, dramatically increased FTIR difference activity is observed where these oxidations are unaccompanied by proton loss.
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Affiliation(s)
- Richard Terrett
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Terry Frankcombe
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia; School of Physical, Environmental and Mathematical Sciences, University of New South Wales, Canberra, ACT 2610, Australia
| | - Ron Pace
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Robert Stranger
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia.
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21
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Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. QM/MM Models of the O2-Evolving Complex of Photosystem II. J Chem Theory Comput 2015; 2:1119-34. [PMID: 26633071 DOI: 10.1021/ct060018l] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This paper introduces structural models of the oxygen-evolving complex of photosystem II (PSII) in the dark-stable S1 state, as well as in the reduced S0 and oxidized S2 states, with complete ligation of the metal-oxo cluster by amino acid residues, water, hydroxide, and chloride. The models are developed according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, applied in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus, recently reported at 3.5 Å resolution. Manganese and calcium ions are ligated consistently with standard coordination chemistry assumptions, supported by biochemical and spectroscopic data. Furthermore, the calcium-bound chloride ligand is found to be bound in a position consistent with pulsed electron paramagnetic resonance data obtained from acetate-substituted PSII. The ligation of protein ligands includes monodentate coordination of D1-D342, CP43-E354, and D1-D170 to Mn(1), Mn(3), and Mn(4), respectively; η(2) coordination of D1-E333 to both Mn(3) and Mn(2); and ligation of D1-E189 and D1-H332 to Mn(2). The resulting QM/MM structural models are consistent with available mechanistic data and also are compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements of PSII. It is, therefore, conjectured that the proposed QM/MM models are particularly relevant to the development and validation of catalytic water-oxidation intermediates.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - José A Gascón
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - James P McEvoy
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Gary W Brudvig
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
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22
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Coe J, Kupitz C, Basu S, Conrad CE, Roy-Chowdhury S, Fromme R, Fromme P. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser. Methods Enzymol 2015; 557:459-82. [PMID: 25950978 PMCID: PMC4558102 DOI: 10.1016/bs.mie.2015.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Photosystem II (PSII) is a membrane protein supercomplex that executes the initial reaction of photosynthesis in higher plants, algae, and cyanobacteria. It captures the light from the sun to catalyze a transmembrane charge separation. In a series of four charge separation events, utilizing the energy from four photons, PSII oxidizes two water molecules to obtain dioxygen, four protons, and four electrons. The light reactions of photosystems I and II (PSI and PSII) result in the formation of an electrochemical transmembrane proton gradient that is used for the production of ATP. Electrons that are subsequently transferred from PSI via the soluble protein ferredoxin to ferredoxin-NADP(+) reductase that reduces NADP(+) to NADPH. The products of photosynthesis and the elemental oxygen evolved sustain all higher life on Earth. All oxygen in the atmosphere is produced by the oxygen-evolving complex in PSII, a process that changed our planet from an anoxygenic to an oxygenic atmosphere 2.5 billion years ago. In this chapter, we provide recent insight into the mechanisms of this process and methods used in probing this question.
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Affiliation(s)
- Jesse Coe
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Chelsie E Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | | | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA.
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23
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Coates CS, Milikisiyants S, Chatterjee R, Whittaker MM, Whittaker JW, Lakshmi KV. Two-Dimensional HYSCORE Spectroscopy of Superoxidized Manganese Catalase: A Model for the Oxygen-Evolving Complex of Photosystem II. J Phys Chem B 2015; 119:4905-16. [DOI: 10.1021/acs.jpcb.5b01602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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, 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
| | - 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
| | - Mei M. Whittaker
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - James W. Whittaker
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239-3098, 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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24
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Pokhrel R, Debus RJ, Brudvig GW. Probing the Effect of Mutations of Asparagine 181 in the D1 Subunit of Photosystem II. Biochemistry 2015; 54:1663-72. [DOI: 10.1021/bi501468h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ravi Pokhrel
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Richard J. Debus
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Gary W. Brudvig
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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25
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Messinger J, Debus R, Dismukes GC. Warwick Hillier: a tribute. PHOTOSYNTHESIS RESEARCH 2014; 122:1-11. [PMID: 25038923 DOI: 10.1007/s11120-014-0025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Warwick Hillier (October 18, 1967-January 10, 2014) made seminal contributions to our understanding of photosynthetic water oxidation employing membrane inlet mass spectrometry and FTIR spectroscopy. This article offers a collection of historical perspectives on the scientific impact of Warwick Hillier's work and tributes to the personal impact his life and ideas had on his collaborators and colleagues.
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Affiliation(s)
- Johannes Messinger
- Department of Chemistry, Chemical Biological Centre (KBC), Umeå University, Linnaeus väg 6, 90187, Umeå, Sweden
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26
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Debus RJ. FTIR studies of metal ligands, networks of hydrogen bonds, and water molecules near the active site Mn₄CaO₅ cluster in Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:19-34. [PMID: 25038513 DOI: 10.1016/j.bbabio.2014.07.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/26/2022]
Abstract
The photosynthetic conversion of water to molecular oxygen is catalyzed by the Mn₄CaO₅ cluster in Photosystem II and provides nearly our entire supply of atmospheric oxygen. The Mn₄CaO₅ cluster accumulates oxidizing equivalents in response to light-driven photochemical events within Photosystem II and then oxidizes two molecules of water to oxygen. The Mn₄CaO₅ cluster converts water to oxygen much more efficiently than any synthetic catalyst because its protein environment carefully controls the cluster's reactivity at each step in its catalytic cycle. This control is achieved by precise choreography of the proton and electron transfer reactions associated with water oxidation and by careful management of substrate (water) access and proton egress. This review describes the FTIR studies undertaken over the past two decades to identify the amino acid residues that are responsible for this control and to determine the role of each. In particular, this review describes the FTIR studies undertaken to characterize the influence of the cluster's metal ligands on its activity, to delineate the proton egress pathways that link the Mn₄CaO₅ cluster with the thylakoid lumen, and to characterize the influence of specific residues on the water molecules that serve as substrate or as participants in the networks of hydrogen bonds that make up the water access and proton egress pathways. This information will improve our understanding of water oxidation by the Mn₄CaO₅ catalyst in Photosystem II and will provide insight into the design of new generations of synthetic catalysts that convert sunlight into useful forms of storable energy. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521-0129, USA.
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27
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Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature 2014; 513:261-5. [PMID: 25043005 DOI: 10.1038/nature13453] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 05/04/2014] [Indexed: 01/17/2023]
Abstract
Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.
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28
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Noguchi T. Fourier transform infrared difference and time-resolved infrared detection of the electron and proton transfer dynamics in photosynthetic water oxidation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:35-45. [PMID: 24998309 DOI: 10.1016/j.bbabio.2014.06.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/25/2014] [Accepted: 06/26/2014] [Indexed: 01/15/2023]
Abstract
Photosynthetic water oxidation, which provides the electrons necessary for CO₂ reduction and releases O₂ and protons, is performed at the Mn₄CaO₅ cluster in photosystem II (PSII). In this review, studies that assessed the mechanism of water oxidation using infrared spectroscopy are summarized focusing on electron and proton transfer dynamics. Structural changes in proteins and water molecules between intermediates known as Si states (i=0-3) were detected using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. Electron flow in PSII and proton release from substrate water were monitored using the infrared changes in ferricyanide as an exogenous electron acceptor and Mes buffer as a proton acceptor. Time-resolved infrared (TRIR) spectroscopy provided information on the dynamics of proton-coupled electron transfer during the S-state transitions. In particular, a drastic proton movement during the lag phase (~200μs) before electron transfer in the S3→S0 transition was detected directly by monitoring the infrared absorption of a polarizable proton in a hydrogen bond network. Furthermore, the proton release pathways in the PSII proteins were analyzed by FTIR difference measurements in combination with site-directed mutagenesis, isotopic substitutions, and quantum chemical calculations. Therefore, infrared spectroscopy is a powerful tool for understanding the molecular mechanism of photosynthetic water oxidation. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
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29
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Debus RJ. Evidence from FTIR Difference Spectroscopy That D1-Asp61 Influences the Water Reactions of the Oxygen-Evolving Mn4CaO5 Cluster of Photosystem II. Biochemistry 2014; 53:2941-55. [DOI: 10.1021/bi500309f] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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30
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Service RJ, Hillier W, Debus RJ. Network of Hydrogen Bonds near the Oxygen-Evolving Mn4CaO5 Cluster of Photosystem II Probed with FTIR Difference Spectroscopy. Biochemistry 2014; 53:1001-17. [DOI: 10.1021/bi401450y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rachel J. Service
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Warwick Hillier
- Research
School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Richard J. Debus
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
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31
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Service RJ, Yano J, Dilbeck PL, Burnap RL, Hillier W, Debus RJ. Participation of glutamate-333 of the D1 polypeptide in the ligation of the Mn₄CaO₅ cluster in photosystem II. Biochemistry 2013; 52:8452-64. [PMID: 24168467 DOI: 10.1021/bi401339f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In the 1.9 Å structural model of photosystem II (PDB: 3ARC), the amino acid residue Glu333 of the D1 polypeptide coordinates to the oxygen-evolving Mn₄CaO₅ cluster. This residue appears to be highly significant in that it bridges the two Mn ions (Mn(B3) and the "dangling" Mn(A4)) that are also bridged by the oxygen atom O5. This oxygen atom has been proposed to be derived from one of two substrate water molecules and to become incorporated into the product dioxygen molecule during the final step in the catalytic cycle. In addition, the backbone nitrogen of D1-Glu333 interacts directly with a nearby Cl⁻ atom. To further explore the influence of this structurally unique residue on the properties of the Mn₄CaO₅ cluster, the D1-E333Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray absorption, and FTIR difference spectroscopy. The kinetics of oxygen release in the mutant were essentially unchanged from those in wild-type. In addition, the oxygen flash yields exhibited normal period-four oscillations having normal S state parameters, although the yields were lower, indicative of the mutant's lower steady-state dioxygen evolution rate of approximately 30% compared to that of the wild-type. The S₁ state Mn-XANES and Mn-EXAFS and S₂ state multiline EPR signals of purified D1-E333Q PSII core complexes closely resembled those of wild-type, aside from having lower amplitudes. The S(n+1)-minus-S(n) FTIR difference spectra showed only minor alterations to the carbonyl, amide, and carboxylate stretching regions. However, the mutation eliminated a negative peak at 3663 cm⁻¹ in the weakly H-bonding O-H stretching region of the S₂-minus-S₁ FTIR difference spectrum and caused an approximately 9 cm⁻¹ downshift of the negative feature in this region of the S₁-minus-S₀ FTIR difference spectrum. We conclude that fully functional Mn₄CaO₅ clusters assemble in the presence of the D1-E333Q mutation but that the mutation decreases the yield of assembled clusters and alters the H-bonding properties of one or more water molecules or hydroxide groups that are located on or near the Mn₄CaO₅ cluster and that either deprotonate or form stronger hydrogen bonds during the S₀ to S₁ and S₁ to S₂ transitions.
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Affiliation(s)
- Rachel J Service
- Department of Biochemistry, University of California , Riverside California 92521, United States
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32
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Nagashima H, Mino H. Highly resolved proton matrix ENDOR of oriented photosystem II membranes in the S2 state. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1165-73. [DOI: 10.1016/j.bbabio.2013.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/26/2013] [Accepted: 06/03/2013] [Indexed: 12/12/2022]
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33
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Pokhrel R, Service RJ, Debus RJ, Brudvig GW. Mutation of Lysine 317 in the D2 Subunit of Photosystem II Alters Chloride Binding and Proton Transport. Biochemistry 2013; 52:4758-73. [DOI: 10.1021/bi301700u] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ravi Pokhrel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107,
United States
| | - Rachel J. Service
- Department
of Biochemistry, University of California, Riverside, California 92521,
United States
| | - Richard J. Debus
- Department
of Biochemistry, University of California, Riverside, California 92521,
United States
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107,
United States
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34
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Experimental demonstration of radicaloid character in a Ru(V)=O intermediate in catalytic water oxidation. Proc Natl Acad Sci U S A 2013; 110:3765-70. [PMID: 23417296 DOI: 10.1073/pnas.1222102110] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water oxidation is the key half reaction in artificial photosynthesis. An absence of detailed mechanistic insight impedes design of new catalysts that are more reactive and more robust. A proposed paradigm leading to enhanced reactivity is the existence of oxyl radical intermediates capable of rapid water activation, but there is a dearth of experimental validation. Here, we show the radicaloid nature of an intermediate reactive toward formation of the O-O bond by assessing the spin density on the oxyl group by Electron Paramagnetic Resonance (EPR). In the study, an (17)O-labeled form of a highly oxidized, short-lived intermediate in the catalytic cycle of the water oxidation catalyst cis,cis-[(2,2-bipyridine)2(H2O)Ru(III)ORu(III)(OH2)(bpy)2](4+) was investigated. It contains Ru centers in oxidation states [4,5], has at least one Ru(V) = O unit, and shows
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35
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Suzuki H, Sugiura M, Noguchi T. Determination of the Miss Probabilities of Individual S-State Transitions during Photosynthetic Water Oxidation by Monitoring Electron Flow in Photosystem II Using FTIR Spectroscopy. Biochemistry 2012; 51:6776-85. [DOI: 10.1021/bi300708a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Suzuki
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Miwa Sugiura
- Cell-Free Science and Technology
Research Center, Ehime University, Matsuyama,
Ehime 790-8577, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8, Honcho, Kawagchi,
Saitama 332-0012, 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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36
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Siegbahn PEM. The Effect of Backbone Constraints: The Case of Water Oxidation by the Oxygen-Evolving Complex in PSII. Chemphyschem 2011; 12:3274-80. [DOI: 10.1002/cphc.201100475] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/18/2011] [Indexed: 11/06/2022]
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37
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Stich TA, Yeagle GJ, Service RJ, Debus RJ, Britt RD. Ligation of D1-His332 and D1-Asp170 to the manganese cluster of photosystem II from Synechocystis assessed by multifrequency pulse EPR spectroscopy. Biochemistry 2011; 50:7390-404. [PMID: 21790179 DOI: 10.1021/bi2010703] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Multifrequency electron spin-echo envelope modulation (ESEEM) spectroscopy is used to ascertain the nature of the bonding interactions of various active site amino acids with the Mn ions that compose the oxygen-evolving cluster (OEC) in photosystem II (PSII) from the cyanobacterium Synechocystis sp. PCC 6803 poised in the S(2) state. Spectra of natural isotopic abundance PSII ((14)N-PSII), uniformly (15)N-labeled PSII ((15)N-PSII), and (15)N-PSII containing (14)N-histidine ((14)N-His/(15)N-PSII) are compared. These complementary data sets allow for a precise determination of the spin Hamiltonian parameters of the postulated histidine nitrogen interaction with the Mn ions of the OEC. These results are compared to those from a similar study on PSII isolated from spinach. Upon mutation of His332 of the D1 polypeptide to a glutamate residue, all isotopically sensitive spectral features vanish. Additional K(a)- and Q-band ESEEM experiments on the D1-D170H site-directed mutant give no indication of new (14)N-based interactions.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
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Najafpour MM. Calcium-manganese oxides as structural and functional models for active site in oxygen evolving complex in photosystem II: Lessons from simple models. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2011; 104:111-7. [DOI: 10.1016/j.jphotobiol.2010.12.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/10/2010] [Accepted: 12/13/2010] [Indexed: 01/12/2023]
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Ho FM. Structural and mechanistic investigations of photosystem II through computational methods. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:106-20. [PMID: 21565158 DOI: 10.1016/j.bbabio.2011.04.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/22/2011] [Accepted: 04/02/2011] [Indexed: 11/17/2022]
Abstract
The advent of oxygenic photosynthesis through water oxidation by photosystem II (PSII) transformed the planet, ultimately allowing the evolution of aerobic respiration and an explosion of ecological diversity. The importance of this enzyme to life on Earth has ironically been paralleled by the elusiveness of a detailed understanding of its precise catalytic mechanism. Computational investigations have in recent years provided more and more insights into the structural and mechanistic details that underlie the workings of PSII. This review will present an overview of some of these studies, focusing on those that have aimed at elucidating the mechanism of water oxidation at the CaMn₄ cluster in PSII, and those exploring the features of the structure and dynamics of this enzyme that enable it to catalyse this energetically demanding reaction. This article is part of a Special Issue entitled: Photosystem II.
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Affiliation(s)
- Felix M Ho
- Deparment of Photochemistry and Molecular Sciences, Angström Laboratory, Uppsala University, Sweden.
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Cox N, Rapatskiy L, Su JH, Pantazis DA, Sugiura M, Kulik L, Dorlet P, Rutherford AW, Neese F, Boussac A, Lubitz W, Messinger J. Effect of Ca2+/Sr2+ substitution on the electronic structure of the oxygen-evolving complex of photosystem II: a combined multifrequency EPR, 55Mn-ENDOR, and DFT study of the S2 state. J Am Chem Soc 2011; 133:3635-48. [PMID: 21341708 DOI: 10.1021/ja110145v] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic structures of the native Mn(4)O(x)Ca cluster and the biosynthetically substituted Mn(4)O(x)Sr cluster of the oxygen evolving complex (OEC) of photosystem II (PSII) core complexes isolated from Thermosynechococcus elongatus, poised in the S(2) state, were studied by X- and Q-band CW-EPR and by pulsed Q-band (55)Mn-ENDOR spectroscopy. Both wild type and tyrosine D less mutants grown photoautotrophically in either CaCl(2) or SrCl(2) containing media were measured. The obtained CW-EPR spectra of the S(2) state displayed the characteristic, clearly noticeable differences in the hyperfine pattern of the multiline EPR signal [Boussac et al. J. Biol. Chem.2004, 279, 22809-22819]. In sharp contrast, the manganese ((55)Mn) ENDOR spectra of the Ca and Sr forms of the OEC were remarkably similar. Multifrequency simulations of the X- and Q-band CW-EPR and (55)Mn-pulsed ENDOR spectra using the Spin Hamiltonian formalism were performed to investigate this surprising result. It is shown that (i) all four manganese ions contribute to the (55)Mn-ENDOR spectra; (ii) only small changes are seen in the fitted isotropic hyperfine values for the Ca(2+) and Sr(2+) containing OEC, suggesting that there is no change in the overall spin distribution (electronic coupling scheme) upon Ca(2+)/Sr(2+) substitution; (iii) the changes in the CW-EPR hyperfine pattern can be explained by a small decrease in the anisotropy of at least two hyperfine tensors. It is proposed that modifications at the Ca(2+) site may modulate the fine structure tensor of the Mn(III) ion. DFT calculations support the above conclusions. Our data analysis also provides strong support for the notion that in the S(2) state the coordination of the Mn(III) ion is square-pyramidal (5-coordinate) or octahedral (6-coordinate) with tetragonal elongation. In addition, it is shown that only one of the currently published OEC models, the Siegbahn structure [Siegbahn, P. E. M. Acc. Chem. Res.2009, 42, 1871-1880, Pantazis, D. A. et al. Phys. Chem. Chem. Phys.2009, 11, 6788-6798], is consistent with all data presented here. These results provide important information for the structure of the OEC and the water-splitting mechanism. In particular, the 5-coordinate Mn(III) is a potential site for substrate 'water' (H(2)O, OH(-)) binding. Its location within the cuboidal structural unit, as opposed to the external 'dangler' position, may have important consequences for the mechanism of O-O bond formation.
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Affiliation(s)
- Nicholas Cox
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
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41
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Li X, Chen G, Schinzel S, Siegbahn PEM. A comparison between artificial and natural water oxidation. Dalton Trans 2011; 40:11296-307. [DOI: 10.1039/c1dt11323b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Service RJ, Yano J, McConnell I, Hwang HJ, Niks D, Hille R, Wydrzynski T, Burnap RL, Hillier W, Debus RJ. Participation of glutamate-354 of the CP43 polypeptide in the ligation of manganese and the binding of substrate water in photosystem II. Biochemistry 2010; 50:63-81. [PMID: 21114287 DOI: 10.1021/bi1015937] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the current X-ray crystallographic structural models of photosystem II, Glu354 of the CP43 polypeptide is the only amino acid ligand of the oxygen-evolving Mn(4)Ca cluster that is not provided by the D1 polypeptide. To further explore the influence of this structurally unique residue on the properties of the Mn(4)Ca cluster, the CP43-E354Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray absorption, FTIR, and mass spectrometry. The kinetics of oxygen release in the mutant were essentially unchanged from those in wild type. In addition, the oxygen flash yields exhibited normal period four oscillations having normal S state parameters, although the yields were lower, correlating with the mutant's lower steady-state rate (approximately 20% compared to wild type). Experiments conducted with H(2)(18)O showed that the fast and slow phases of substrate water exchange in CP43-E354Q thylakoid membranes were accelerated 8.5- and 1.8-fold, respectively, in the S(3) state compared to wild type. Purified oxygen-evolving CP43-E354Q PSII core complexes exhibited a slightly altered S(1) state Mn-EXAFS spectrum, a slightly altered S(2) state multiline EPR signal, a substantially altered S(2)-minus-S(1) FTIR difference spectrum, and an unusually long lifetime for the S(2) state (>10 h) in a substantial fraction of reaction centers. In contrast, the S(2) state Mn-EXAFS spectrum was nearly indistinguishable from that of wild type. The S(2)-minus-S(1) FTIR difference spectrum showed alterations throughout the amide and carboxylate stretching regions. Global labeling with (15)N and specific labeling with l-[1-(13)C]alanine revealed that the mutation perturbs both amide II and carboxylate stretching modes and shifts the symmetric carboxylate stretching modes of the α-COO(-) group of D1-Ala344 (the C-terminus of the D1 polypeptide) to higher frequencies by 3-4 cm(-1) in both the S(1) and S(2) states. The EPR and FTIR data implied that 76-82% of CP43-E354Q PSII centers can achieve the S(2) state and that most of these can achieve the S(3) state, but no evidence for advancement beyond the S(3) state was observed in the FTIR data, at least not in a majority of PSII centers. Although the X-ray absorption and EPR data showed that the CP43-E354Q mutation only subtly perturbs the structure and spin state of the Mn(4)Ca cluster in the S(2) state, the FTIR and H(2)(18)O exchange data show that the mutation strongly influences other properties of the Mn(4)Ca cluster, altering the response of numerous carboxylate and amide groups to the increased positive charge that develops on the cluster during the S(1) to S(2) transition and weakening the binding of both substrate water molecules (or water-derived ligands), especially the one that exchanges rapidly in the S(3) state. The FTIR data provide evidence that CP43-Glu354 coordinates to the Mn(4)Ca cluster in the S(1) state as a bridging ligand between two metal ions but provide no compelling evidence that this residue changes its coordination mode during the S(1) to S(2) transition. The H(2)(18)O exchange data provide evidence that CP43-Glu354 interacts with the Mn ion that ligates the substrate water molecule (or water-derived ligand) that is in rapid exchange in the S(3) state.
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Affiliation(s)
- Rachel J Service
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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Service RJ, Hillier W, Debus RJ. Evidence from FTIR difference spectroscopy of an extensive network of hydrogen bonds near the oxygen-evolving Mn(4)Ca cluster of photosystem II involving D1-Glu65, D2-Glu312, and D1-Glu329. Biochemistry 2010; 49:6655-69. [PMID: 20593803 DOI: 10.1021/bi100730d] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analyses of the refined X-ray crystallographic structures of photosystem II (PSII) at 2.9-3.5 A have revealed the presence of possible channels for the removal of protons from the catalytic Mn(4)Ca cluster during the water-splitting reaction. As an initial attempt to verify these channels experimentally, the presence of a network of hydrogen bonds near the Mn(4)Ca cluster was probed with FTIR difference spectroscopy in a spectral region sensitive to the protonation states of carboxylate residues and, in particular, with a negative band at 1747 cm(-1) that is often observed in the S(2)-minus-S(1) FTIR difference spectrum of PSII from the cyanobacterium Synechocystis sp. PCC 6803. On the basis of its 4 cm(-1) downshift in D(2)O, this band was assigned to the carbonyl stretching vibration (C horizontal lineO) of a protonated carboxylate group whose pK(a) decreases during the S(1) to S(2) transition. The positive charge that forms on the Mn(4)Ca cluster during the S(1) to S(2) transition presumably causes structural perturbations that are transmitted to this carboxylate group via electrostatic interactions and/or an extended network of hydrogen bonds. In an attempt to identify the carboxylate group that gives rise to this band, the FTIR difference spectra of PSII core complexes from the mutants D1-Asp61Ala, D1-Glu65Ala, D1-Glu329Gln, and D2-Glu312Ala were examined. In the X-ray crystallographic models, these are the closest carboxylate residues to the Mn(4)Ca cluster that do not ligate Mn or Ca and all are highly conserved. The 1747 cm(-1) band is present in the S(2)-minus-S(1) FTIR difference spectrum of D1-Asp61Ala but absent from the corresponding spectra of D1-Glu65Ala, D2-Glu312Ala, and D1-Glu329Gln. The band is also sharply diminished in magnitude in the wild type when samples are maintained at a relative humidity of </=85%. It is proposed that D1-Glu65, D2-Glu312, and D1-Glu329 participate in a common network of hydrogen bonds that includes water molecules and the carboxylate group that gives rise to the 1747 cm(-1) band. It is further proposed that the mutation of any of these three residues, or partial dehydration caused by maintaining samples at a relative humidity of <or=85%, disrupts the network sufficiently that the structural perturbations associated with the S(1) to S(2) transition are no longer transmitted to the carboxylate group that gives rise to the 1747 cm(-1) band. Because D1-Glu329 is located approximately 20 A from D1-Glu65 and D2-Glu312, the postulated network of hydrogen bonds must extend for at least 20 A across the lumenal face of the Mn(4)Ca cluster. The D1-Asp61Ala, D1-Glu65Ala, and D2-Glu312Ala mutations also appear to substantially decrease the fraction of PSII reaction centers that undergo the S(3) to S(0) transition in response to a saturating flash. This behavior is consistent with D1-Asp61, D1-Glu65, and D2-Glu312 participating in a dominant proton egress channel that links the Mn(4)Ca cluster with the thylakoid lumen.
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Affiliation(s)
- Rachel J Service
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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44
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Katsuda M, Hishikawa E, Mitani M, Yoshioka Y. Theoretical study of electronic structures of [(H2O)3(O-)Mn(μ-oxo)2Mn(OH2)4]q+ (q = 2 or 3) with Mn–O bond. Phys Chem Chem Phys 2010; 12:2730-9. [DOI: 10.1039/b914793d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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Sugiura M, Rappaport F, Hillier W, Dorlet P, Ohno Y, Hayashi H, Boussac A. Evidence that D1-His332 in photosystem II from Thermosynechococcus elongatus interacts with the S3-state and not with the S2-state. Biochemistry 2009; 48:7856-66. [PMID: 19624137 DOI: 10.1021/bi901067b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygen evolution by Photosystem II (PSII) is catalyzed by a Mn(4)Ca cluster. Thus far, from the crystallographic three-dimensional (3D) structures, seven amino acid residues have been identified as possible ligands of the Mn(4)Ca cluster. Among them, there is only one histidine, His332, which belongs to the D1 polypeptide. The relationships of the D1-His332 amino acid with kinetics and thermodynamic properties of the Mn(4)Ca cluster in the S(2)- and S(3)-states of the catalytic cycle were investigated in purified PSII from Thermosynechococcus elongatus. This was done by examining site-directed D1-His332Gln and D1-His332Ser mutants by a variety of spectroscopic techniques such as time-resolved UV-visible absorption change spectroscopy, cw- and pulse-EPR, thermoluminescence, and measurement of substrate water exchange. Both mutants grew photo-autotrophically and active PSII could be purified. On the basis of the parameters assessed in this work, the D1-His332(Gln, Ser) mutations had no effect in the S(2)-state. Electron spin-echo envelope modulation (ESEEM) spectroscopy also showed that possible interactions between the nuclear spin of the nitrogen(s) of D1-His332 with the electronic spin S = 1/2 of the Mn(4)Ca cluster in the S(2)-state were not detectable and that the D1-His332Ser mutation did not affect the detected hyperfine couplings. In contrast, the following changes were observed in the S(3)-state of the D1-His332 mutants: (1) The redox potential of the S(3)/S(2) couple was slightly increased by < or = 20 meV, (2) The S(3)-EPR spectrum was slightly modified, (3) The D1-His332Gln mutation resulted in a approximately 3 fold decrease of the slow (tightly bound) exchange rate and a approximately 2 fold increase of the fast exchange rate of the water substrate molecules. All these results suggest that the D1-His332 would be more involved in S(3) than in S(2). This could be one element of the conformational changes put forward in the S(2) to S(3) transition.
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Affiliation(s)
- Miwa Sugiura
- Cell-Free Science and Technology Research Center, Ehime University, Bunkyo-cho, Matsuyama Ehime, 790-8577, Japan.
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46
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Cox N, Hughes JL, Steffen R, Smith PJ, Rutherford AW, Pace RJ, Krausz E. Identification of the QY Excitation of the Primary Electron Acceptor of Photosystem II: CD Determination of Its Coupling Environment. J Phys Chem B 2009; 113:12364-74. [DOI: 10.1021/jp808796x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Joseph L. Hughes
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Ronald Steffen
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Paul J. Smith
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - A. William Rutherford
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Ron J. Pace
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Elmars Krausz
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and iBiTec-S, CNRS URA 2096, Bât 532, CEA Saclay, 91191 Gif-sur-Yvette, France
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47
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Suzuki H, Sugiura M, Noguchi T. Monitoring Proton Release during Photosynthetic Water Oxidation in Photosystem II by Means of Isotope-Edited Infrared Spectroscopy. J Am Chem Soc 2009; 131:7849-57. [DOI: 10.1021/ja901696m] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Suzuki
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, and Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Miwa Sugiura
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, and Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, and Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
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48
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Gauthier A, Carpentier R. Disorganization of the Mn4Ca complex of photosystem II by ruthenium red: a thermoluminescence study. LUMINESCENCE 2009; 24:108-14. [DOI: 10.1002/bio.1082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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49
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Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat Struct Mol Biol 2009; 16:334-42. [PMID: 19219048 DOI: 10.1038/nsmb.1559] [Citation(s) in RCA: 867] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 01/14/2009] [Indexed: 12/11/2022]
Abstract
Photosystem II (PSII) is a large homodimeric protein-cofactor complex located in the photosynthetic thylakoid membrane that acts as light-driven water:plastoquinone oxidoreductase. The crystal structure of PSII from Thermosynechococcus elongatus at 2.9-A resolution allowed the unambiguous assignment of all 20 protein subunits and complete modeling of all 35 chlorophyll a molecules and 12 carotenoid molecules, 25 integral lipids and 1 chloride ion per monomer. The presence of a third plastoquinone Q(C) and a second plastoquinone-transfer channel, which were not observed before, suggests mechanisms for plastoquinol-plastoquinone exchange, and we calculated other possible water or dioxygen and proton channels. Putative oxygen positions obtained from a Xenon derivative indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII. The chloride position suggests a role in proton-transfer reactions because it is bound through a putative water molecule to the Mn(4)Ca cluster at a distance of 6.5 A and is close to two possible proton channels.
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50
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Siegbahn PEM. A structure-consistent mechanism for dioxygen formation in photosystem II. Chemistry 2008; 14:8290-302. [PMID: 18680116 DOI: 10.1002/chem.200800445] [Citation(s) in RCA: 198] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In recent DFT studies a new mechanism for O-O bond formation at the oxygen evolving center (OEC) in photosystem II has been suggested. With the structure of the S(4) state required for that mechanism, the structures of the lower S states are investigated herein by adding protons and electrons. A model was used including the full amino acids for the ones ligating the OEC, and in which the backbone positions were held fixed from the X-ray structure. The only charged second-shell ligand Arg357 was also included. An optimized structure for the S(1) state was reached with a large similarity to one of those suggested by EXAFS. A full catalytic cycle was derived which can rationalize the structural relaxation in the S(2) to S(3) transition, and the fact that only an electron leaves in the transition before. Water is suggested to bind to the OEC in the S(2) to S(3), and S(4) to S(0) transitions. A new possibility for water exchange is suggested from the final energy diagram. The optimal O-O bond formation occurs between an oxygen radical and an oxo ligand. The alternative mechanism, where the oxygen radical reacts with an external water, has a barrier about 20 kcal mol(-1) higher.
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Affiliation(s)
- Per E M Siegbahn
- Department of Physics, ALBA NOVA, Stockholm University, 106 91 Stockholm, Sweden.
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