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Affiliation(s)
- Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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2
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Baituti B. Computational studies of the Mn 4/Ca cluster in photosystem II. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Computational chemistry with the data from more detailed X-ray diffraction (XRD) oxygen evolving complex (OEC) structure has been used extensively of late in exploring the mechanisms of water oxidation in the OEC. The study reported in this paper involves density functional theory (DFT) calculations to investigate whether the data are in agreement with the four manganese ions in the OEC, being organized as a ‘3[Formula: see text]1’ (trimer plus one) model [Gatt et al. Angewandte Chemie International Edition, 51, 12025–12028, 2012; Petrie et al. Chemistry - A European Journal, 21, 6780–6792, 2015; Terrett et al. Chemical Communications, 50, 3187–3190, 2014] or ‘dimer of dimers’ model. [Terrett et al. Journal of Inorganic Biochemistry, 162, 178–189, 2016]. The data analysis method used involves quantum chemical DFT calculations on relevant models of the OEC cluster. DFT calculations were performed using both the so-called ‘open’ and ‘closed’ forms [Terrett et al. Journal of Inorganic Biochemistry, 162, 178–189, 2016] of the S2 OEC structure models with total spin ([Formula: see text]) 1/2, 7/2, 9/2 and 15/2 within the MnIII MnIV MnIII MnIII ‘low’ oxidation paradigm to examine exchange coupling within the OEC cluster. The results show that the [Formula: see text]-coupling in the ‘closed’ form: [Formula: see text][Formula: see text]cm[Formula: see text], [Formula: see text][Formula: see text]cm[Formula: see text], [Formula: see text][Formula: see text]cm[Formula: see text] and [Formula: see text]–[Formula: see text][Formula: see text]cm[Formula: see text]. In the ‘closed’ form, [Formula: see text] and [Formula: see text] represent the two largest exchange interactions within the manganese cluster, whereas [Formula: see text] and [Formula: see text] are small and almost net cancel. The magnetic coupling between the four Mn ions is close to ‘dimer of dimers’, with both dimers anti-ferromagnetically coupled internally and with weak inter-dimer net coupling.
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Affiliation(s)
- Bernard Baituti
- Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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3
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Beal NJ, Corry TA, O'Malley PJ. A Comparison of Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters for Intermediates Involved in the S 2 to S 3 State Transition of Nature's Oxygen Evolving Complex. J Phys Chem B 2018; 122:1394-1407. [PMID: 29300480 DOI: 10.1021/acs.jpcb.7b10843] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A broken symmetry density functional theory (BS-DFT) magnetic analysis of the S2, S2YZ•, and S3 states of Nature's oxygen evolving complex is performed for both the native Ca and Sr substituted forms. Good agreement with experiment is observed between the tyrosyl calculated g-tensor and 1H hyperfine couplings for the native Ca form. Changes in the hydrogen bonding environment of the tyrosyl radical in S2YZ• caused by Sr substitution lead to notable changes in the calculated g-tensor of the tyrosyl radical. Comparison of calculated and experimental 55Mn hyperfine couplings for the S3 state presently favors an open cubane form of the complex with an additional OH ligand coordinating to MnD. In Ca models, this additional ligation can arise by closed-cubane form deprotonation of the Ca ligand W3 in the S2YZ• state accompanied by spontaneous movement to the vacant Mn coordination site or by addition of an external OH group. For the Sr form, no spontaneous movement of W3 to the vacant Mn coordination site is observed in contrast to the native Ca form, a difference which may lead to the reduced catalytic activity of the Sr substituted form. BS-DFT studies on peroxo models of S3 as indicated by a recent X-ray free electron laser (XFEL) crystallography study give rise to a structural model compatible with experimental data and an S = 3 ground state compatible with EPR studies.
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Affiliation(s)
- Nathan J Beal
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - Thomas A Corry
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - Patrick J O'Malley
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
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4
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Shoji M, Isobe H, Shen JR, Yamaguchi K. Geometric and electronic structures of the synthetic Mn₄CaO₄ model compound mimicking the photosynthetic oxygen-evolving complex. Phys Chem Chem Phys 2017; 18:11330-40. [PMID: 27055567 DOI: 10.1039/c5cp07226c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(Bu(t)COO)8(py)(Bu(t)COOH)2] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan and Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan.
| | - Hiroshi Isobe
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-0043, Japan and Handairigaku Techno-Research (NPO), Toyonaka, Osaka 560-0043, Japan
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Nagashima H, Nakajima Y, Shen JR, Mino H. Proton Matrix ENDOR Studies on Ca2+-depleted and Sr2+-substituted Manganese Cluster in Photosystem II. J Biol Chem 2015; 290:28166-28174. [PMID: 26438823 DOI: 10.1074/jbc.m115.675496] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 01/08/2023] Open
Abstract
Proton matrix ENDOR spectra were measured for Ca(2+)-depleted and Sr(2+)-substituted photosystem II (PSII) membrane samples from spinach and core complexes from Thermosynechococcus vulcanus in the S2 state. The ENDOR spectra obtained were similar for untreated PSII from T. vulcanus and spinach, as well as for Ca(2+)-containing and Sr(2+)-substituted PSII, indicating that the proton arrangements around the manganese cluster in cyanobacterial and higher plant PSII and Ca(2+)-containing and Sr(2+)-substituted PSII are similar in the S2 state, in agreement with the similarity of the crystal structure of both Ca(2+)-containing and Sr(2+)-substituted PSII in the S1 state. Nevertheless, slightly different hyperfine separations were found between Ca(2+)-containing and Sr(2+)-substituted PSII because of modifications of the water protons ligating to the Sr(2+) ion. Importantly, Ca(2+) depletion caused the loss of ENDOR signals with a 1.36-MHz separation because of the loss of the water proton W4 connecting Ca(2+) and YZ directly. With respect to the crystal structure and the functions of Ca(2+) in oxygen evolution, it was concluded that the roles of Ca(2+) and Sr(2+) involve the maintenance of the hydrogen bond network near the Ca(2+) site and electron transfer pathway to the manganese cluster.
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Affiliation(s)
- Hiroki Nagashima
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602, Japan
| | - Yoshiki Nakajima
- Photosynthesis Research Center, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Hiroyuki Mino
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602, Japan.
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Sproviero EM, McEvoy JP, Gascón JA, Brudvig GW, Batista VS. Computational insights into the O2-evolving complex of photosystem II. PHOTOSYNTHESIS RESEARCH 2008; 97:91-114. [PMID: 18483777 PMCID: PMC2728911 DOI: 10.1007/s11120-008-9307-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Accepted: 04/10/2008] [Indexed: 05/04/2023]
Abstract
Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies.
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Computational studies of the O(2)-evolving complex of photosystem II and biomimetic oxomanganese complexes. Coord Chem Rev 2008; 252:395-415. [PMID: 19190716 DOI: 10.1016/j.ccr.2007.09.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In recent years, there has been considerable interest in studies of catalytic metal clusters in metalloproteins based on Density Functional Theory (DFT) quantum mechanics/molecular mechanics (QM/MM) hybrid methods. These methods explicitly include the perturbational influence of the surrounding protein environment on the structural/functional properties of the catalytic centers. In conjunction with recent breakthroughs in X-ray crystallography and advances in spectroscopic and biophysical studies, computational chemists are trying to understand the structural and mechanistic properties of the oxygen-evolving complex (OEC) embedded in photosystem II (PSII). Recent studies include the development of DFT-QM/MM computational models of the Mn(4)Ca cluster, responsible for photosynthetic water oxidation, and comparative quantum mechanical studies of biomimetic oxomanganese complexes. A number of computational models, varying in oxidation and protonation states and ligation of the catalytic center by amino acid residues, water, hydroxide and chloride have been characterized along the PSII catalytic cycle of water splitting. The resulting QM/MM models are consistent with available mechanistic data, Fourier-transform infrared (FTIR) spectroscopy, X-ray diffraction data and extended X-ray absorption fine structure (EXAFS) measurements. Here, we review these computational efforts focused towards understanding the catalytic mechanism of water oxidation at the detailed molecular level.
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8
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Abstract
Water oxidation at photosystem II Mn-cluster is mediated by the redox-active tyrosine Y(Z). We calculated the redox potential (E(m)) of Y(Z) and its symmetrical counterpart Y(D), by solving the linearized Poisson-Boltzmann equation. The calculated E(m)(Y( )/Y(-)) were +926 mV/+694 mV for Y(Z)/Y(D) with the Mn-cluster in S2 state. Together with the asymmetric position of the Mn-cluster relative to Y(Z/D), differences in H-bond network between Y(Z) (Y(Z)/D1-His(190)/D1-Asn(298)) and Y(D) (Y(D)/D2-His(189)/D2-Arg(294)/CP47-Glu(364)) are crucial for E(m)(Y(Z/D)). When D1-His(190) is protonated, corresponding to a thermally activated state, the calculated E(m)(Y(Z)) was +1216 mV, which is as high as the E(m) for P(D1/D2). We observed deprotonation at CP43-Arg(357) upon S-state transition, which may suggest its involvement in the proton exit pathway. E(m)(Y(D)) was affected by formation of P(D2)(+) (but not P(D1)(+)) and sensitive to the protonation state of D2-Arg(180). This points to an electrostatic link between Y(D) and P(D2).
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Affiliation(s)
- Hiroshi Ishikita
- Institute of Chemistry and Biochemistry, Free University of Berlin, Berlin, Germany
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Mukhopadhyay S, Mandal SK, Bhaduri S, Armstrong WH. Manganese clusters with relevance to photosystem II. Chem Rev 2005; 104:3981-4026. [PMID: 15352784 DOI: 10.1021/cr0206014] [Citation(s) in RCA: 481] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sumitra Mukhopadhyay
- Department of Chemistry, Eugene F Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, USA
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Hsieh WY, Campbell KA, Gregor W, David Britt R, Yoder DW, Penner-Hahn JE, Pecoraro VL. The first spectroscopic model for the S1 state multiline signal of the OEC. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:149-57. [PMID: 15100027 DOI: 10.1016/j.bbabio.2003.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Revised: 12/05/2003] [Accepted: 12/05/2003] [Indexed: 11/18/2022]
Abstract
The parallel-mode electron paramagnetic resonance (EPR) spectrum of the S(1) state of the oxygen-evolving complex (OEC) shows a multiline signal centered around g=12, indicating an integer spin system. The series of [Mn(2)(2-OHsalpn)(2)] complexes were structurally characterized in four oxidation levels (Mn(II)(2), Mn(II)Mn(III), Mn(III)(2), and Mn(III)Mn(IV)). By using bulk electrolysis, the [Mn(III)Mn(IV)(2-OHsalpn)(2)(OH)] is oxidized to a species that contains Mn(IV) oxidation state as detected by X-ray absorption near edge spectroscopy (XANES) and that can be formulated as Mn(IV)(4) tetramer. The parallel-mode EPR spectrum of this multinuclear Mn(IV)(4) complex shows 18 well-resolved hyperfine lines center around g=11 with an average hyperfine splitting of 36 G. This EPR spectrum is very similar to that found in the S(1) state of the OEC. This is the first synthetic manganese model complex that shows an S(1)-like multiline spectrum in parallel-mode EPR.
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Affiliation(s)
- Wen-Yuan Hsieh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan MI 48109-1055, USA
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11
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Hughes JL, Prince BJ, Krausz E, Smith PJ, Pace RJ, Riesen H. Highly Efficient Spectral Hole-Burning in Oxygen-Evolving Photosystem II Preparations. J Phys Chem B 2004. [DOI: 10.1021/jp0492523] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph L. Hughes
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, Faculties Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Physical, Environmental and Mathematical Sciences, University College, The University of New South Wales, ADFA, Canberra ACT 2600, Australia
| | - Barry J. Prince
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, Faculties Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Physical, Environmental and Mathematical Sciences, University College, The University of New South Wales, ADFA, Canberra ACT 2600, Australia
| | - Elmars Krausz
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, Faculties Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Physical, Environmental and Mathematical Sciences, University College, The University of New South Wales, ADFA, Canberra ACT 2600, Australia
| | - Paul J. Smith
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, Faculties Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Physical, Environmental and Mathematical Sciences, University College, The University of New South Wales, ADFA, Canberra ACT 2600, Australia
| | - Ron J. Pace
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, Faculties Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Physical, Environmental and Mathematical Sciences, University College, The University of New South Wales, ADFA, Canberra ACT 2600, Australia
| | - Hans Riesen
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, Faculties Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Physical, Environmental and Mathematical Sciences, University College, The University of New South Wales, ADFA, Canberra ACT 2600, Australia
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12
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Petrie S, Mukhopadhyay S, Armstrong WH, Stranger R. Theoretical analysis of the [Mn2(μ-oxo)2(μ-carboxylato)2]+core. Phys Chem Chem Phys 2004. [DOI: 10.1039/b407512a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Dau H, Liebisch P, Haumann M. The structure of the manganese complex of Photosystem II in its dark-stable S1-state—EXAFS results in relation to recent crystallographic data. Phys Chem Chem Phys 2004. [DOI: 10.1039/b408146c] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mino H, Ishii A, Ono TA. Nonlineal relationship between g=2 doublet and multiline signals in Ca(2+)-depleted Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2003; 1606:127-36. [PMID: 14507433 DOI: 10.1016/s0005-2728(03)00107-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Illuminating of the Ca(2+)-depleted PS II in the S(2) state for a short period induced the doublet signal at g=2 with concomitant diminution of the multiline signal, both in the presence and absence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). In the absence of DCMU, the doublet signal decayed (t(1/2) approximately 7 min) during subsequent dark incubation at 273 K and the multiline signal was regenerated to the original amplitude with the same kinetics of the doublet decay. In the presence of DCMU, the doublet signal decayed much faster (t(1/2) approximately 1 min) by charge recombination with Q(A)(-), while the time course of the multiline recovery was inherently identical with that observed in the absence of DCMU. A simple theoretical consideration indicates the direct conversion from the doublet-signal state to the multiline state with no intermediate state between them. Lengthy dark storage at 77 K led to disappearance of the DCMU-affected doublet signal and a Fe(2+)/Q(A)(-) electron spin resonance (ESR) signal, but no recovery of the multiline signal. Notably, the multiline signal was restored by subsequent dark incubation at 273 K. The charge recombination between Q(A)(-) and the doublet signal species led to a thermoluminescence band at 7 degrees C in a medium at pH 5.5. The peak position shifted to 17 degrees C at pH 7.0, presumably due to a pH-dependent change in the redox property of a donor-side radical species responsible for the doublet signal. Based on these results, redox events in the Ca(2+)-depleted PS II are discussed in contradistinction with the normal processes in oxygen-evolving PS II.
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Affiliation(s)
- Hiroyuki Mino
- Laboratory for Photo-Biology(1), The Institute of Physical and Chemical Research, RIKEN Photodynamics Research Center, 519-1399 Aoba, Aramaki, Aoba, Sendai 980-0845, Japan.
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15
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Current awareness in phytochemical analysis. PHYTOCHEMICAL ANALYSIS : PCA 2001; 12:215-222. [PMID: 11705030 DOI: 10.1002/pca.555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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