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. [PMID: 39037338 DOI: 10.1039/d4cp01307g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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Debus RJ, Oyala PH. Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O 2-Evolving Mn 4CaO 5 Cluster in Photosystem II. J Phys Chem B 2024; 128:3870-3884. [PMID: 38602496 DOI: 10.1021/acs.jpcb.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The O2-evolving Mn4CaO5 cluster in photosystem II is ligated by six carboxylate residues. One of these is D170 of the D1 subunit. This carboxylate bridges between one Mn ion (Mn4) and the Ca ion. A second carboxylate ligand is D342 of the D1 subunit. This carboxylate bridges between two Mn ions (Mn1 and Mn2). D170 and D342 are located on opposite sides of the Mn4CaO5 cluster. Recently, it was shown that the D170E mutation perturbs both the intricate networks of H-bonds that surround the Mn4CaO5 cluster and the equilibrium between different conformers of the cluster in two of its lower oxidation states, S1 and S2, while still supporting O2 evolution at approximately 50% the rate of the wild type. In this study, we show that the D342E mutation produces much the same alterations to the cluster's FTIR and EPR spectra as D170E, while still supporting O2 evolution at approximately 20% the rate of the wild type. Furthermore, the double mutation, D170E + D342E, behaves similarly to the two single mutations. We conclude that D342E alters the equilibrium between different conformers of the cluster in its S1 and S2 states in the same manner as D170E and perturbs the H-bond networks in a similar fashion. This is the second identification of a Mn4CaO5 metal ligand whose mutation influences the equilibrium between the different conformers of the S1 and S2 states without eliminating O2 evolution. This finding has implications for our understanding of the mechanism of O2 formation in terms of catalytically active/inactive conformations of the Mn4CaO5 cluster in its lower oxidation states.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106, United States
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3
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Lee SJ, Kim GM, Kim CL. Self-lubrication and tribological properties of polymer composites containing lubricant. RSC Adv 2023; 13:3541-3551. [PMID: 36756588 PMCID: PMC9890944 DOI: 10.1039/d2ra08262d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
The purpose of this study was to improve the tribological properties of polydimethylsiloxane (PDMS) by mixing lubricants into it. The chemical composition, physical/chemical bonding state, and mechanical properties of the PDMS/lubricant composites (PLCs), prepared by mixing PDMS and lubricants at different ratios, were analyzed. With increasing lubricant content, the friction coefficient initially decreased, reaching a minimum value at a PDMS/lubricant ratio of 100 : 10; however, it gradually increased with a further increase in the lubricant content. The mechanical properties of PLCs with lubricant contents of 10% and higher decreased owing to the lubricant addition, so that the contact area with the sliding counter tip increased with lubricant content, but the frictional resistance was still decreased owing to the self-lubricating effect. In addition, owing to the effect of the lubricating film, there was no direct contact between the PLC surface and counter tip, and almost no damage was done to the PLC surface. Finite element analysis of the changes in stress during indentation and sliding confirmed that the stress applied to the PLCs was lower than that for bare PDMS.
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Affiliation(s)
- Sung-Jun Lee
- Department of Mechanical Engineering, Chosun University Gwangju 61452 Republic of Korea
| | - Gang-Min Kim
- Korea Automotive Technology InstituteYeongam-gun58463Republic of Korea
| | - Chang-Lae Kim
- Department of Mechanical Engineering, Chosun University Gwangju 61452 Republic of Korea
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4
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Kimura Y, Imanishi M, Li Y, Yura Y, Ohno T, Saga Y, Madigan MT, Wang-Otomo ZY. Identification of metal-sensitive structural changes in the Ca 2+-binding photocomplex from Thermochromatium tepidum by isotope-edited vibrational spectroscopy. J Chem Phys 2022; 156:105101. [DOI: 10.1063/5.0075600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Calcium ions play a dual role in expanding the spectral diversity and structural stability of photocomplexes from several Ca2+-requiring purple sulfur phototrophic bacteria. Here, metal-sensitive structural changes in the isotopically labeled light-harvesting 1 reaction center (LH1-RC) complexes from the thermophilic purple sulfur bacterium Thermochromatium ( Tch.) tepidum were investigated by perfusion-induced attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The ATR-FTIR difference spectra induced by exchanges between native Ca2+ and exogenous Ba2+ exhibited interconvertible structural and/or conformational changes in the metal binding sites at the LH1 C-terminal region. Most of the characteristic Ba2+/Ca2+ difference bands were detected even when only Ca ions were removed from the LH1-RC complexes, strongly indicating the pivotal roles of Ca2+ in maintaining the LH1-RC structure of Tch. tepidum. Upon 15N-, 13C- or 2H-labeling, the LH1-RC complexes exhibited characteristic 15N/14N-, 13C/12C-, or 2H/1H-isotopic shifts for the Ba2+/Ca2+ difference bands. Some of the 15N/14N or 13C/12C bands were also sensitive to further 2H-labelings. Given the band frequencies and their isotopic shifts along with the structural information of the Tch. tepidum LH1-RC complexes, metal-sensitive FTIR bands were tentatively identified to the vibrational modes of the polypeptide main chains and side chains comprising the metal binding sites. Furthermore, important new IR marker bands highly sensitive to the LH1 BChl a conformation in the Ca2+-bound states were revealed based on both ATR-FTIR and near-infrared Raman analyses. The present approach provides valuable insights concerning the dynamic equilibrium between the Ca2+- and Ba2+-bound states statically resolved by x-ray crystallography.
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Affiliation(s)
- Yukihiro Kimura
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Michie Imanishi
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yong Li
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yuki Yura
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Ohno
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yoshitaka Saga
- Department of Chemistry, Faculty of Science and Engineering, Kindai University, Higashi-Osaka 577-8502, Japan
| | - Michael T. Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901, USA
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5
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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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6
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Wang M, Zhang Y, Chen C, Zhang C, Jiang J, Weng Y. Structural Reorganization of a Synthetic Mimic of the Oxygen-Evolving Center in Multiple Redox Transitions Revealed by Electrochemical FTIR Spectra. J Phys Chem Lett 2021; 12:9830-9839. [PMID: 34605651 DOI: 10.1021/acs.jpclett.1c02689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In photosynthesis, the protein-bound natural oxygen-evolving center (OEC) undergoes multiple oxidation-state transitions in the light-driven water splitting reactions with a stepwise change in the oxidation potential. Because the protein is vulnerable to electrochemical oxidation, the multiple oxidation/reduction-state transitions can hardly be achieved by electrochemical oxidation with a continuous change in the oxidation potential. An OEC mimic that can undergo four redox transitions has been synthesized (Zhang, C., Science, 2015, 348, 690-693). Here we report an electrochemical FTIR spectroscopic study of this synthetic complex at its multiple oxidation states in the low-frequency region for Mn-O bonds. Compared with those of the native OEC induced by pulsed laser flashes, our results also show the existence of two structural isomers in the S2 state, with the closed cubane conformer being more stable than the open cubane conformer, in contrast to that of the native OEC in which the open form is more stable.
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Affiliation(s)
- Mohan Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changhui Chen
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunxi Zhang
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Yuxiang Weng
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523000, China
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7
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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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8
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Quinone transport in the closed light-harvesting 1 reaction center complex from the thermophilic purple bacterium Thermochromatium tepidum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148307. [PMID: 32926863 DOI: 10.1016/j.bbabio.2020.148307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 11/22/2022]
Abstract
Redox-active quinones play essential roles in efficient light energy conversion in type-II reaction centers of purple phototrophic bacteria. In the light-harvesting 1 reaction center (LH1-RC) complex of purple bacteria, QB is converted to QBH2 upon light-induced reduction and QBH2 is transported to the quinone pool in the membrane through the LH1 ring. In the purple bacterium Rhodobacter sphaeroides, the C-shaped LH1 ring contains a gap for quinone transport. In contrast, the thermophilic purple bacterium Thermochromatium (Tch.) tepidum has a closed O-shaped LH1 ring that lacks a gap, and hence the mechanism of photosynthetic quinone transport is unclear. Here we detected light-induced Fourier transform infrared (FTIR) signals responsible for changes of QB and its binding site that accompany photosynthetic quinone reduction in Tch. tepidum and characterized QB and QBH2 marker bands based on their 15N- and 13C-isotopic shifts. Quinone exchanges were monitored using reconstituted photosynthetic membranes comprised of solubilized photosynthetic proteins, membrane lipids, and exogenous ubiquinone (UQ) molecules. In combination with 13C-labeling of the LH1-RC and replacement of native UQ8 by ubiquinones of different tail lengths, we demonstrated that quinone exchanges occur efficiently within the hydrophobic environment of the lipid membrane and depend on the side chain length of UQ. These results strongly indicate that unlike the process in Rba. sphaeroides, quinone transport in Tch. tepidum occurs through the size-restricted hydrophobic channels in the closed LH1 ring and are consistent with structural studies that have revealed narrow hydrophobic channels in the Tch. tepidum LH1 transmembrane region.
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9
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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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10
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Imanishi M, Takenouchi M, Takaichi S, Nakagawa S, Saga Y, Takenaka S, Madigan MT, Overmann J, Wang-Otomo ZY, Kimura Y. A Dual Role for Ca 2+ in Expanding the Spectral Diversity and Stability of Light-Harvesting 1 Reaction Center Photocomplexes of Purple Phototrophic Bacteria. Biochemistry 2019; 58:2844-2852. [PMID: 31145583 DOI: 10.1021/acs.biochem.9b00351] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The light-harvesting 1 reaction center (LH1-RC) complex in the purple sulfur bacterium Thiorhodovibrio ( Trv.) strain 970 cells exhibits its LH1 Q y transition at 973 nm, the lowest-energy Q y absorption among purple bacteria containing bacteriochlorophyll a (BChl a). Here we characterize the origin of this extremely red-shifted Q y transition. Growth of Trv. strain 970 did not occur in cultures free of Ca2+, and elemental analysis of Ca2+-grown cells confirmed that purified Trv. strain 970 LH1-RC complexes contained Ca2+. The LH1 Q y band of Trv. strain 970 was blue-shifted from 959 to 875 nm upon Ca2+ depletion, but the original spectral properties were restored upon Ca2+ reconstitution, which also occurs with the thermophilic purple bacterium Thermochromatium ( Tch.) tepidum. The amino acid sequences of the LH1 α- and β-polypeptides from Trv. strain 970 closely resemble those of Tch. tepidum; however, Ca2+ binding in the Trv. strain 970 LH1-RC occurred more selectively than in Tch. tepidum LH1-RC and with a reduced affinity. Ultraviolet resonance Raman analysis indicated that the number of hydrogen-bonding interactions between BChl a and LH1 proteins of Trv. strain 970 was significantly greater than for Tch. tepidum and that Ca2+ was indispensable for maintaining these bonds. Furthermore, perfusion-induced Fourier transform infrared analyses detected Ca2+-induced conformational changes in the binding site closely related to the unique spectral properties of Trv. strain 970. Collectively, our results reveal an ecological strategy employed by Trv. strain 970 of integrating Ca2+ into its LH1-RC complex to extend its light-harvesting capacity to regions of the near-infrared spectrum unused by other purple bacteria.
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Affiliation(s)
- Michie Imanishi
- Graduate School of Agricultural Science , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Mizuki Takenouchi
- Faculty of Science , Ibaraki University , Bunkyo, Mito 310-8512 , Japan
| | - Shinichi Takaichi
- Faculty of Life Sciences , Tokyo University of Agriculture , Setagaya, Tokyo 156-8502 , Japan
| | - Shiori Nakagawa
- Department of Chemistry , Kindai University , Higashi-Osaka, Osaka 577-8502 , Japan
| | - Yoshitaka Saga
- Department of Chemistry , Kindai University , Higashi-Osaka, Osaka 577-8502 , Japan
| | - Shinji Takenaka
- Graduate School of Agricultural Science , Kobe University , Nada, Kobe 657-8501 , Japan
| | - Michael T Madigan
- Department of Microbiology , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures , 38124 Braunschweig , Germany.,Microbiology , Braunschweig University of Technology , 38106 Braunschweig , Germany
| | | | - Yukihiro Kimura
- Graduate School of Agricultural Science , Kobe University , Nada, Kobe 657-8501 , Japan
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11
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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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12
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Ghosh I, Banerjee G, Kim CJ, Reiss K, Batista VS, Debus RJ, Brudvig GW. D1-S169A Substitution of Photosystem II Perturbs Water Oxidation. Biochemistry 2019; 58:1379-1387. [DOI: 10.1021/acs.biochem.8b01184] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Victor S. Batista
- 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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13
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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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14
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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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15
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Nagao R, Ueoka-Nakanishi H, Noguchi T. D1-Asn-298 in photosystem II is involved in a hydrogen-bond network near the redox-active tyrosine Y Z for proton exit during water oxidation. J Biol Chem 2017; 292:20046-20057. [PMID: 29046348 DOI: 10.1074/jbc.m117.815183] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/04/2017] [Indexed: 01/19/2023] Open
Abstract
In photosynthetic water oxidation, two water molecules are converted into one oxygen molecule and four protons at the Mn4CaO5 cluster in photosystem II (PSII) via the S-state cycle. Efficient proton exit from the catalytic site to the lumen is essential for this process. However, the exit pathways of individual protons through the PSII proteins remain to be identified. In this study, we examined the involvement of a hydrogen-bond network near the redox-active tyrosine YZ in proton transfer during the S-state cycle. We focused on spectroscopic analyses of a site-directed variant of D1-Asn-298, a residue involved in a hydrogen-bond network near YZ We found that the D1-N298A mutant of Synechocystis sp. PCC 6803 exhibits an O2 evolution activity of ∼10% of the wild-type. D1-N298A and the wild-type D1 had very similar features of thermoluminescence glow curves and of an FTIR difference spectrum upon YZ oxidation, suggesting that the hydrogen-bonded structure of YZ and electron transfer from the Mn4CaO5 cluster to YZ were little affected by substitution. In the D1-N298A mutant, however, the flash-number dependence of delayed luminescence showed a monotonic increase without oscillation, and FTIR difference spectra of the S-state cycle indicated partial and significant inhibition of the S2 → S3 and S3 → S0 transitions, respectively. These results suggest that the D1-N298A substitution inhibits the proton transfer processes in the S2 → S3 and S3 → S0 transitions. This in turn indicates that the hydrogen-bond network near YZ can be functional as a proton transfer pathway during photosynthetic water oxidation.
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Affiliation(s)
- Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
| | - Hanayo Ueoka-Nakanishi
- 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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16
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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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17
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Bovi D, Capone M, Narzi D, Guidoni L. Vibrational fingerprints of the Mn 4 CaO 5 cluster in Photosystem II by mixed quantum-classical molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1669-77. [DOI: 10.1016/j.bbabio.2016.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/16/2016] [Accepted: 07/12/2016] [Indexed: 11/16/2022]
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18
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Redox potential of the terminal quinone electron acceptor QB in photosystem II reveals the mechanism of electron transfer regulation. Proc Natl Acad Sci U S A 2015; 113:620-5. [PMID: 26715751 DOI: 10.1073/pnas.1520211113] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photosystem II (PSII) extracts electrons from water at a Mn4CaO5 cluster using light energy and then transfers them to two plastoquinones, the primary quinone electron acceptor QA and the secondary quinone electron acceptor QB. This forward electron transfer is an essential process in light energy conversion. Meanwhile, backward electron transfer is also significant in photoprotection of PSII proteins. Modulation of the redox potential (Em) gap of QA and QB mainly regulates the forward and backward electron transfers in PSII. However, the full scheme of electron transfer regulation remains unresolved due to the unknown Em value of QB. Here, for the first time (to our knowledge), the Em value of QB reduction was measured directly using spectroelectrochemistry in combination with light-induced Fourier transform infrared difference spectroscopy. The Em(QB (-)/QB) was determined to be approximately +90 mV and was virtually unaffected by depletion of the Mn4CaO5 cluster. This insensitivity of Em(QB (-)/QB), in combination with the known large upshift of Em(QA (-)/QA), explains the mechanism of PSII photoprotection with an impaired Mn4CaO5 cluster, in which a large decrease in the Em gap between QA and QB promotes rapid charge recombination via QA (-).
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19
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Nagao R, Tomo T, Noguchi T. Effects of Extrinsic Proteins on the Protein Conformation of the Oxygen-Evolving Center in Cyanobacterial Photosystem II As Revealed by Fourier Transform Infrared Spectroscopy. Biochemistry 2015; 54:2022-31. [DOI: 10.1021/acs.biochem.5b00053] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryo Nagao
- Division
of Material Science, Graduate School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
| | - Tatsuya Tomo
- Department
of Biology, Faculty of Science, Tokyo University of Science, Kagurazaka
1-3, Shinjuku-ku, Tokyo 162-8601, Japan
- PRESTO, Japan Science and Technology Agency (JST), 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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20
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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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21
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Xerri B, Petitjean H, Dupeyrat F, Flament JP, Lorphelin A, Vidaud C, Berthomieu C, Berthomieu D. Mid- and Far-Infrared Marker Bands of the Metal Coordination Sites of the Histidine Side Chains in the Protein Cu,Zn-Superoxide Dismutase. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Kato Y, Noguchi T. Long-Range Interaction between the Mn4CaO5 Cluster and the Non-heme Iron Center in Photosystem II as Revealed by FTIR Spectroelectrochemistry. Biochemistry 2014; 53:4914-23. [DOI: 10.1021/bi500549b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yuki Kato
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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23
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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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24
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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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25
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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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26
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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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27
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Li Y, Kimura Y, Arikawa T, Wang-Otomo ZY, Ohno T. ATR–FTIR Detection of Metal-Sensitive Structural Changes in the Light-Harvesting 1 Reaction Center Complex from the Thermophilic Purple Sulfur Bacterium Thermochromatium tepidum. Biochemistry 2013; 52:9001-8. [DOI: 10.1021/bi401033y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yong Li
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yukihiro Kimura
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Teruhisa Arikawa
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | | | - Takashi Ohno
- Department
of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
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28
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Uno C, Nagao R, Suzuki H, Tomo T, Noguchi T. Structural Coupling of Extrinsic Proteins with the Oxygen-Evolving Center in Red Algal Photosystem II As Revealed by Light-Induced FTIR Difference Spectroscopy. Biochemistry 2013; 52:5705-7. [DOI: 10.1021/bi4009787] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chihiro Uno
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Nagao
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroyuki Suzuki
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Department of Biology, Faculty
of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Tatsuya Tomo
- Department of Biology, Faculty
of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi,
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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29
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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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30
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Suzuki H, Yu J, Kobayashi T, Nakanishi H, Nixon PJ, Noguchi T. Functional roles of D2-Lys317 and the interacting chloride ion in the water oxidation reaction of photosystem II as revealed by fourier transform infrared analysis. Biochemistry 2013; 52:4748-57. [PMID: 23786399 PMCID: PMC3777104 DOI: 10.1021/bi301699h] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosynthetic water oxidation in plants and cyanobacteria is catalyzed by a Mn4CaO5 cluster within the photosystem II (PSII) protein complex. Two Cl(-) ions bound near the Mn4CaO5 cluster act as indispensable cofactors, but their functional roles remain to be clarified. We have investigated the role of the Cl(-) ion interacting with D2-K317 (designated Cl-1) by Fourier transform infrared spectroscopy (FTIR) analysis of the D2-K317R mutant of Synechocystis sp. PCC 6803 in combination with Cl(-)/NO3(-) replacement. The D2-K317R mutation perturbed the bands in the regions of the COO(-) stretching and backbone amide vibrations in the FTIR difference spectrum upon the S1 → S2 transition. In addition, this mutation altered the (15)N isotope-edited NO3(-) bands in the spectrum of NO3(-)-treated PSII. These results provide the first experimental evidence that the Cl-1 site is coupled with the Mn4CaO5 cluster and its interaction is affected by the S1 → S2 transition. It was also shown that a negative band at 1748 cm(-1) arising from COOH group(s) was altered to a positive intensity by the D2-K317R mutation as well as by NO3(-) treatment, suggesting that the Cl-1 site affects the pKa of COOH/COO(-) group(s) near the Mn4CaO5 cluster in a common hydrogen bond network. Together with the observation that the efficiency of the S3 → S0 transition significantly decreased in the core complexes of D2-K317R upon moderate dehydration, it is suggested that D2-K317 and Cl-1 are involved in a proton transfer pathway from the Mn4CaO5 cluster to the lumen, which functions in the S3 → S0 transition.
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Affiliation(s)
- Hiroyuki Suzuki
- Division of Material Science, Graduate School of Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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31
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Vita N, Brubach JB, Hienerwadel R, Bremond N, Berthomieu D, Roy P, Berthomieu C. Electrochemically Induced Far-Infrared Difference Spectroscopy on Metalloproteins Using Advanced Synchrotron Technology. Anal Chem 2013; 85:2891-8. [DOI: 10.1021/ac303511g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nicolas Vita
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Jean-Blaise Brubach
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Rainer Hienerwadel
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Lab Genet Biophys Plantes, Aix-Marseille Université, Marseille, F-13009,
France
- Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Marseille,
F-13009, France
| | - Nicolas Bremond
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue
de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Pascale Roy
- Société Civile Synchrotron SOLEIL, L’Orme des Merisiers,
St-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France
| | - Catherine Berthomieu
- Lab Interactions Protein Metal, Commissariat à l’Energie Atomique (CEA), DSV, IBEB, Saint-Paul-lez-Durance,
F-13108, France
- Centre National de la Recherche Scientifique, UMR Biol Veget et Microbiol
Environ, Saint-Paul-lez-Durance, F-13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
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32
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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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33
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Noguchi T, Suzuki H, Tsuno M, Sugiura M, Kato C. Time-Resolved Infrared Detection of the Proton and Protein Dynamics during Photosynthetic Oxygen Evolution. Biochemistry 2012; 51:3205-14. [DOI: 10.1021/bi300294n] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Takumi Noguchi
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Hiroyuki Suzuki
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Masaya Tsuno
- Division of Material Science,
Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, 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, Kawauchi,
Saitama 332-0012, Japan
| | - Chihiro Kato
- Kanagawa Industrial Technology Center, Ebina, Kanagawa 243-0435, Japan
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34
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Marboutin L, Petitjean H, Xerri B, Vita N, Dupeyrat F, Flament JP, Berthomieu D, Berthomieu C. Profiling the Active Site of a Copper Enzyme through Its Far-Infrared Fingerprint. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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35
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Marboutin L, Petitjean H, Xerri B, Vita N, Dupeyrat F, Flament JP, Berthomieu D, Berthomieu C. Profiling the Active Site of a Copper Enzyme through Its Far-Infrared Fingerprint. Angew Chem Int Ed Engl 2011; 50:8062-6. [DOI: 10.1002/anie.201102014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Indexed: 12/16/2022]
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36
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Tsuno M, Suzuki H, Kondo T, Mino H, Noguchi T. Interaction and inhibitory effect of ammonium cation in the oxygen evolving center of photosystem II. Biochemistry 2011; 50:2506-14. [PMID: 21338049 DOI: 10.1021/bi101952g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosynthetic O(2) evolution takes place at the Mn cluster in photosystem II (PSII) by oxidation of water. It has been proposed that ammonia, one of water analogues, functions as an inhibitor of O(2) evolution at alkaline pH. However, the detailed mechanism of inhibition has not been understood yet. In this study, we investigated the mechanism of ammonia inhibition by examining the NH(4)Cl-induced inhibition of O(2) evolution in a wide pH range (pH 5.0-8.0) and by detecting the interaction site using Fourier transform infrared (FTIR) spectroscopy. In addition to intact PSII membranes from spinach, PSII membranes depleted of the PsbP and PsbQ extrinsic proteins were used as samples to avoid the effect of the release of these proteins by salt treatments. In both types of samples, oxygen evolution activity decreased by approximately 40% by addition of 100 mM NH(4)Cl in the range of pH 5.0-8.0. The presence of inhibition at acidic pH without significant pH dependence strongly suggests that NH(4)(+) cation functions as a major inhibitor in the acidic pH region, where neutral NH(3) scarcely exists in the buffer. The NH(4)Cl treatment at pH 6.5 and 5.5 induced prominent changes in the COO(-) stretching regions in FTIR difference spectra upon the S(1) → S(2) transition measured at 283 K. The NH(4)Cl concentration dependence of the amplitude of the spectral changes showed a good correlation with that of the inhibition of O(2) evolution. From this observation, it is proposed that NH(4)(+) cation interacts with carboxylate groups coupled to the Mn cluster as direct ligands or proton transfer mediators, causing inhibition of the O(2) evolving reaction.
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Affiliation(s)
- Masaya Tsuno
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Shimada Y, Suzuki H, Tsuchiya T, Mimuro M, Noguchi T. Structural Coupling of an Arginine Side Chain with the Oxygen-Evolving Mn4Ca Cluster in Photosystem II As Revealed by Isotope-Edited Fourier Transform Infrared Spectroscopy. J Am Chem Soc 2011; 133:3808-11. [DOI: 10.1021/ja200186h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuichiro Shimada
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroyuki Suzuki
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Tohru Tsuchiya
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Mamoru Mimuro
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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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: 84] [Impact Index Per Article: 6.0] [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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Iizasa M, Suzuki H, Noguchi T. Orientations of Carboxylate Groups Coupled to the Mn Cluster in the Photosynthetic Oxygen-Evolving Center As Studied by Polarized ATR-FTIR Spectroscopy. Biochemistry 2010; 49:3074-82. [DOI: 10.1021/bi1002647] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Mitsuhiro Iizasa
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Hiroyuki Suzuki
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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Xerri B, Flament JP, Petitjean H, Berthomieu C, Berthomieu D. Vibrational Modeling of Copper−Histamine Complexes: Metal−Ligand IR Modes Investigation. J Phys Chem B 2009; 113:15119-27. [DOI: 10.1021/jp905917z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bertrand Xerri
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Jean-Pierre Flament
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Hugo Petitjean
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Catherine Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Dorothee Berthomieu
- Institut Charles Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM1-UM2, 8, rue de l’Ecole Normale, 34296 Montpellier cedex 5, France, Université Lille1, Sciences et Technologies, Laboratoire de Physique des Lasers, Atomes et Molécules (UMR, CNRS 8523) and CERLA (FR 2416 CNRS), 59655 Villeneuve d’Ascq Cedex, France, and CEA, DSV, IBEB, Laboratoire des Interactions Protéine Métal, UMR 6191 CNRS-CEA-Université Aix-Marseille, CEA-Cadarache, Saint-Paul-lez-Durance, F-13108, France
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Suzuki H, Sugiura M, Noguchi T. Monitoring water reactions during the S-state cycle of the photosynthetic water-oxidizing center: detection of the DOD bending vibrations by means of Fourier transform infrared spectroscopy. Biochemistry 2008; 47:11024-30. [PMID: 18821774 DOI: 10.1021/bi801580e] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosynthetic water oxidation takes place in the water-oxidizing center (WOC) of photosystem II (PSII). To clarify the mechanism of water oxidation, detecting water molecules in the WOC and monitoring their reactions at the molecular level are essential. In this study, we have for the first time detected the DOD bending vibrations of functional D 2O molecules during the S-state cycle of the WOC by means of Fourier transform infrared (FTIR) difference spectroscopy. Flash-induced FTIR difference spectra upon S-state transitions were measured using the PSII core complexes from Thermosynechococcus elongatus moderately deuterated with D 2 (16)O and D 2 (18)O. D 2 (16)O-minus-D 2 (18)O double difference spectra at individual S-state transitions exhibited six to eight peaks arising from the D (16)OD/D (18)OD bending vibrations in the 1250-1150 cm (-1) region. This observation indicates that at least two water molecules, not in any deprotonated forms, participate in the reaction at each S-state transition throughout the cycle. Most of the peaks exhibited clear counter peaks with opposite signs at different transitions, reflecting a series of reactions of water molecules at the catalytic site. In contrast, negative bands at approximately 1240 cm (-1) in the S 2 --> S 3, S 3 --> S 0, and possibly S 0 --> S 1 transitions, for which no clear counter peaks were found in other transitions, can be interpreted as insertion of substrate water into the WOC from a water cluster in the proteins. The characteristics of the weakly D-bonded OD stretching bands were consistent with the insertion of substrate from internal water molecules in the S 2 --> S 3 and S 3 --> S 0 transitions. The results of this study show that FTIR detection of the DOD bending vibrations is a powerful method for investigating the molecular mechanism of photosynthetic water oxidation as well as other enzymatic reactions involving functional water molecules.
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Affiliation(s)
- Hiroyuki Suzuki
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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43
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Strickler MA, Hwang HJ, Burnap RL, Yano J, Walker LM, Service RJ, Britt RD, Hillier W, Debus RJ. Glutamate-354 of the CP43 polypeptide interacts with the oxygen-evolving Mn4Ca cluster of photosystem II: a preliminary characterization of the Glu354Gln mutant. Philos Trans R Soc Lond B Biol Sci 2008; 363:1179-87; discussion 1187-8. [PMID: 17954433 DOI: 10.1098/rstb.2007.2213] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the recent X-ray crystallographic structural models of photosystem II, Glu354 of the CP43 polypeptide is assigned as a ligand of the O2-evolving Mn4Ca cluster. In this communication, a preliminary characterization of the CP43-Glu354Gln mutant of the cyanobacterium Synechocystis sp. PCC 6803 is presented. The steady-state rate of O2 evolution in the mutant cells is only approximately 20% compared with the wild-type, but the kinetics of O2 release are essentially unchanged and the O2-flash yields show normal period-four oscillations, albeit with lower overall intensity. Purified PSII particles exhibit an essentially normal S2 state multiline electron paramagnetic resonance (EPR) signal, but exhibit a substantially altered S2-minus-S1 Fourier transform infrared (FTIR) difference spectrum. The intensities of the mutant EPR and FTIR difference spectra (above 75% compared with wild-type) are much greater than the O2 signals and suggest that CP43-Glu354Gln PSII reaction centres are heterogeneous, with a minority fraction able to evolve O2 with normal O2 release kinetics and a majority fraction unable to advance beyond the S2 or S3 states. The S2-minus-S1 FTIR difference spectrum of CP43-Glu354Gln PSII particles is altered in both the symmetric and asymmetric carboxylate stretching regions, implying either that CP43-Glu354 is exquisitely sensitive to the increased charge that develops on the Mn4Ca cluster during the S1-->S2 transition or that the CP43-Glu354Gln mutation changes the distribution of Mn(III) and Mn(IV) oxidation states within the Mn4Ca cluster in the S1 and/or S2 states.
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Affiliation(s)
- Melodie A Strickler
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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Noguchi T. FTIR detection of water reactions in the oxygen-evolving centre of photosystem II. Philos Trans R Soc Lond B Biol Sci 2008; 363:1189-94; discussion 1194-5. [PMID: 17965007 DOI: 10.1098/rstb.2007.2214] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Flash-induced Fourier transform infrared (FTIR) difference spectroscopy has been used to study the water-oxidizing reactions in the oxygen-evolving centre of photosystem II. Reactions of water molecules were directly monitored by detecting the OH stretching bands of weakly H-bonded OH of water in the 3700-3500 cm(-1) region in FTIR difference spectra during S-state cycling. In the S1-->S2 transition, a band shift from 3588 to 3617 cm(-1) was observed, indicative of a weakened H-bond. Decoupling experiments using D2O:H2O (1:1) showed that this OH arose from a water molecule with an asymmetric H-bonding structure and this asymmetry became more significant upon S2 formation. In the S2-->S3, S3-->S0 and S0-->S1 transitions, negative bands were observed at 3634, 3621 and 3612 cm(-1), respectively, representing formation of a strong H-bond or a proton release reaction. In addition, using complex spectral features in the carboxylate stretching region (1600-1300 cm-(1)) as 'fingerprints' of individual S-state transitions, pH dependency of the transition efficiencies and the effect of dehydration were examined to obtain the information of proton release and water insertion steps in the S-state cycle. Low-pH inhibition of the S2-->S3, S3-->S0 and S0-->S1 transitions was consistent with a view that protons are released in the three transitions other than S1-->S2, while relatively high susceptibility to dehydration in the S2-->S3 and S3-->S0 transitions suggested the insertion of substrate water into the system during these transitions. Thus, a possible mechanism of water oxidation to explain the FTIR data is proposed.
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Affiliation(s)
- Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan.
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45
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NOGUCHI T. Fourier transform infrared analysis of the photosynthetic oxygen-evolving center. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.05.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Abstract
Photosynthetic water oxidation is catalyzed by a unique Mn(4)Ca cluster in Photosystem II. The ligation environment of the Mn(4)Ca cluster optimizes the cluster's reactivity at each step in the catalytic cycle and minimizes the release of toxic, partly oxidized intermediates. However, our understanding of the cluster's ligation environment remains incomplete. Although the recent X-ray crystallographic structural models have provided great insight and are consistent with most conclusions of earlier site-directed mutagenesis studies, the ligation environments of the Mn(4)Ca cluster in the two available structural models differ in important respects. Furthermore, while these structural models and the earlier mutagenesis studies agree on the identity of most of the Mn(4)Ca cluster's amino acid ligands, they disagree on the identity of others. This review describes mutant characterizations that have been undertaken to probe the ligation environment of the Mn(4)Ca cluster, some of which have been inspired by the recent X-ray crystallographic structural models. Many of these characterizations have involved Fourier Transform Infrared (FTIR) difference spectroscopy because of the extreme sensitivity of this form of spectroscopy to the dynamic structural changes that occur during an enzyme's catalytic cycle.
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Affiliation(s)
- Richard J. Debus
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521-0129
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47
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Grafton AK. Vibalizer: A free, web-based tool for rapid, quantitative comparison and analysis of calculated vibrational modes. J Comput Chem 2007; 28:1290-305. [PMID: 17299728 DOI: 10.1002/jcc.20642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This report describes the development and applications of a software package called Vibalizer, the first and only method that provides free, fast, interactive, and quantitative comparison and analysis of calculated vibrational modes. Using simple forms and menus in a web-based interface, Vibalizer permits the comparison of vibrational modes from different, but similar molecules and also performs rapid calculation and comparison of isotopically substituted molecules' normal modes. Comparing and matching complex vibrational modes can be completed in seconds with Vibalizer, whereas matching vibrational modes manually can take hours and gives only qualitative comparisons subject to human error and differing individual judgments. In addition to these core features, Vibalizer also provides several other useful features, including the ability to automatically determine first-approximation mode descriptions, to help users analyze the results of vibrational frequency calculations. Because the software can be dimensioned to handle almost arbitrarily large systems, Vibalizer may be of particular use when analyzing the vibrational modes of complex systems such as proteins and extended materials systems. Additionally, the ease of use of the Vibalizer interface and the straightforward interpretation of results may find favor with educators who incorporate molecular modeling into their classrooms. The Vibalizer interface is available for free use at http://www.compchem.org, and it is also available as a locally-installable package that will run on a Linux-based web server.
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Affiliation(s)
- Anthony K Grafton
- Division of Science, Lyon College, P.O. Box 2317, Batesville, Arkansas 72503, USA.
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48
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Noguchi T. Light-induced FTIR difference spectroscopy as a powerful tool toward understanding the molecular mechanism of photosynthetic oxygen evolution. PHOTOSYNTHESIS RESEARCH 2007; 91:59-69. [PMID: 17279438 DOI: 10.1007/s11120-007-9137-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 01/15/2007] [Indexed: 05/06/2023]
Abstract
The molecular mechanism of photosynthetic oxygen evolution remains a mystery in photosynthesis research. Although recent X-ray crystallographic studies of the photosystem II core complex at 3.0-3.5 A resolutions have revealed the structure of the oxygen-evolving center (OEC), with approximate positions of the Mn and Ca ions and the amino acid ligands, elucidation of its detailed structure and the reactions during the S-state cycle awaits further spectroscopic investigations. Light-induced Fourier transform infrared (FTIR) difference spectroscopy was first applied to the OEC in 1992 as detection of its structural changes upon the S(1)-->S(2) transition, and spectra during the S-state cycle induced by consecutive flashes were reported in 2001. These FTIR spectra provide extensive structural information on the amino acid side groups, polypeptide chains, metal core, and water molecules, which constitute the OEC and are involved in its reaction. FTIR spectroscopy is thus becoming a powerful tool in investigating the reaction mechanism of photosynthetic oxygen evolution. In this mini-review, the measurement method of light-induced FTIR spectra of OEC is introduced and the results obtained thus far using this technique are summarized.
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Affiliation(s)
- Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan.
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49
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Hasegawa K, Ono TA. Vibrational Analyses of Di-μ-oxo-Bridged Manganese Dimers Based on Density Functional Theory Calculations. Theoretical Evaluation of Mn–O Vibrations of the Mn-Cluster Core for Photosynthetic Oxygen-Evolving Complex. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2006. [DOI: 10.1246/bcsj.79.1025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Berthomieu C, Marboutin L, Dupeyrat F, Bouyer P. Electrochemically induced FTIR difference spectroscopy in the mid- to far infrared (200 μm) domain: A new setup for the analysis of metal–ligand interactions in redox proteins. Biopolymers 2006; 82:363-7. [PMID: 16453337 DOI: 10.1002/bip.20469] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the setup of an electrochemical cell with chemical-vapor deposition diamond windows and the use of a Bruker 66 SX FTIR spectrometer equipped with DTGS and Si-bolometer detectors and KBr and mylar beam splitters, to record on the same sample, FTIR difference spectra corresponding to the structural changes associated with the change in redox state of active sites in proteins in the whole 1800-50 cm(-1) region. With cytochrome c we show that reliable reduced-minus-oxidized FTIR difference spectra are obtained, which correspond to single molecular vibrations. Redox-sensitive IR modes of the cytochrome c are detected until 140 cm(-1) with a good signal to noise. This new setup is promising to analyze the infrared spectral region where metal-ligand vibrations are expected to contribute and to extend the analysis of vibrational properties to metal sites or redox states not accessible to (resonance) Raman spectroscopy.
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Affiliation(s)
- Catherine Berthomieu
- Laboratoire des Interactions Protéine Métal, DSV-DEVM, UMR 6191 CNRS-CEA-Univ. Aix-Marseille II, CEA-Cadarache, 13108 Saint Paul-lez-Durance Cedex, France.
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