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Kuleta P, Pietras R, Andrys-Olek J, Wójcik-Augustyn A, Osyczka A. Probing molecular interactions of semiquinone radicals at quinone reduction sites of cytochrome bc1 by X-band HYSCORE EPR spectroscopy and quantum mechanical calculations. Phys Chem Chem Phys 2023; 25:21935-21943. [PMID: 37551546 DOI: 10.1039/d3cp02433d] [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: 08/09/2023]
Abstract
Quinone redox reactions involve a semiquinone (SQ) intermediate state. The catalytic sites in enzymes stabilize the SQ state via various molecular interactions, such as hydrogen bonding to oxygens of the two carbonyls of the benzoquinone ring. To understand how these interactions contribute to SQ stabilization, we examined SQ in the quinone reduction site (Qi) of cytochrome bc1 using electron paramagnetic resonance (ESEEM, HYSCORE) at the X-band and quantum mechanical (QM) calculations. We compared native enzyme (WT) with a H217R mutant (replacement of histidine that interacts with one carbonyl of the occupant of Qi to arginine) in which the SQ stability has previously been shown to markedly increase. The 14N region of the HYSCORE 2D spectrum for SQi in WT had a shape typical of histidine residue, while in H217R, the spectrum shape changed significantly and appeared similar to the pattern described for SQ liganded natively by arginine in cytochrome bo3. Parametrization of hyperfine and quadrupolar interactions of SQi with surrounding magnetic nuclei (1H, 14N) allowed us to assign specific nitrogens of H217 or R217 as ligands of SQi in WT and H217R, respectively. This was further substantiated by qualitative agreement between the experimental (EPR-derived) and theoretical (QM-derived) parameters. The proton (1H) region of the HYSCORE spectrum in both WT and H217R was very similar and indicative of interactions with two protons, which in view of the QM calculations, were identified as directly involved in the formation of a H-bond with the two carbonyl oxygens of SQ (interaction of H217 or R217 with O4 and D252 with O1). In view of these assignments, we explain how different SQ ligands effectively influence SQ stability. We also propose that the characteristic X-band HYSCORE pattern and parameters of H217R are highly specific to the interaction of SQ with the nitrogen of arginine. These features can thus be considered as potential markers of the interaction of arginine with SQ in other proteins.
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Affiliation(s)
- Patryk Kuleta
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland.
| | - Rafał Pietras
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland.
| | - Justyna Andrys-Olek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland.
| | - Anna Wójcik-Augustyn
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland.
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland.
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2
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Wikström M, Djurabekova A, Sharma V. On the role of ubiquinone in the proton translocation mechanism of respiratory complex I. FEBS Lett 2023; 597:224-236. [PMID: 36180980 DOI: 10.1002/1873-3468.14506] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 01/26/2023]
Abstract
Complex I converts oxidoreduction energy into a proton electrochemical gradient across the inner mitochondrial or bacterial cell membrane. This gradient is the primary source of energy for aerobic synthesis of ATP. Oxidation of reduced nicotinamide adenine dinucleotide (NADH) by ubiquinone (Q) yields NAD+ and ubiquinol (QH2 ), which is tightly coupled to translocation of four protons from the negatively to the positively charged side of the membrane. Electrons from NADH oxidation reach the iron-sulfur centre N2 positioned near the bottom of a tunnel that extends circa 30 Å from the membrane domain into the hydrophilic domain of the complex. The tunnel is occupied by ubiquinone, which can take a distal position near the N2 centre or proximal positions closer to the membrane. Here, we review important structural, kinetic and thermodynamic properties of ubiquinone that define its role in complex I function. We suggest that this function exceeds that of a mere substrate or electron acceptor and propose that ubiquinone may be the redox element of complex I coupling electron transfer to proton translocation.
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Affiliation(s)
- Mårten Wikström
- HiLIFE Institute of Biotechnology, University of Helsinki, Finland
| | | | - Vivek Sharma
- HiLIFE Institute of Biotechnology, University of Helsinki, Finland.,Department of Physics, University of Helsinki, Finland
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3
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Capacity and kinetics of light-induced cytochrome oxidation in intact cells of photosynthetic bacteria. Sci Rep 2022; 12:14298. [PMID: 35995915 PMCID: PMC9395421 DOI: 10.1038/s41598-022-18399-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/10/2022] [Indexed: 11/08/2022] Open
Abstract
Light-induced oxidation of the reaction center dimer and periplasmic cytochromes was detected by fast kinetic difference absorption changes in intact cells of wild type and cytochrome mutants (cycA, cytC4 and pufC) of Rubrivivax gelatinosus and Rhodobacter sphaeroides. Constant illumination from a laser diode or trains of saturating flashes enabled the kinetic separation of acceptor and donor redox processes, and the electron contribution from the cyt bc1 complex via periplasmic cytochromes. Under continuous excitation, concentrations of oxidized cytochromes increased in three phases where light intensity, electron transfer rate and the number of reduced cytochromes were the rate liming steps, respectively. By choosing suitable flash timing, gradual steps of cytochrome oxidation in whole cells were observed; each successive flash resulted in a smaller, damped oxidation. We attribute this damping to lowered availability of reduced cytochromes resulting from both exchange (unbinding/binding) of the cytochromes and electron transfer at the reaction center interface since a similar effect is observed upon deletion of genes encoding periplasmic cytochromes. In addition, we present a simple model to calculate the damping effect; application of this method may contribute to understanding the function of the diverse range of c-type cytochromes in the electron transport chains of anaerobic phototrophic bacteria.
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4
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Time-resolved infrared absorption spectroscopy applied to photoinduced reactions: how and why. Photochem Photobiol Sci 2022; 21:557-584. [DOI: 10.1007/s43630-022-00180-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
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5
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Tani K, Kanno R, Ji XC, Hall M, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY. Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum. Biochemistry 2021; 60:2483-2491. [PMID: 34323477 DOI: 10.1021/acs.biochem.1c00360] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodospirillum (Rsp.) rubrum is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) a esterified at the propionic acid side chain by geranylgeraniol (BChl aG) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from Rsp. rubrum remains at low resolutions. Using cryo-EM, here we present a robust new view of the Rsp. rubrum LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol side chains of BChl aG coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls aG. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution Rsp. rubrum LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.
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Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan
| | - Ryo Kanno
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Xuan-Cheng Ji
- Faculty of Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Malgorzata Hall
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan
| | - Michael T Madigan
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan
| | - Bruno M Humbel
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
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6
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Białek R, Thakur K, Ruff A, Jones MR, Schuhmann W, Ramanan C, Gibasiewicz K. Insight into Electron Transfer from a Redox Polymer to a Photoactive Protein. J Phys Chem B 2020; 124:11123-11132. [PMID: 33236901 PMCID: PMC7735723 DOI: 10.1021/acs.jpcb.0c08714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/10/2020] [Indexed: 11/29/2022]
Abstract
Biohybrid photoelectrochemical systems in photovoltaic or biosensor applications have gained considerable attention in recent years. While the photoactive proteins engaged in such systems usually maintain an internal charge separation quantum yield of nearly 100%, the subsequent steps of electron and hole transfer beyond the protein often limit the overall system efficiency and their kinetics remain largely uncharacterized. To reveal the dynamics of one of such charge-transfer reactions, we report on the reduction of Rhodobacter sphaeroides reaction centers (RCs) by Os-complex-modified redox polymers (P-Os) characterized using transient absorption spectroscopy. RCs and P-Os were mixed in buffered solution in different molar ratios in the presence of a water-soluble quinone as an electron acceptor. Electron transfer from P-Os to the photoexcited RCs could be described by a three-exponential function, the fastest lifetime of which was on the order of a few microseconds, which is a few orders of magnitude faster than the internal charge recombination of RCs with fully separated charge. This was similar to the lifetime for the reduction of RCs by their natural electron donor, cytochrome c2. The rate of electron donation increased with increasing ratio of polymer to protein concentrations. It is proposed that P-Os and RCs engage in electrostatic interactions to form complexes, the sizes of which depend on the polymer-to-protein ratio. Our findings throw light on the processes within hydrogel-based biophotovoltaic devices and will inform the future design of materials optimally suited for this application.
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Affiliation(s)
- Rafał Białek
- Faculty
of Physics, Adam Mickiewicz University, Poznań, ul. Uniwersytetu
Poznańskiego 2, 61-614 Poznań, Poland
| | - Kalyani Thakur
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Adrian Ruff
- Analytical
Chemistry—Center for Electrochemical Sciences, Faculty of Biochemistry
and Chemistry, Faculty of Biochemistry and Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Michael R. Jones
- School
of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Wolfgang Schuhmann
- Analytical
Chemistry—Center for Electrochemical Sciences, Faculty of Biochemistry
and Chemistry, Faculty of Biochemistry and Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Charusheela Ramanan
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Krzysztof Gibasiewicz
- Faculty
of Physics, Adam Mickiewicz University, Poznań, ul. Uniwersytetu
Poznańskiego 2, 61-614 Poznań, Poland
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7
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Oja V, Laisk A. Time- and reduction-dependent rise of photosystem II fluorescence during microseconds-long inductions in leaves. PHOTOSYNTHESIS RESEARCH 2020; 145:209-225. [PMID: 32918663 DOI: 10.1007/s11120-020-00783-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/02/2020] [Indexed: 05/16/2023]
Abstract
Lettuce (Lactuca sativa) and benth (Nicotiana benthamiana) leaves were illuminated with 720 nm background light to mix S-states and oxidize electron carriers. Green-filtered xenon flashes of different photon dose were applied and O2 evolution induced by a flash was measured. After light intensity gradient across the leaf was mathematically considered, the flash-induced PSII electron transport (= 4·O2 evolution) exponentially increased with the flash photon dose in any differential layer of the leaf optical density. This proved the absence of excitonic connectivity between PSII units. Time courses of flash light intensity and 680 nm chlorophyll fluorescence emission were recorded. While with connected PSII the sigmoidal fluorescence rise has been explained by quenching of excitation in closed PSII by its open neighbors, in the absence of connectivity the sigmoidicity indicates gradual rise of the fluorescence yield of an individual closed PSII during the induction. Two phases were discerned: the specific fluorescence yield immediately increased from Fo to 1.8Fo in a PSII, whose reaction center became closed; fluorescence yield of the closed PSII was keeping time-dependent rise from 1.8Fo to about 3Fo, approaching the flash fluorescence yield Ff = 0.6Fm during 40 μs. The time-dependent fluorescence rise was resolved from the quenching by 3Car triplets and related to protein conformational change. We suggest that QA reduction induces a conformational change, which by energetic or structural means closes the gate for excitation entrance into the central radical pair trap-efficiently when QB cannot accept the electron, but less efficiently when it can.
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Affiliation(s)
- Vello Oja
- Institute of Technology, University of Tartu, Nooruse st. 1, 50411, Tartu, Estonia
| | - Agu Laisk
- Institute of Technology, University of Tartu, Nooruse st. 1, 50411, Tartu, Estonia.
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8
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Maróti P. Chemical rescue of H + delivery in proton transfer mutants of reaction center of photosynthetic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:317-324. [PMID: 30707884 DOI: 10.1016/j.bbabio.2019.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/05/2018] [Accepted: 01/25/2019] [Indexed: 11/27/2022]
Abstract
In the native and most mutant reaction centers of bacterial photosynthesis, the electron transfer is coupled to proton transfer and is rate limiting for the second reduction of QB- → QBH2. In the presence of divalent metal ions (e.g. Cd2+) or in some ("proton transfer") mutants (L210DN/M17DN or L213DN), the proton delivery to QB- is made rate limiting and the properties of the proton pathway can be directly examined. We found that small weak acids and buffers in large concentrations (up to 1 M) were able to rescue the severely impaired proton transfer capability differently depending on the location of the defects: lesions at the protein surface (proton gate H126H/H128H + Cd2+), beneath the surface (M17DN + Cd2+, L210DN/M17DN) or deep inside the protein (L213DN) could be completely, partially or to very small extent recovered, respectively. Small zwitterionic acids (azide/hydrazoic acid) and buffers (tricine) proved to be highly effective rescuers consistent with their enhanced binding affinity and access to any of the proton acceptors (including QB- itself) in the pathway. As a consequence, back titration of the protons at L212Glu could be observed as a pH-dependence of the rate constant of the charge recombination in the presence of azide or formate. Model calculations support the collective influence of the acid cluster on the change of the protonation states upon extension of the cluster with the bound small acid. In proton transfer mutants, the rescuing agents decreased the free energy of activation together with their enthalpic and entropic components. This is in agreement with the hypothesis that they function as protein-penetrating protonophores delivering protons into the chain and select dominating paths out of many alternate routes. We estimate that the proton delivery will be accelerated in one pathway out of 100-200 alternate pathways. The implications for design of the chemical recovery of impaired intra-protein proton transfer pathways in proton transfer mutants are discussed.
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Affiliation(s)
- Péter Maróti
- Institute of Medical Physics, University of Szeged, Hungary.
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9
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Ptushenko VV, Krishtalik LI. Reorganization energies of the electron transfer reactions involving quinones in the reaction center of Rhodobacter sphaeroides. PHOTOSYNTHESIS RESEARCH 2018; 138:167-175. [PMID: 30022339 DOI: 10.1007/s11120-018-0560-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
In framework of the continuum electrostatics theory, the reorganization energies of the electron transfers QA--QB (fast phase), Bph--QA, P+-QA-, and P+-QB- in the photosynthetic bacterial reaction center have been calculated. The calculations were based on the static dielectric permittivity spatial distribution derived from the data on the electrogenesis, with the corresponding characteristic times relatively close to the reaction times of QA--QB (fast phase) and Bph--QA but much shorter than those times of the latter two recombination reactions. The calculated reorganization energies were reasonably close to the experimental estimates for QA--QB (fast phase) and Bph--QA but substantially lower than those of P+-QA- and P+-QB-. A higher effective dielectric permittivity contributes to this effect, but the dominant contribution is most probably made by a non-dielectric relaxation, especially for the P+-QB- recombination influenced by the proton transfer. This situation calls for reconsidering of the current electron transfer rate estimates.
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Affiliation(s)
- Vasily V Ptushenko
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - Lev I Krishtalik
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia.
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10
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Schulz CE, Dutta AK, Izsák R, Pantazis DA. Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones. J Comput Chem 2018; 39:2439-2451. [PMID: 30281169 DOI: 10.1002/jcc.25570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/07/2022]
Abstract
Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T0 ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Christine E Schulz
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Achintya Kumar Dutta
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Róbert Izsák
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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11
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Sipka G, Kis M, Maróti P. Characterization of mercury(II)-induced inhibition of photochemistry in the reaction center of photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 2018; 136:379-392. [PMID: 29285578 DOI: 10.1007/s11120-017-0474-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Mercuric contamination of aqueous cultures results in impairment of viability of photosynthetic bacteria primarily by inhibition of the photochemistry of the reaction center (RC) protein. Isolated reaction centers (RCs) from Rhodobacter sphaeroides were exposed to Hg2+ ions up to saturation concentration (~ 103 [Hg2+]/[RC]) and the gradual time- and concentration-dependent loss of the photochemical activity was monitored. The vast majority of Hg2+ ions (about 500 [Hg2+]/[RC]) had low affinity for the RC [binding constant Kb ~ 5 mM-1] and only a few (~ 1 [Hg2+]/[RC]) exhibited strong binding (Kb ~ 50 μM-1). Neither type of binding site had specific and harmful effects on the photochemistry of the RC. The primary charge separation was preserved even at saturation mercury(II) concentration, but essential further steps of stabilization and utilization were blocked already in the 5 < [Hg2+]/[RC] < 50 range whose locations were revealed. (1) The proton gate at the cytoplasmic site had the highest affinity for Hg2+ binding (Kb ~ 0.2 μM-1) and blocked the proton uptake. (2) Reduced affinity (Kb ~ 0.05 μM-1) was measured for the mercury(II)-binding site close to the secondary quinone that resulted in inhibition of the interquinone electron transfer. (3) A similar affinity was observed close to the bacteriochlorophyll dimer causing slight energetic changes as evidenced by a ~ 30 nm blue shift of the red absorption band, a 47 meV increase in the redox midpoint potential, and a ~ 20 meV drop in free energy gap of the primary charge pair. The primary quinone was not perturbed upon mercury(II) treatment. Although the Hg2+ ions attack the RC in large number, the exertion of the harmful effect on photochemistry is not through mass action but rather a couple of well-defined targets. Bound to these sites, the Hg2+ ions can destroy H-bond structures, inhibit protein dynamics, block conformational gating mechanisms, and modify electrostatic profiles essential for electron and proton transfer.
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Affiliation(s)
- Gábor Sipka
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
- Department of Plant Biology, Hungarian Academy of Science, Biological Research Centre, Szeged, Hungary
| | - Mariann Kis
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
| | - Péter Maróti
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary.
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12
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Noji T, Matsuo M, Takeda N, Sumino A, Kondo M, Nango M, Itoh S, Dewa T. Lipid-Controlled Stabilization of Charge-Separated States (P+QB–) and Photocurrent Generation Activity of a Light-Harvesting–Reaction Center Core Complex (LH1-RC) from Rhodopseudomonas palustris. J Phys Chem B 2018; 122:1066-1080. [DOI: 10.1021/acs.jpcb.7b09973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tomoyasu Noji
- The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), Osaka City University, Sugimoto-cho, Sumiyoshi-ku, Osaka 558−8585, Japan
| | - Mikano Matsuo
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Nobutaka Takeda
- Department
of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Ayumi Sumino
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Masaharu Kondo
- Department
of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Mamoru Nango
- The OCU Advanced Research Institute for Natural Science & Technology (OCARINA), Osaka City University, Sugimoto-cho, Sumiyoshi-ku, Osaka 558−8585, Japan
| | - Shigeru Itoh
- Division
of Material Sciences (Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464−8602, Japan
| | - Takehisa Dewa
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department
of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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13
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Pietras R, Sarewicz M, Osyczka A. Distinct properties of semiquinone species detected at the ubiquinol oxidation Qo site of cytochrome bc1 and their mechanistic implications. J R Soc Interface 2017; 13:rsif.2016.0133. [PMID: 27194483 PMCID: PMC4892266 DOI: 10.1098/rsif.2016.0133] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/18/2016] [Indexed: 12/23/2022] Open
Abstract
The two-electron ubiquinol oxidation or ubiquinone reduction typically involves semiquinone (SQ) intermediates. Natural engineering of ubiquinone binding sites of bioenergetic enzymes secures that SQ is sufficiently stabilized, so that it does not leave the site to membranous environment before full oxidation/reduction is completed. The ubiquinol oxidation Qo site of cytochrome bc1 (mitochondrial complex III, cytochrome b6f in plants) has been considered an exception with catalytic reactions assumed to involve highly unstable SQ or not to involve any SQ intermediate. This view seemed consistent with long-standing difficulty in detecting any reaction intermediates at the Qo site. New perspective on this issue is now offered by recent, independent reports on detection of SQ in this site. Each of the described SQs seems to have different spectroscopic properties leaving space for various interpretations and mechanistic considerations. Here, we comparatively reflect on those properties and their consequences on the SQ stabilization, the involvement of SQ in catalytic reactions, including proton transfers, and the reactivity of SQ with oxygen associated with superoxide generation activity of the Qo site.
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Affiliation(s)
- Rafał Pietras
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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14
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Sun C. Removal of the H subunit results in enhanced exposure of the semiquinone sites in the LM dimer from Rhodobacter sphaeroides to oxidation by ferricyanide and by O 2. PHOTOSYNTHESIS RESEARCH 2017; 133:371-377. [PMID: 28540587 DOI: 10.1007/s11120-017-0404-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
Bacterial reaction centers (RC) from Rhodobacter sphaeroides have been widely used to functionalize electrodes and to generate photocurrent. However, in most studies, direct electron transfer from the semiquinone to the electrode was not observed because the H subunit of the RC shields the semiquinone. It is demonstrated in the current work that removal of the H subunit effectively exposes the semiquinone sites in the LM dimer. This is demonstrated by measuring the second-order rate constant for the reaction between ferricyanide and the anionic semiquinone Q A- formed by an actinic flash. The rate constant increases 1000-fold for Q A- oxidation by ferricyanide in the LM dimer compared to the intact RC. The second-order rate constant approaches the diffusion limit of 6 × 109 M-1·s-1 at low pH, but it decreases steadily when the pH is above 6.5. This pH dependence suggests that the protonation state of the LM dimer plays an important role in controlling the electron transfer kinetics. It is also shown that the addition of exogenous ubiquinone to replenish the QB site, which is mostly empty in the LM dimer, leads to oxidation of Q A- by O2 following an actinic flash. It is concluded that removal of the H subunit results in exposure of the semiquinone sites of the LM dimer to externally added oxidants and may provide a strategy for enhancing direct electron transfer from the RC to an electrode.
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Affiliation(s)
- Chang Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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15
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Mezzetti A, Leibl W. Time-resolved infrared spectroscopy in the study of photosynthetic systems. PHOTOSYNTHESIS RESEARCH 2017; 131:121-144. [PMID: 27678250 DOI: 10.1007/s11120-016-0305-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.
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Affiliation(s)
- Alberto Mezzetti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7197, Laboratoire de Réactivité de Surfaces, 4 Pl. Jussieu, 75005, Paris, France.
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Winfried Leibl
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
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16
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Pan J, Saer R, Lin S, Beatty JT, Woodbury NW. Electron Transfer in Bacterial Reaction Centers with the Photoactive Bacteriopheophytin Replaced by a Bacteriochlorophyll through Coordinating Ligand Substitution. Biochemistry 2016; 55:4909-18. [DOI: 10.1021/acs.biochem.6b00317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie Pan
- The
Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - Rafael Saer
- Department
of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Su Lin
- The
Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - J. Thomas Beatty
- Department
of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Neal W. Woodbury
- The
Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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17
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Maróti P, Govindjee. The two last overviews by Colin Allen Wraight (1945-2014) on energy conversion in photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 2016; 127:257-71. [PMID: 26216496 DOI: 10.1007/s11120-015-0175-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/17/2015] [Indexed: 09/18/2024]
Abstract
Colin Allen Wraight (1945-2014) was a well-known biophysicist and biochemist of our times-formerly Professor of Biochemistry, Biophysics and Plant Biology, and Head of the Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. (See a detailed Tribute to him by Govindjee et al., Photosynth Res, 2015.) During the latter part of his life, Colin had (1) given an excellent lecture in 2008 on the overall topic of the molecular mechanisms in biological energy conversion, focusing on how an ubiquinone is reduced to ubiquinol at the so-called "two electron gate", and (2) presented a review poster on the design features of long distance proton transport in biological systems, with focus on photosynthetic bacteria (a pdf file of the original is available from one of us, Govindjee). We present here for historical purpose, a complete transcript of his 2008 lecture and his 2013 poster, which have been annotated and expanded by the authors of this paper. The major theme is: electron and proton transfer in biological systems, with emphasis on bacterial reaction centers. The figures, some of which were prepared by us, are presented in sequence for both the lecture and the poster. A common bibliography is provided at the end of the paper, which is divided into two parts: (I) The Lecture; and (II) The Poster.
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Affiliation(s)
- Péter Maróti
- Department of Medical Physics and Informatics, University of Szeged, Rerrich Béla tér 1. III. em., Szeged, 6720, Hungary.
| | - Govindjee
- Department of Plant Biology, Department of Biochemistry, and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL, 61801, USA.
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18
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Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Hydrogen bond network around the semiquinone of the secondary quinone acceptor Q(B) in bacterial photosynthetic reaction centers. J Phys Chem B 2015; 119:5805-14. [PMID: 25885036 DOI: 10.1021/acs.jpcb.5b03434] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By utilizing a combined pulsed EPR and DFT approach, the high-resolution structure of the QB site semiquinone (SQB) was determined. The development of such a technique is crucial toward an understanding of protein-bound semiquinones on the structural level, as (i) membrane protein crystallography typically results in low resolution structures, and (ii) obtaining protein crystals in the semiquinone form is rarely feasible. The SQB hydrogen bond network was investigated with Q- (∼34 GHz) and X-band (∼9.7 GHz) pulsed EPR spectroscopy on fully deuterated reactions centers from Rhodobacter sphaeroides. Simulations in the SQB g-tensor reference frame provided the principal values and directions of the H-bond proton hyperfine tensors. Three protons were detected, one with an anisotropic tensor component, T = 4.6 MHz, assigned to the histidine NδH of His-L190, and two others with similar anisotropic constants T = 3.2 and 3.0 MHz assigned to the peptide NpH of Gly-L225 and Ile-L224, respectively. Despite the strong similarity in the peptide couplings, all hyperfine tensors were resolved in the Q-band ENDOR spectra. The Euler angles describing the series of rotations that bring the hyperfine tensors into the SQB g-tensor reference frame were obtained by least-squares fitting of the spectral simulations to the ENDOR data. These Euler angles show the locations of the hydrogen bonded protons with respect to the semiquinone. Our geometry optimized model of SQB used in previous DFT work is in strong agreement with the angular constraints from the spectral simulations, providing the foundation for future joint pulsed EPR and DFT semiquinone structural determinations in other proteins.
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Affiliation(s)
- Alexander T Taguchi
- #Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,‡Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Patrick J O'Malley
- ⊥School of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
| | - Colin A Wraight
- #Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,§Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sergei A Dikanov
- ‡Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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19
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Asztalos E, Sipka G, Maróti P. Fluorescence relaxation in intact cells of photosynthetic bacteria: donor and acceptor side limitations of reopening of the reaction center. PHOTOSYNTHESIS RESEARCH 2015; 124:31-44. [PMID: 25527461 DOI: 10.1007/s11120-014-0070-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/12/2014] [Indexed: 06/04/2023]
Abstract
The dark relaxation of the yield of variable BChl fluorescence in the 10(-5)-10 s time range is measured after laser diode (808 nm) excitation of variable duration in intact cells of photosynthetic bacteria Rba. sphaeroides, Rsp. rubrum, and Rvx. gelatinosus under various treatments of redox agents, inhibitors, and temperature. The kinetics of the relaxation is complex and much wider extended than a monoexponential function. The longer is the excitation, the slower is the relaxation which is determined by the redox states, sizes, and accessibility of the pools of cytochrome [Formula: see text] and quinone for donor and acceptor side-limited bacterial strains, respectively. The kinetics of fluorescence decay reflects the opening kinetics of the closed RC. The relaxation is controlled preferentially by the rate of re-reduction of the oxidized dimer by mobile cytochrome [Formula: see text] in Rba. sphaeroides and Rsp. rubrum and by the rate constant of the [Formula: see text] interquinone electron transfer, (350 μs)(-1) and/or the quinol/quinone exchange at the acceptor side in Rvx. gelatinosus. The commonly used acceptor side inhibitors (e.g., terbutryn) demonstrate kinetically limited block of re-oxidation of the primary quinone. The observations are interpreted in frame of a minimum kinetic and energetic model of electron transfer reactions in bacterial RC of intact cells.
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Affiliation(s)
- Emese Asztalos
- Department of Medical Physics, University of Szeged, Szeged, Rerrich Béla tér 1, 6720, Hungary
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20
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Maróti Á, Wraight CA, Maróti P. Protonated rhodosemiquinone at the Q(B) binding site of the M265IT mutant reaction center of photosynthetic bacterium Rhodobacter sphaeroides. Biochemistry 2015; 54:2095-103. [PMID: 25760888 DOI: 10.1021/bi501553t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The second electron transfer from primary ubiquinone Q(A) to secondary ubiquinone Q(B) in the reaction center (RC) from Rhodobacter sphaeroides involves a protonated Q(B)(-) intermediate state whose low pK(a) makes direct observation impossible. Here, we replaced the native ubiquinone with low-potential rhodoquinone at the Q(B) binding site of the M265IT mutant RC. Because the in situ midpoint redox potential of Q(A) of this mutant was lowered approximately the same extent (≈100 mV) as that of Q(B) upon exchange of ubiquinone with low-potential rhodoquinone, the inter-quinone (Q(A) → Q(B)) electron transfer became energetically favorable. After subsequent saturating flash excitations, a period of two damped oscillations of the protonated rhodosemiquinone was observed. The Q(B)H(•) was identified by (1) the characteristic band at 420 nm of the absorption spectrum after the second flash and (2) weaker damping of the oscillation at 420 nm (due to the neutral form) than at 460 nm (attributed to the anionic form). The appearance of the neutral semiquinone was restricted to the acidic pH range, indicating a functional pK(a) of <5.5, slightly higher than that of the native ubisemiquinone (pK(a) < 4.5) at pH 7. The analysis of the pH and temperature dependencies of the rates of the second electron transfer supports the concept of the pH-dependent pK(a) of the semiquinone at the Q(B) binding site. The local electrostatic potential is severely modified by the strongly interacting neighboring acidic cluster, and the pK(a) of the semiquinone is in the middle of the pH range of the complex titration. The kinetic and thermodynamic data are discussed according to the proton-activated electron transfer mechanism combined with the pH-dependent functional pK(a) of the semiquinone at the Q(B) site of the RC.
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Affiliation(s)
| | - Colin A Wraight
- §Center for Biophysics and Computational Biology and Department of Plant Biology, University of Illinois, Urbana, Illinois 61801-3838, United States
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21
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The rate of second electron transfer to Q B − in bacterial reaction center of impaired proton delivery shows hydrogen-isotope effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:223-230. [DOI: 10.1016/j.bbabio.2014.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/31/2014] [Accepted: 11/05/2014] [Indexed: 11/21/2022]
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22
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Gerencsér L, Boros B, Derrien V, Hanson DK, Wraight CA, Sebban P, Maróti P. Stigmatellin probes the electrostatic potential in the QB site of the photosynthetic reaction center. Biophys J 2015; 108:379-94. [PMID: 25606686 DOI: 10.1016/j.bpj.2014.11.3463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/13/2014] [Accepted: 11/19/2014] [Indexed: 11/25/2022] Open
Abstract
The electrostatic potential in the secondary quinone (QB) binding site of the reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides determines the rate and free energy change (driving force) of electron transfer to QB. It is controlled by the ionization states of residues in a strongly interacting cluster around the QB site. Reduction of the QB induces change of the ionization states of residues and binding of protons from the bulk. Stigmatellin, an inhibitor of the mitochondrial and photosynthetic respiratory chain, has been proven to be a unique voltage probe of the QB binding pocket. It binds to the QB site with high affinity, and the pK value of its phenolic group monitors the local electrostatic potential with high sensitivity. Investigations with different types of detergent as a model system of isolated RC revealed that the pK of stigmatellin was controlled overwhelmingly by electrostatic and slightly by hydrophobic interactions. Measurements showed a high pK value (>11) of stigmatellin in the QB pocket of the dark-state wild-type RC, indicating substantial negative potential. When the local electrostatics of the QB site was modulated by a single mutation, L213Asp → Ala, or double mutations, L213Asp-L212Glu → Ala-Ala (AA), the pK of stigmatellin dropped to 7.5 and 7.4, respectively, which corresponds to a >210 mV increase in the electrostatic potential relative to the wild-type RC. This significant pK drop (ΔpK > 3.5) decreased dramatically to (ΔpK > 0.75) in the RC of the compensatory mutant (AA+M44Asn → AA+M44Asp). Our results indicate that the L213Asp is the most important actor in the control of the electrostatic potential in the QB site of the dark-state wild-type RC, in good accordance with conclusions of former studies using theoretical calculations or light-induced charge recombination assay.
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Affiliation(s)
- László Gerencsér
- Department of Biophysics, University of Szeged, Szeged, Hungary; Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Bogáta Boros
- Department of Biophysics, University of Szeged, Szeged, Hungary
| | - Valerie Derrien
- Laboratoire de Chimie Physique, University of Paris-Sud, Orsay, France
| | - Deborah K Hanson
- Biosciences Divisions, Argonne National Laboratory, Argonne, Illinois
| | - Colin A Wraight
- Department of Biochemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois
| | - Pierre Sebban
- Laboratoire de Chimie Physique, University of Paris-Sud, Orsay, France
| | - Péter Maróti
- Department of Biophysics, University of Szeged, Szeged, Hungary.
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23
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Hasan K, Reddy KVR, Eßmann V, Górecki K, Conghaile PÓ, Schuhmann W, Leech D, Hägerhäll C, Gorton L. Electrochemical Communication Between Electrodes andRhodobacter capsulatusGrown in Different Metabolic Modes. ELECTROANAL 2014. [DOI: 10.1002/elan.201400456] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Hyperfine and nuclear quadrupole tensors of nitrogen donors in the Q(A) site of bacterial reaction centers: correlation of the histidine N(δ) tensors with hydrogen bond strength. J Phys Chem B 2014; 118:9225-37. [PMID: 25026433 PMCID: PMC4126732 DOI: 10.1021/jp5051029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
X-
and Q-band pulsed EPR spectroscopy was applied to study the
interaction of the QA site semiquinone (SQA)
with nitrogens from the local protein environment in natural abundance 14N and in 15N uniformly labeled photosynthetic
reaction centers of Rhodobacter sphaeroides. The hyperfine and nuclear quadrupole tensors for His-M219 Nδ and Ala-M260 peptide nitrogen (Np) were
estimated through simultaneous simulation of the Q-band 15N Davies ENDOR, X- and Q-band 14,15N HYSCORE, and X-band 14N three-pulse ESEEM spectra, with support from DFT calculations.
The hyperfine coupling constants were found to be a(14N) = 2.3 MHz, T = 0.3 MHz for His-M219
Nδ and a(14N) = 2.6 MHz, T = 0.3 MHz for Ala-M260 Np. Despite that His-M219
Nδ is established as the stronger of the two H-bond
donors, Ala-M260 Np is found to have the larger value of a(14N). The nuclear quadrupole coupling constants
were estimated as e2Qq/4h = 0.38 MHz, η = 0.97 and e2Qq/4h = 0.74 MHz, η = 0.59 for His-M219 Nδ and Ala-M260 Np, respectively. An analysis of the available
data on nuclear quadrupole tensors for imidazole nitrogens found in
semiquinone-binding proteins and copper complexes reveals these systems
share similar electron occupancies of the protonated nitrogen orbitals.
By applying the Townes–Dailey model, developed previously for
copper complexes, to the semiquinones, we find the asymmetry parameter
η to be a sensitive probe of the histidine Nδ–semiquinone hydrogen bond strength. This is supported by
a strong correlation observed between η and the isotropic coupling
constant a(14N) and is consistent with
previous computational works and our own semiquinone-histidine model
calculations. The empirical relationship presented here for a(14N) and η will provide an important
structural characterization tool in future studies of semiquinone-binding
proteins.
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Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, §Department of Biochemistry, and ∥Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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25
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Olson TL, Williams JC, Allen JP. The three-dimensional structures of bacterial reaction centers. PHOTOSYNTHESIS RESEARCH 2014; 120:87-98. [PMID: 23575738 DOI: 10.1007/s11120-013-9821-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
This review presents a broad overview of the research that enabled the structure determination of the bacterial reaction centers from Blastochloris viridis and Rhodobacter sphaeroides, with a focus on the contributions from Duysens, Clayton, and Feher. Early experiments performed in the laboratory of Duysens and others demonstrated the utility of spectroscopic techniques and the presence of photosynthetic complexes in both oxygenic and anoxygenic photosynthesis. The laboratories of Clayton and Feher led efforts to isolate and characterize the bacterial reaction centers. The availability of well-characterized preparations of pure and stable reaction centers allowed the crystallization and subsequent determination of the structures using X-ray diffraction. The three-dimensional structures of reaction centers revealed an overall arrangement of two symmetrical branches of cofactors surrounded by transmembrane helices from the L and M subunits, which also are related by the same twofold symmetry axis. The structure has served as a framework to address several issues concerning bacterial photosynthesis, including the directionality of electron transfer, the properties of the reaction center-cytochrome c 2 complex, and the coupling of proton and electron transfer. Together, these research efforts laid the foundation for ongoing efforts to address an outstanding question in oxygenic photosynthesis, namely the molecular mechanism of water oxidation.
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Affiliation(s)
- T L Olson
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-1604, USA
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26
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Zhang X, Gunner MR. Affinity and activity of non-native quinones at the Q(B) site of bacterial photosynthetic reaction centers. PHOTOSYNTHESIS RESEARCH 2014; 120:181-96. [PMID: 23715773 PMCID: PMC4442677 DOI: 10.1007/s11120-013-9850-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 05/08/2013] [Indexed: 05/11/2023]
Abstract
Purple, photosynthetic reaction centers from Rhodobacter sphaeroides bacteria use ubiquinone (UQ10) as both primary (Q(A)) and secondary (Q(B)) electron acceptors. Many quinones reconstitute Q(A) function, while a few will act as Q(B). Nine quinones were tested for their ability to bind and reconstitute Q(A) and Q(B) functions. Only ubiquinone (UQ) reconstitutes both functions in the same protein. The affinities of the non-native quinones for the Q(B) site were determined by a competitive inhibition assay. The affinities of benzoquinones, naphthoquinone (NQ), and 2-methyl-NQ for the Q(B) site are 7 ± 3 times weaker than that at Q(A) site. However, di-ortho-substituted NQs and anthraquinone bind tightly to the Q(A) site (K d ≤ 200 nM), and ≥1,000 times more weakly to the Q(B) site, perhaps setting a limit on the size of the site. With a low-potential electron donor, 2-methyl, 3-dimethylamino-1,4-NQ, (Me-diMeAm-NQ) at Q(A), Q(B) reduction is 260 meV, more favorable than with UQ as Q(A). Electron transfer from Me-diMeAm-NQ at the Q(A) site to NQ at the Q(B) site can be detected. In the Q(B) site, the NQ semiquinone is estimated to be ≈60-100 meV higher in energy than the UQ semiquinone, while in the Q(A) site, the semiquinone energy level is similar or lower with NQ than with UQ. Thus, the NQ semiquinone is more stable in the Q(A) than in the Q(B) site. In contrast, the native UQ semiquinone is ≈60 meV lower in energy in the Q(B) than in the Q(A) site, stabilizing forward electron transfer from Q(A) to Q(B).
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Affiliation(s)
| | - M. R. Gunner
- To whom correspondence should be addressed. Telephone: 212-650-5557. Fax: 212-650-6940
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27
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Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Nuclear hyperfine and quadrupole tensor characterization of the nitrogen hydrogen bond donors to the semiquinone of the QB site in bacterial reaction centers: a combined X- and S-band (14,15)N ESEEM and DFT study. J Phys Chem B 2014; 118:1501-9. [PMID: 24437652 PMCID: PMC3983398 DOI: 10.1021/jp411023k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
secondary quinone anion radical QB– (SQB) in reaction centers of Rhodobacter
sphaeroides interacts with Nδ of
His-L190 and Np (peptide nitrogen) of Gly-L225 involved
in hydrogen bonds to the QB carbonyls. In this work, S-band
(∼3.6 GHz) ESEEM was used with the aim of obtaining a complete
characterization of the nuclear quadrupole interaction (nqi) tensors
for both nitrogens by approaching the cancelation condition between
the isotropic hyperfine coupling and 14N Zeeman frequency
at lower microwave frequencies than traditional X-band (9.5 GHz).
By performing measurements at S-band, we found a dominating contribution
of Nδ in the form of a zero-field nqi triplet at
0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e2qQ/4h = 0.4 MHz and associated asymmetry parameter η =
0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of
1D and 2D 14,15N X-band and three-pulse 14N
S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the
contribution of Np to the S-band spectrum is suppressed
by its strong nqi and weak isotropic hfi comparable to the level of
hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations
and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to
full tensor characterizations.
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Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, ‡Department of Biochemistry, §Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Taguchi AT, Mattis AJ, O'Malley PJ, Dikanov SA, Wraight CA. Tuning cofactor redox potentials: the 2-methoxy dihedral angle generates a redox potential difference of >160 mV between the primary (Q(A)) and secondary (Q(B)) quinones of the bacterial photosynthetic reaction center. Biochemistry 2013; 52:7164-6. [PMID: 24079813 DOI: 10.1021/bi4011896] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from Rhodobacter sphaeroides. (13)C hyperfine sublevel correlation measurements of the 2-methoxy in the semiquinone states, SQA and SQB, were compared with quantum mechanics calculations of the (13)C couplings as a function of the dihedral angle. X-ray structures support dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of ~180 mV. This is consistent with the failure of a ubiquinone analogue lacking the 2-methoxy to function as QB in mutant reaction centers with a ΔEm of ≈160-195 mV.
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Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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29
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Zhao N, Hastings G. On the Nature of the Hydrogen Bonds to Neutral Ubiquinone in the QA Binding Site in Purple Bacterial Photosynthetic Reaction Centers. J Phys Chem B 2013; 117:8705-13. [DOI: 10.1021/jp403833y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Nan Zhao
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia 30303, United States
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia 30303, United States
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30
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Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Conformational differences between the methoxy groups of QA and QB site ubisemiquinones in bacterial reaction centers: a key role for methoxy group orientation in modulating ubiquinone redox potential. Biochemistry 2013; 52:4648-55. [PMID: 23745576 DOI: 10.1021/bi400489b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquinone is an almost universal, membrane-associated redox mediator. Its ability to accept either one or two electrons allows it to function in critical roles in biological electron transport. The redox properties of ubiquinone in vivo are determined by its environment in the binding sites of proteins and by the dihedral angle of each methoxy group relative to the ring plane. This is an attribute unique to ubiquinone among natural quinones and could account for its widespread function with many different redox complexes. In this work, we use the photosynthetic reaction center as a model system for understanding the role of methoxy conformations in determining the redox potential of the ubiquinone/semiquinone couple. Despite the abundance of X-ray crystal structures for the reaction center, quinone site resolution has thus far been too low to provide a reliable measure of the methoxy dihedral angles of the primary and secondary quinones, QA and QB. We performed 2D ESEEM (HYSCORE) on isolated reaction centers with ubiquinones (13)C-labeled at the headgroup methyl and methoxy substituents, and have measured the (13)C isotropic and anisotropic components of the hyperfine tensors. Hyperfine couplings were compared to those derived by DFT calculations as a function of methoxy torsional angle allowing estimation of the methoxy dihedral angles for the semiquinones in the QA and QB sites. Based on this analysis, the orientation of the 2-methoxy groups are distinct in the two sites, with QB more out of plane by 20-25°. This corresponds to an ≈50 meV larger electron affinity for the QB quinone, indicating a substantial contribution to the experimental difference in redox potentials (60-75 mV) of the two quinones. The methods developed here can be readily extended to ubiquinone-binding sites in other protein complexes.
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Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, §Department of Biochemistry, and ‡Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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31
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Pan J, Saer RG, Lin S, Guo Z, Beatty JT, Woodbury NW. The Protein Environment of the Bacteriopheophytin Anion Modulates Charge Separation and Charge Recombination in Bacterial Reaction Centers. J Phys Chem B 2013; 117:7179-89. [DOI: 10.1021/jp400132k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Pan
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - Rafael G. Saer
- Department of Microbiology and
Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada
V6T 1Z3
| | - Su Lin
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- Department of Chemistry and
Biochemistry, Arizona State University,
Tempe, Arizona 85287-1604, United States
| | - Zhi Guo
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - J. Thomas Beatty
- Department of Microbiology and
Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada
V6T 1Z3
| | - Neal W. Woodbury
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- Department of Chemistry and
Biochemistry, Arizona State University,
Tempe, Arizona 85287-1604, United States
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32
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Onidas D, Sipka G, Asztalos E, Maróti P. Mutational control of bioenergetics of bacterial reaction center probed by delayed fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1191-9. [PMID: 23685111 DOI: 10.1016/j.bbabio.2013.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/01/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
The free energy gap between the metastable charge separated state P(+)QA(-) and the excited bacteriochlorophyll dimer P* was measured by delayed fluorescence of the dimer in mutant reaction center proteins of the photosynthetic bacterium Rhodobacter sphaeroides. The mutations were engineered both at the donor (L131L, M160L, M197F and M202H) and acceptor (M265I and M234E) sides. While the donor side mutations changed systematically the number of H-bonds to P, the acceptor side mutations modified the energetics of QA by altering the van-der-Waals and electronic interactions (M265IT) and H-bond network to the acidic cluster around QB (M234EH, M234EL, M234EA and M234ER). All mutants decreased the free energy gap of the wild type RC (~890meV), i.e. destabilized the P(+)QA(-) charge pair by 60-110meV at pH8. Multiple modifications in the hydrogen bonding pattern to P resulted in systematic changes of the free energy gap. The destabilization showed no pH-dependence (M234 mutants) or slight increase (WT, donor-side mutants and M265IT above pH8) with average slope of 10-15meV/pH unit over the 6-10.5pH range. In wild type and donor-side mutants, the free energy change of the charge separation consisted of mainly enthalpic term but the acceptor side mutants showed increased entropic (even above that of enthalpic) contributions. This could include softening the structure of the iron ligand (M234EH) and the QA binding pocket (M265IT) and/or increase of the multiplicity of the electron transfer of charge separation in the acceptor side upon mutation.
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Affiliation(s)
- Delphine Onidas
- Laboratoire de Chimie Physique UMR 8000, Batiment 350, Orsay-Cedex, Université de Paris-Sud, 91405, France
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33
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New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory. Biochem J 2012; 442:27-37. [PMID: 22054235 DOI: 10.1042/bj20111540] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.
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34
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Calculated vibrational properties of pigments in protein binding sites. Proc Natl Acad Sci U S A 2011; 108:10526-31. [PMID: 21670247 DOI: 10.1073/pnas.1104046108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FTIR difference spectroscopy is widely used to probe molecular bonding interactions of protein-bound electron transfer cofactors. The technique is particularly attractive because it provides information on both neutral and radical cofactor states. Such dual information is not easily obtainable using other techniques. Although FTIR difference spectroscopy has been used to study cofactors in biological protein complexes, in nearly all cases interpretation of the spectra has been purely qualitative. Virtually no computational work has been undertaken in an attempt to model the spectra. To address this problem we have developed the use of ONIOM (our own N-layered integrated molecular Orbital + Molecular mechanics package) (quantum mechanical:molecular mechanics) methods to calculate FTIR difference spectra associated with protein-bound cofactors. As a specific example showing the utility of the approach we have calculated isotope edited FTIR difference spectra associated with unlabeled and labeled ubiquinones in the Q(A) binding site in Rhodobacter sphaeroides photosynthetic reaction centers. The calculated spectra are in remarkable agreement with experiment. Such agreement cannot be obtained by considering ubiquinone molecules in the gas phase or in solution. A calculation including the protein environment is required. The ONIOM calculated spectra agree well with experiment but indicate a very different interpretation of the experimental data compared to that proposed previously. In particular the calculations do not predict that one of the carbonyl groups of Q(A) is very strongly hydrogen bonded. We show that a computational-based interpretation of FTIR difference spectra associated with protein-bound cofactors is now possible. This approach will be applicable to FTIR studies of many cofactor-containing proteins.
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35
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Martin E, Samoilova RI, Narasimhulu KV, Wraight CA, Dikanov SA. Hydrogen bonds between nitrogen donors and the semiquinone in the Q(B) site of bacterial reaction centers. J Am Chem Soc 2010; 132:11671-7. [PMID: 20672818 DOI: 10.1021/ja104134e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosynthetic reaction centers from Rhodobacter sphaeroides have identical ubiquinone-10 molecules functioning as primary (Q(A)) and secondary (Q(B)) electron acceptors. X-band 2D pulsed EPR spectroscopy, called HYSCORE, was applied to study the interaction of the Q(B) site semiquinone with nitrogens from the local protein environment in natural and (15)N uniformly labeled reactions centers. (14)N and (15)N HYSCORE spectra of the Q(B) semiquinone show the interaction with two nitrogens carrying transferred unpaired spin density. Quadrupole coupling constants estimated from (14)N HYSCORE spectra indicate them to be a protonated nitrogen of an imidazole residue and amide nitrogen of a peptide group. (15)N HYSCORE spectra allowed estimation of the isotropic and anisotropic couplings with these nitrogens. From these data, we calculated the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen and analyzed the contribution of different factors to the anisotropic hyperfine tensors. The hyperfine coupling of other protein nitrogens with the semiquinone is weak (<0.1 MHz). These results clearly indicate that the Q(B) semiquinone forms hydrogen bonds with two nitrogens and provide quantitative characteristics of the hyperfine couplings with these nitrogens, which can be used in theoretical modeling of the Q(B) site. On the basis of the quadrupole coupling constant, one nitrogen can only be assigned to N(delta) of His-L190, consistent with all existing structures. However, we cannot specify between two candidates the residue corresponding to the second nitrogen. Further work employing multifrequency spectroscopic approaches or selective isotope labeling would be desirable for unambiguous assignment of this nitrogen.
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Affiliation(s)
- Erik Martin
- Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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