1
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Taguchi AT, Wraight CA, Dikanov SA. Influence of Polar Mutations on the Electronic and Structural Properties of QA-· in Bacterial Reaction Centers. J Phys Chem B 2022; 126:6210-6220. [PMID: 35960270 DOI: 10.1021/acs.jpcb.2c04371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction centers from Rhodobacter sphaeroides with residue M265 mutated from isoleucine to threonine, serine, and asparagine (M265IT, M265IS, and M265IN, respectively) in the QA-· state are studied by high-resolution electron spin echo envelope modulation (ESEEM) and electron nuclear double resonance spectroscopy methods to investigate the structural characteristics of these mutants influencing the redox properties of the QA site. All three mutants decrease the redox midpoint potential (Em) of QA by ∼0.1 V, yet the mechanism for this drop in Em is unclear. In this work, we examine (i) the hydrogen bonding interactions between QA-· and residues histidine M219 and alanine M260, (ii) the electron spin density distribution of the semiquinone, and (iii) the orientations of the ubiquinone methoxy substituents. 13C measurements show no significant contribution of methoxy dihedral angles to the observed decrease in Em for the QA mutants. Instead, 14N three-pulse ESEEM data suggest that electrostatic or hydrogen bond formation between the mutated M265 side chain and His-M219 Nδ may be involved in the observed lowering of the QA midpoint potential. For mutant M265IN, analysis of the proton hyperfine couplings reveals a weakened hydrogen bond network, resulting in an altered QA-· spin density distribution. The magnetic resonance study presented here is most consistent with an electrostatic or structural perturbation of the His-M219 Nδ hydrogen bond in these mutants as a mechanism for the ∼0.1 V decrease in QA Em.
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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.,RubrYc Therapeutics, 733 Industrial Road, San Carlos, California 94403, United States
| | - Colin A Wraight
- 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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2
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Ding Z, Sun C, Yi SM, Gennis RB, Dikanov SA. The Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Accommodates Menaquinone and Stabilizes a Functional Menasemiquinone. Biochemistry 2019; 58:4559-4569. [PMID: 31644263 DOI: 10.1021/acs.biochem.9b00750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytochrome bo3, one of three terminal oxygen reductases in the aerobic respiratory chain of Escherichia coli, has been well characterized as a ubiquinol oxidase. The ability of cytochrome bo3 to catalyze the two-electron oxidation of ubiquinol-8 requires the enzyme to stabilize the one-electron oxidized ubisemiquinone species that is a transient intermediate in the reaction. Cytochrome bo3 has been shown recently to also utilize demethylmenaquinol-8 as a substrate that, along with menaquinol-8, replaces ubiquinol-8 when E. coli is grown under microaerobic or anaerobic conditions. In this work, we show that its steady-state turnover with 2,3-dimethyl-1,4-naphthoquinol, a water-soluble menaquinol analogue, is just as efficient as with ubiquinol-1. Using pulsed electron paramagnetic resonance spectroscopy, we demonstrate that the same residues in cytochrome bo3 that stabilize the semiquinone state of ubiquinone also stabilize the semiquinone state of menaquinone, with the hydrogen bond strengths and the distribution of unpaired spin density accommodated for the different substrate. Catalytic function with menaquinol is more tolerant of mutations at the active site than with ubiquinol. A mutation of one of the stabilizing residues (R71H in subunit I) that eliminates the ubiquinol oxidase activity of cytochrome bo3 does not abolish activity with soluble menaquinol analogues.
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Affiliation(s)
- Ziqiao Ding
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Chang Sun
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sophia M Yi
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Robert B Gennis
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Center for Biophysics and Computational Biology , 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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3
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Taguchi AT, O’Malley PJ, Wraight CA, Dikanov SA. Determination of the Complete Spin Density Distribution in 13C-Labeled Protein-Bound Radical Intermediates Using Advanced 2D Electron Paramagnetic Resonance Spectroscopy and Density Functional Theory. J Phys Chem B 2017; 121:10256-10268. [DOI: 10.1021/acs.jpcb.7b10036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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
| | | | - 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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Yi SM, Taguchi AT, Samoilova RI, O'Malley PJ, Gennis RB, Dikanov SA. Plasticity in the High Affinity Menaquinone Binding Site of the Cytochrome aa3-600 Menaquinol Oxidase from Bacillus subtilis. Biochemistry 2015. [PMID: 26196462 DOI: 10.1021/acs.biochem.5b00528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome aa3-600 is a terminal oxidase in the electron transport pathway that contributes to the electrochemical membrane potential by actively pumping protons. A notable feature of this enzyme complex is that it uses menaquinol as its electron donor instead of cytochrome c when it reduces dioxygen to water. The enzyme stabilizes a menasemiquinone radical (SQ) at a high affinity site that is important for catalysis. One of the residues that interacts with the semiquinone is Arg70. We have made the R70H mutant and have characterized the menasemiquinone radical by advanced X- and Q-band EPR. The bound SQ of the R70H mutant exhibits a strong isotropic hyperfine coupling (a(14)N ≈ 2.0 MHz) with a hydrogen bonded nitrogen. This nitrogen originates from a histidine side chain, based on its quadrupole coupling constant, e(2)qQ/h = 1.44 MHz, typical for protonated imidazole nitrogens. In the wild-type cyt aa3-600, the SQ is instead hydrogen bonded with Nε from the Arg70 side chain. Analysis of the (1)H 2D electron spin echo envelope modulation (ESEEM) spectra shows that the mutation also changes the number and strength of the hydrogen bonds between the SQ and the surrounding protein. Despite the alterations in the immediate environment of the SQ, the R70H mutant remains catalytically active. These findings are in contrast to the equivalent mutation in the close homologue, cytochrome bo3 ubiquinol oxidase from Escherichia coli, where the R71H mutation eliminates function.
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Affiliation(s)
- Sophia M Yi
- §Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - 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
| | - Rimma I Samoilova
- ⊥V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Patrick J O'Malley
- ∥School of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
| | - Robert B Gennis
- §Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,†Center for Biophysics and Computational Biology, 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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Vennam PR, Fisher N, Krzyaniak MD, Kramer DM, Bowman MK. A caged, destabilized, free radical intermediate in the q-cycle. Chembiochem 2013; 14:1745-53. [PMID: 24009094 PMCID: PMC3951126 DOI: 10.1002/cbic.201300265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 11/12/2022]
Abstract
The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase (Qo ) sites, in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models have been proposed. In previous work, we trapped a Q-cycle semiquinone anion intermediate, termed SQo , in bacterial cytochrome bc1 by rapid freeze-quenching. In this work, we apply pulsed-EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and can even be destabilized with respect to solution. It is trapped in Qo at a site that is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analyses show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves "stripping" of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL while minimizing certain Q-cycle bypass reactions, including oxidation of prereduced cytochrome b and reduction of O2 .
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Affiliation(s)
- Preethi R. Vennam
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - Nicholas Fisher
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Matthew D. Krzyaniak
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - David M. Kramer
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Michael K. Bowman
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
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6
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Dikanov SA. Resolving protein-semiquinone interactions by two-dimensional ESEEM spectroscopy. ELECTRON PARAMAGNETIC RESONANCE 2012. [DOI: 10.1039/9781849734837-00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S. A. Dikanov
- University of Illinois at Urbana-Champaign, Department of Veterinary Clinical Medicine 190 MSB, 506 S. Mathews Ave., Urbana IL 61801 USA
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Chatterjee R, Coates CS, Milikisiyants S, Poluektov OG, Lakshmi KV. Structure and Function of Quinones in Biological Solar Energy Transduction: A High-Frequency D-Band EPR Spectroscopy Study of Model Benzoquinones. J Phys Chem B 2011; 116:676-82. [DOI: 10.1021/jp210156a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Ruchira Chatterjee
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Christopher S. Coates
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Sergey Milikisiyants
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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8
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Srinivasan N, Chatterjee R, Milikisiyants S, Golbeck JH, Lakshmi KV. Effect of Hydrogen Bond Strength on the Redox Properties of Phylloquinones: A Two-Dimensional Hyperfine Sublevel Correlation Spectroscopy Study of Photosystem I. Biochemistry 2011; 50:3495-501. [DOI: 10.1021/bi102056q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nithya Srinivasan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ruchira Chatterjee
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Sergey Milikisiyants
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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9
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Martin E, Samoilova RI, Narasimhulu KV, Lin TJ, O'Malley PJ, Wraight CA, Dikanov SA. Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site. J Am Chem Soc 2011; 133:5525-37. [PMID: 21417328 DOI: 10.1021/ja2001538] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.
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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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10
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Witwicki M, Jezierska J. Effects of Solvents, Ligand Aromaticity, and Coordination Sphere on the g Tensor of Anionic o-Semiquinone Radicals Complexed by Mg2+ Ions: DFT Studies. J Phys Chem B 2011; 115:3172-84. [DOI: 10.1021/jp110515j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, 14 F. Joliot-Curie St., Wroclaw 50-283, Poland
| | - Julia Jezierska
- Faculty of Chemistry, Wroclaw University, 14 F. Joliot-Curie St., Wroclaw 50-283, Poland
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11
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Wu J, Huang F, Lü X, Chen P. One-pot synthesis of BiSbO4 nanophotocatalyst with enhanced visible-light performance. CrystEngComm 2011. [DOI: 10.1039/c1ce05025g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Savitsky A, Malferrari M, Francia F, Venturoli G, Möbius K. Bacterial Photosynthetic Reaction Centers in Trehalose Glasses: Coupling between Protein Conformational Dynamics and Electron-Transfer Kinetics as Studied by Laser-Flash and High-Field EPR Spectroscopies. J Phys Chem B 2010; 114:12729-43. [DOI: 10.1021/jp105801q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Savitsky
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Marco Malferrari
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Francesco Francia
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Giovanni Venturoli
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Klaus Möbius
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
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14
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Keßen S, Teutloff C, Kern J, Zouni A, Bittl R. High-Field 2H-Mims-ENDOR Spectroscopy on PSII Single Crystals: Hydrogen Bonding of YD. Chemphyschem 2010; 11:1275-82. [DOI: 10.1002/cphc.200901019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Kothe G, Thurnauer MC. What you get out of high-time resolution electron paramagnetic resonance: example from photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 2009; 102:349-365. [PMID: 19350413 DOI: 10.1007/s11120-009-9419-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 03/19/2009] [Indexed: 05/27/2023]
Abstract
The primary energy conversion steps of natural photosynthesis proceed via light-induced radical ion pairs as short-lived intermediates. Time-resolved electron paramagnetic resonance (EPR) experiments of photosynthetic reaction centers monitor the key charge separated state between the oxidized primary electron donor and reduced quinone acceptor, e.g., P(+)(865)Q(-)(A) of purple photosynthetic bacteria. The time-resolved EPR spectra of P(+)(865)Q(-)(A) are indicative of a spin-correlated radical pair that is created from the excited singlet state of P(865) in an ultra-fast photochemical reaction. Importantly, the spin-correlated radical pair nature of the charge separated state is a common feature of all photosynthetic reaction centers, which gives rise to several interesting spin phenomena such as quantum oscillations, observed at short delay times after optical excitation. In this review, we describe details of the quantum oscillation phenomenon and present a complete analysis of the data obtained from the charge separated state of purple bacteria, P(+)(865)Q(-)(A). The analysis and simulation of the quantum oscillations yield the three-dimensional structure of P(+)(865)Q(-)(A) in the photosynthetic membrane on a nanosecond time scale after light-induced charge separation. Comparison with crystallographic data reveals that the position of Q(-)(A) is essentially the same as in the X-ray structure. However, the head group of Q(-)(A) has undergone a 60° rotation in the ring plane relative to its orientation in the crystal structure. The results are discussed within the framework of the previously suggested conformational gating mechanism for electron transfer from Q(-)(A) to the secondary quinone acceptor Q(B).
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Affiliation(s)
- Gerd Kothe
- Department of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany.
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16
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Weyers AM, Chatterjee R, Milikisiyants S, Lakshmi KV. Structure and Function of Quinones in Biological Solar Energy Transduction: A Differential Pulse Voltammetry, EPR, and Hyperfine Sublevel Correlation (HYSCORE) Spectroscopy Study of Model Benzoquinones. J Phys Chem B 2009; 113:15409-18. [DOI: 10.1021/jp907379d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amanda M. Weyers
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Ruchira Chatterjee
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Sergey Milikisiyants
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180
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Teutloff C, Pudollek S, Keßen S, Broser M, Zouni A, Bittl R. Electronic structure of the tyrosine D radical and the water-splitting complex from pulsed ENDOR spectroscopy on photosystem II single crystals. Phys Chem Chem Phys 2009; 11:6715-26. [DOI: 10.1039/b908093g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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Cernescu A, Maly T, Prisner TF. 2D-REFINE spectroscopy: separation of overlapping hyperfine spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 192:78-84. [PMID: 18343175 DOI: 10.1016/j.jmr.2008.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 02/04/2008] [Accepted: 02/04/2008] [Indexed: 05/26/2023]
Abstract
We show on a mixture of three spectrally overlapping paramagnetic compounds TEMPO, BDPA and CuHis that it is possible to separate their field-swept and hyperfine spectra based on the difference in their longitudinal relaxation times T1. This was achieved in a two-dimensional experiment, where one dimension corresponds to the spectral domain and the second dimension encodes the relaxation behavior of the individual compound. Inverse Laplace Transform with respect to this domain separates the field-swept and hyperfine spectra of the individual compounds in the relaxation rate domain. This extends our formerly proposed Relaxation Filtered Hyperfine (REFINE) method to be applicable to more than two spectrally overlapping spectra by adding a further dimension to the chosen EPR experiment.
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Affiliation(s)
- Adrian Cernescu
- Institute for Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, Marie-Curie Str. 11, D-60439 Frankfurt am Main, Germany
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High-Field/High-Frequency Electron Paramagnetic Resonance Involving Single- and Multiple-Transition Schemes. BIOPHYSICAL TECHNIQUES IN PHOTOSYNTHESIS 2008. [DOI: 10.1007/978-1-4020-8250-4_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Heinen U, Utschig LM, Poluektov OG, Link G, Ohmes E, Kothe G. Structure of the charge separated state P865(+)Q(A)- in the photosynthetic reaction centers of Rhodobacter sphaeroides by quantum beat oscillations and high-field electron paramagnetic resonance: evidence for light-induced Q(A)- reorientation. J Am Chem Soc 2007; 129:15935-46. [PMID: 18052250 DOI: 10.1021/ja075065h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of the secondary radical pair, P865(+)Q(A)-, in fully deuterated and Zn-substituted reaction centers (RCs) of the purple bacterium Rhodobacter sphaeroides R-26 has been determined by high-time resolution and high-field electron paramagnetic resonance (EPR). A computer analysis of quantum beat oscillations, observed in a two-dimensional Q-band (34 GHz) EPR experiment, provides the orientation of the various magnetic tensors of P865(+)Q(A)- with respect to a magnetic reference frame. The orientation of the g-tensor of P865(+) in an external reference system is adapted from a single-crystal W-band (95 GHz) EPR study [Klette, R.; Törring, J. T.; Plato, M.; Möbius, K.; Bönigk, B.; Lubitz, W. J. Phys. Chem. 1993, 97, 2015-2020]. Thus, we obtain the three-dimensional structure of the charge separated state P865(+)Q(A)- on a nanosecond time scale after light-induced charge separation. Comparison with crystallographic data reveals that the position of the quinone is essentially the same as that in the X-ray structure. However, the head group of Q(A)- has undergone a 60 degrees rotation in the ring plane relative to its orientation in the crystal structure. Analysis suggests that the two different QA conformations are functionally relevant states which control the electron-transfer kinetics from Q(A)- to the secondary quinone acceptor QB. It appears that the rate-limiting step of this reaction is a reorientation of Q(A)- in its binding pocket upon light-induced reduction. The new kinetic model accounts for striking observations by Kleinfeld et al. who reported that electron transfer from Q(A)- to QB proceeds in RCs cooled to cryogenic temperature under illumination but does not proceed in RCs cooled in the dark [Kleinfeld, D.; Okamura, M. Y.; Feher, G. Biochemistry 1984, 23, 5780-5786].
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Affiliation(s)
- Ulrich Heinen
- Department of Physical Chemistry, University of Freiburg, Albertstrasse 21, D-79104 Freiburg, Germany
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21
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Kacprzak S, Kaupp M, MacMillan F. Protein-cofactor interactions and EPR parameters for the Q(H) quinone binding site of quinol oxidase. A density functional study. J Am Chem Soc 2007; 128:5659-71. [PMID: 16637632 DOI: 10.1021/ja053988b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent multifrequency EPR studies of the "high-affinity" quinone binding site of quinol oxidase (Q(H) site) have suggested a very asymmetric hydrogen-bonding environment for the semiquinone radical anion state. Single-sided hydrogen bonding to the O1 carbonyl position was one of the proposals, which contrasts with some previous experimental indications. Here density functional calculations of the EPR parameters (g-tensors, 13C, 1H, and 17O hyperfine tensors) for a wide variety of supermolecular model complexes have been used to provide insight into the detailed relations among structure, environment, and EPR parameters of ubisemiquinone radical anions. A single-sided binding model is not able to account for the experimentally observed low g(x) component of the g-tensor or for the observed magnitude of the asymmetry of the 13C carbonyl HFC tensors. Based on the detailed comparison between computation and experiment, a model with two hydrogen bonds to O1 and one hydrogen bond to O4 is suggested for the Q(H) site, but a model with one more hydrogen bond on each side cannot be excluded. Several general conclusions on the interrelations between EPR parameters and hydrogen bond patterns of ubisemiquinones in proteins are provided.
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Affiliation(s)
- Sylwia Kacprzak
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D 97074 Würzburg, Germany
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22
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Epel B, Niklas J, Sinnecker S, Zimmermann H, Lubitz W. Phylloquinone and related radical anions studied by pulse electron nuclear double resonance spectroscopy at 34 GHz and density functional theory. J Phys Chem B 2007; 110:11549-60. [PMID: 16771431 DOI: 10.1021/jp060548d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1H hyperfine (hf) coupling constants of semiquinone radical anions of 1,4-naphthoquinone, 2-methyl-1,4-naphthoquinone, and 2-methyl-3-phytyl-1,4-naphthoquinone in frozen alcoholic solutions were measured using pulse Q-band electron nuclear double resonance spectroscopy. The resolved signals of the quinone protons as well as from hydrogen bond and solvent shell protons were analyzed and assigned. Both in-plane and out-of-plane hydrogen bonding with respect to the pi-plane of the radical is observed. Interactions with nonexchangeable protons from the surrounding matrix are detected and assigned to solvent protons above and below the quinone plane. Density functional theory was used to calculate spin Hamiltonian parameters of the radical anions. Solvent molecules of the first solvent shell that provide hydrogen bonds to the quinones were included in the geometry optimization. The conductor-like screening model was employed to introduce additional effects of the solvent cage. From a comparison of the experimental and calculated hf tensors it is concluded that four solvent molecules are coordinated via hydrogen bonds to the quinone oxygens. For all radicals very good agreement between experimental and calculated data is observed. The influence of different substituents on the spin density distribution and hydrogen bond geometries is discussed.
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Affiliation(s)
- Boris Epel
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim/Ruhr, Germany
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Flores M, Isaacson R, Abresch E, Calvo R, Lubitz W, Feher G. Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: II. Geometry of the hydrogen bonds to the primary quinone formula by 1H and 2H ENDOR spectroscopy. Biophys J 2006; 92:671-82. [PMID: 17071655 PMCID: PMC1751397 DOI: 10.1529/biophysj.106.092460] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The geometry of the hydrogen bonds to the two carbonyl oxygens of the semiquinone Q(A)(. -) in the reaction center (RC) from the photosynthetic purple bacterium Rhodobacter sphaeroides R-26 were determined by fitting a spin Hamiltonian to the data derived from (1)H and (2)H ENDOR spectroscopies at 35 GHz and 80 K. The experiments were performed on RCs in which the native Fe(2+) (high spin) was replaced by diamagnetic Zn(2+) to prevent spectral line broadening of the Q(A)(. -) due to magnetic coupling with the iron. The principal components of the hyperfine coupling and nuclear quadrupolar coupling tensors of the hydrogen-bonded protons (deuterons) and their principal directions with respect to the quinone axes were obtained by spectral simulations of ENDOR spectra at different magnetic fields on frozen solutions of deuterated Q(A)(. -) in H(2)O buffer and protonated Q(A)(. -) in D(2)O buffer. Hydrogen-bond lengths were obtained from the nuclear quadrupolar couplings. The two hydrogen bonds were found to be nonequivalent, having different directions and different bond lengths. The H-bond lengths r(OH) are 1.73 +/- 0.03 Angstrom and 1.60 +/- 0.04 Angstrom, from the carbonyl oxygens O(1) and O(4) to the NH group of Ala M260 and the imidazole nitrogen N(delta) of His M219, respectively. The asymmetric hydrogen bonds of Q(A)(. -) affect the spin density distribution in the quinone radical and its electronic structure. It is proposed that the H-bonds play an important role in defining the physical properties of the primary quinone, which affect the electron transfer processes in the RC.
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Affiliation(s)
- M Flores
- Department of Physics, University of California at San Diego, La Jolla, California, USA
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Borovykh IV, Ceola S, Gajula P, Gast P, Steinhoff HJ, Huber M. Distance between a native cofactor and a spin label in the reaction centre of Rhodobacter sphaeroides by a two-frequency pulsed electron paramagnetic resonance method and molecular dynamics simulations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 180:178-85. [PMID: 16515869 DOI: 10.1016/j.jmr.2006.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 12/31/2005] [Accepted: 02/06/2006] [Indexed: 05/06/2023]
Abstract
The distance between the paramagnetic state of a native cofactor and a spin label is measured in the photosynthetic reaction centre from the bacterium Rhodobacter sphaeroides R26. A two-frequency pulsed electron paramagnetic resonance method [double-electron-electron spin resonance (DEER)] is used. A distance of 3.05 nm between the semiquinone anion state of the primary acceptor (Q(A)) and the spin label at the native cysteine at position 156 in the H-subunit is found. Molecular-dynamics (MD) simulations are performed to interpret the distance. A 6 ns run comprising the entire RC protein yields a distance distribution that is close to the experimental one. The average distance found by the MD simulation is smaller than the distance obtained by DEER by at least 0.2 nm. To better represent the experiments performed at low temperature (60K), a MD method to mimic the freezing-in of the room-temperature conformations is introduced. Both MD methods yield similar distances, but the second method has a trend towards a wider distance distribution.
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Affiliation(s)
- Igor V Borovykh
- Fachbereich Physik, Universität Osnabrück, P.O. Box, 49069 Osnabrueck, Germany
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Flores M, Isaacson R, Abresch E, Calvo R, Lubitz W, Feher G. Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: I. Identification of the ENDOR lines associated with the hydrogen bonds to the primary quinone QA*-. Biophys J 2006; 90:3356-62. [PMID: 16473904 PMCID: PMC1432105 DOI: 10.1529/biophysj.105.077883] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen bonds are important in determining the structure and function of biomolecules. Of particular interest are hydrogen bonds to quinones, which play an important role in the bioenergetics of respiration and photosynthesis. In this work we investigated the hydrogen bonds to the two carbonyl oxygens of the semiquinone QA*- in the well-characterized reaction center from the photosynthetic bacterium Rhodobacter sphaeroides R-26. We used electron paramagnetic resonance and electron nuclear double resonance techniques at 35 GHz at a temperature of 80 K. The goal of this study was to identify and assign sets of 1H-ENDOR lines to protons hydrogen bonded to each of the two oxygens. This was accomplished by preferentially exchanging the hydrogen bond on one of the oxygens with deuterium while concomitantly monitoring the changes in the amplitudes of the 1H-ENDOR lines. The preferential deuteration of one of the oxygens was made possible by the different 1H --> 2H exchange times of the protons bonded to the two oxygens. The assignment of the 1H-ENDOR lines sets the stage for the determination of the geometries of the H-bonds by a detailed field selection ENDOR study to be presented in a future article.
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Affiliation(s)
- M Flores
- Department of Physics, University of California at San Diego, La Jolla, California, USA
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26
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Goldfarb D. High field ENDOR as a characterization tool for functional sites in microporous materials. Phys Chem Chem Phys 2006; 8:2325-43. [PMID: 16710481 DOI: 10.1039/b601513c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The determination of the details of the spatial and electronic structure of functional sites (centers) in any system, be it in materials chemistry or in biology, is the first step towards understanding their function. When such sites happen to be paramagnetic in any point of their activity cycle, the tool box offered by a variety of high resolution electron paramagnetic resonance (EPR) spectroscopic techniques becomes very attractive for their characterization. This tool box has been considerably expanded by the developments in high field (HF) EPR in general, and HF electron nuclear double resonance (ENDOR), in particular. These have led to numerous new applications in the fields of biology, physics, chemistry and materials sciences. This overview focuses specifically on recent applications of pulsed HF ENDOR spectroscopy to microporous materials, such as zeotype materials, presenting the new opportunities it offers. First, a brief description of the theoretical basis required for the analysis of the HF ENDOR spectrum is given, followed by a description of the pulsed techniques used to record spectra and assign the signals, along with a brief presentation of the required instrumentation. Next, specific applications are given, including transition metal ions and complexes exchanged into zeolite cages, transition metal substitution into frameworks of zeolites, aluminophosphate molecular sieves, and silicious mesoporous materials, the interaction of NO with Lewis sites in zeolite cages and trapped S. We end with a discussion of the advantages and the shortcomings of the method and conclude with a future outlook.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel.
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27
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Sinnecker S, Flores M, Lubitz W. Protein–cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: Effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study. Phys Chem Chem Phys 2006; 8:5659-70. [PMID: 17149487 DOI: 10.1039/b612568a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.
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Affiliation(s)
- Sebastian Sinnecker
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany
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28
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Poluektov OG, Utschig LM, Dubinskij AA, Thurnauer MC. Electron transfer pathways and protein response to charge separation in photosynthetic reaction centers: time-resolved high-field ENDOR of the spin-correlated radical pair P865(+)QA(-). J Am Chem Soc 2005; 127:4049-59. [PMID: 15771542 DOI: 10.1021/ja043063g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently we reported the first observation of time-resolved (TR) high-frequency (HF) electron nuclear double resonance (ENDOR) of the transient charge separated state P865(+)Q(-)A in purple photosynthetic bacterial reaction centers (RC) (Poluektov, O. G., et al. J. Am. Chem. Soc. 2004, 126, 1644-1645). The high resolution and orientational selectivity of HF ENDOR allows us to directly probe protein environments by spectrally selecting specific nuclei in isotopically labeled samples. A new phenomenon associated with the spin correlated radical pair (SCRP) nature of P865(+)Q(-)A was observed. The TR-HF ENDOR spectra of protein nuclei (protons) surrounding deuterated QA(-) exhibit a derivative-like, complicated line shape, which differs considerably from the HF ENDOR spectrum of the protein nuclei surrounding thermally equilibrated QA(-). Here, a theoretical analysis of these observations is presented that shows that the positions and amplitudes of ENDOR lines contain information on hyperfine interactions (HFI) of a particular nucleus (a proton of the protein) with both correlated electron spins. Thus, spin density delocalization in the protein environment between the SCRP donor and acceptor molecules can be revealed via HF ENDOR. Novel approaches for acquiring and analyzing SCRP ENDOR that simplify interpretation of the spectra are discussed. Furthermore, we report here that the positions of the ENDOR lines of the SCRP shift with an increase in the time after laser flash, which initiates electron transfer. These shifts provide direct spectroscopic evidence of reorganization of the protein environment to accommodate the donor-acceptor charge-separated state P865(+)QA(-).
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Affiliation(s)
- Oleg G Poluektov
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
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29
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Borrelli R, Di Donato M, Peluso A. Role of intramolecular vibrations in long-range electron transfer between pheophytin and ubiquinone in bacterial photosynthetic reaction centers. Biophys J 2005; 89:830-41. [PMID: 15894646 PMCID: PMC1366633 DOI: 10.1529/biophysj.105.060574] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamics of the elementary electron transfer step between pheophytin and primary ubiquinone in bacterial photosynthetic reaction centers is investigated by using a discrete state approach, including only the intramolecular normal modes of vibration of the two redox partners. The whole set of normal coordinates of the acceptor and donor groups have been employed in the computations of the Hamiltonian matrix, to reliably account both for shifts and mixing of the normal coordinates, and for changes in vibrational frequencies upon ET. It is shown that intramolecular modes provide not only a discrete set of states more strongly coupled to the initial state but also a quasicontinuum of weakly coupled states, which account for the spreading of the wave packet after ET. The computed transition probabilities are sufficiently high for asserting that electron transfer from bacteriopheophytin to the primary quinone can occur via tunneling solely promoted by intramolecular modes; the transition times, computed for different values of the electronic energy difference and coupling term, are of the same order of magnitude (10(2) ps) of the observed one.
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30
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Möbius K, Savitsky A, Schnegg A, Plato M, Fuchs M. High-field EPR spectroscopy applied to biological systems: characterization of molecular switches for electron and ion transfer. Phys Chem Chem Phys 2005; 7:19-42. [DOI: 10.1039/b412180e] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Okamoto K, Ohkubo K, Kadish KM, Fukuzumi S. Remarkable Accelerating Effects of Ammonium Cations on Electron-Transfer Reactions of Quinones by Hydrogen Bonding with Semiquinone Radical Anions. J Phys Chem A 2004. [DOI: 10.1021/jp046078+] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
▪ Abstract Two current frontiers in EPR research are high-field ([Formula: see text]) electron paramagnetic resonance (EPR) and high-field electron-nuclear double resonance (ENDOR). This review focuses on recent advances in high-field ENDOR and its applications to the study of proteins containing native paramagnetic sites. It concentrates on two aspects; the first concerns the determination of the location of protons and is related to the site geometry, and the second focuses on the spin density distribution within the site, which is inherent to the electronic structure. Both spin density and proton locations can be derived from ligand hyperfine couplings determined by ENDOR measurements. A brief description of the experimental methods is presented along with a discussion of the advantages and disadvantages of high-field ENDOR compared with conventional X-band (∼ 9.5 GHz) experiments. Specific examples of both protein single crystals and frozen solutions are then presented. These include the determination of the coordinates of water ligand protons in the Mn(II) site of concanavalin A, the detection of hydrogen bonds in a quinone radical in the bacterial photosynthetic reaction center as well as in the tyrosyl radical in ribonuclease reductase, and the study of the spin distribution in copper proteins. The copper proteins discussed are the type I copper of azurin and the binuclear CuA center in a number of proteins. The last part of the review presents a brief discussion of the interpretation of hyperfine couplings using quantum chemical calculations, primarily density functional theory (DFT) methods. Such methods are becoming an integral part of the data analysis tools, as they can facilitate signal assignment and provide the ultimate relation between the experimental hyperfine couplings and the electronic wave function.
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Affiliation(s)
- D Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel 76100.
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33
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Di Donato M, Peluso A, Villani G. Electron Transfer between Quinones in Photosynthetic Reaction Centers. J Phys Chem B 2004. [DOI: 10.1021/jp036678t] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mariangela Di Donato
- Dipartimento di Chimica, Università di Salerno, I-84081 Baronissi, Salerno, Italy,and Istituto per i Processi Chimico Fisici, IPCF, CNR, via G. Moruzzi 1, I-56124, Pisa, Italy
| | - Andrea Peluso
- Dipartimento di Chimica, Università di Salerno, I-84081 Baronissi, Salerno, Italy,and Istituto per i Processi Chimico Fisici, IPCF, CNR, via G. Moruzzi 1, I-56124, Pisa, Italy
| | - Giovanni Villani
- Dipartimento di Chimica, Università di Salerno, I-84081 Baronissi, Salerno, Italy,and Istituto per i Processi Chimico Fisici, IPCF, CNR, via G. Moruzzi 1, I-56124, Pisa, Italy
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Cozzoli P, Comparelli R, Fanizza E, Curri M, Agostiano A. Photocatalytic activity of organic-capped anatase TiO2 nanocrystals in homogeneous organic solutions. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2003. [DOI: 10.1016/j.msec.2003.09.101] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Grimaldi S, Ostermann T, Weiden N, Mogi T, Miyoshi H, Ludwig B, Michel H, Prisner TF, MacMillan F. Asymmetric binding of the high-affinity Q(H)(*)(-) ubisemiquinone in quinol oxidase (bo3) from Escherichia coli studied by multifrequency electron paramagnetic resonance spectroscopy. Biochemistry 2003; 42:5632-9. [PMID: 12741819 DOI: 10.1021/bi034010z] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ubiquinone-2 (UQ-2) selectively labeled with (13)C (I =(1)/(2)) at either the position 1- or the 4-carbonyl carbon is incorporated into the ubiquinol oxidase bo(3) from Escherichia coli in which the native quinone (UQ-8) has been previously removed. The resulting stabilized anion radical in the high-affinity quinone-binding site (Q(H)(*)(-)) is investigated using multifrequency (9, 34, and 94 GHz) electron paramagnetic resonance (EPR) spectroscopy. The corresponding spectra reveal dramatic differences in (13)C hyperfine couplings indicating a strongly asymmetric spin density distribution over the quinone headgroup. By comparison with previous results on labeled ubisemiquinones in proteins as well as in organic solvents, it is concluded that Q(H)(*)(-) is most probably bound to the protein via a one-sided hydrogen bond or a strongly asymmetric hydrogen-bonding network. This observation is discussed with regard to the function of Q(H) in the enzyme and contrasted with the information available on other protein-bound semiquinone radicals.
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Affiliation(s)
- S Grimaldi
- Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität Frankfurt, Centre for Biological Magnetic Resonance, Frankfurt am Main, Germany
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37
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Schnegg A, Fuhs M, Rohrer M, Lubitz W, Prisner TF, Möbius K. Molecular Dynamics of QA-• and QB-• in Photosynthetic Bacterial Reaction Centers Studied by Pulsed High-Field EPR at 95 GHz. J Phys Chem B 2002. [DOI: 10.1021/jp0203907] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Schnegg
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, 60439 Frankfurt, Germany, and Max-Planck-Institut für Strahlenchemie, 45470 Mülheim an der Ruhr, Germany
| | - M. Fuhs
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, 60439 Frankfurt, Germany, and Max-Planck-Institut für Strahlenchemie, 45470 Mülheim an der Ruhr, Germany
| | - M. Rohrer
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, 60439 Frankfurt, Germany, and Max-Planck-Institut für Strahlenchemie, 45470 Mülheim an der Ruhr, Germany
| | - W. Lubitz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, 60439 Frankfurt, Germany, and Max-Planck-Institut für Strahlenchemie, 45470 Mülheim an der Ruhr, Germany
| | - T. F. Prisner
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, 60439 Frankfurt, Germany, and Max-Planck-Institut für Strahlenchemie, 45470 Mülheim an der Ruhr, Germany
| | - K. Möbius
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, Marie Curie Strasse 11, 60439 Frankfurt, Germany, and Max-Planck-Institut für Strahlenchemie, 45470 Mülheim an der Ruhr, Germany
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38
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NILSSON JARVID, LYUBARTSEV ALEXANDER, ERIKSSON LEIFA, LAAKSONEN AATTO. Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds. Mol Phys 2001. [DOI: 10.1080/00268970110072403] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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40
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Abstract
Pulsed electron paramagnetic resonance (EPR) methods such as ESEEM, PELDOR, relaxation time measurements, transient EPR, high-field/high-frequency EPR, and pulsed ENDOR, have been used successfully to investigate the local structure and dynamics of paramagnetic centers in biological samples. These methods allow different contributions to the EPR spectra to be distinguished and can help unravel complicated EPR spectra consisting of overlapping resonance lines, as are often found in disordered protein samples. The basic principles, specific potentials, technical requirements, and limitations of these advanced EPR techniques will be reviewed together with recent applications to metal centers, organic radicals, and spin labels in proteins.
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Affiliation(s)
- T Prisner
- Institute for Physical and Theoretical Chemistry, J. W. Goethe-University Frankfurt, Marie-Curie-Strasse 11, Frankfurt am Main, D-60439 Germany.
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41
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Abstract
Numerous model studies of organic redox cofactor activity have appeared in the latter half of 1998 and the first half of 1999. These investigations include the use of solution models to explore flavin-dependent, quinone-dependent and pyrroloquinone-dependent redox processes, the exploration of flavin and quinone redox events using organized interfaces, and the application of computational methods to increase the understanding of flavin-catalyzed, nicotinamide-catalyzed and quinone-catalyzed redox processes.
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Affiliation(s)
- V M Rotello
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA.
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42
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Schäfer KO, Bittl R, Zweygart W, Lendzian F, Haselhorst G, Weyhermüller T, Wieghardt K, Lubitz W. Electronic Structure of Antiferromagnetically Coupled Dinuclear Manganese (MnIIIMnIV) Complexes Studied by Magnetic Resonance Techniques. J Am Chem Soc 1998. [DOI: 10.1021/ja9827548] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kai-Oliver Schäfer
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Robert Bittl
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Wolfgang Zweygart
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Friedhelm Lendzian
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Gabriele Haselhorst
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Thomas Weyhermüller
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Karl Wieghardt
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
| | - Wolfgang Lubitz
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie (PC 14), Technische Universität Berlin, Strasse des 17 Juni 135, D-10623 Berlin, FRG, and Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim a.d. Ruhr, FRG
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Kamlowski A, Zech SG, Fromme P, Bittl R, Lubitz W, Witt HT, Stehlik D. The Radical Pair State in Photosystem I Single Crystals: Orientation Dependence of the Transient Spin-Polarized EPR Spectra. J Phys Chem B 1998. [DOI: 10.1021/jp9817022] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas Kamlowski
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Stephan G. Zech
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Petra Fromme
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Robert Bittl
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Wolfgang Lubitz
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Horst T. Witt
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Dietmar Stehlik
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany, and Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
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