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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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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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Richardson KH, Seif-Eddine M, Sills A, Roessler MM. Controlling and exploiting intrinsic unpaired electrons in metalloproteins. Methods Enzymol 2022; 666:233-296. [PMID: 35465921 DOI: 10.1016/bs.mie.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.
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Affiliation(s)
| | - Maryam Seif-Eddine
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Adam Sills
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Maxie M Roessler
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom.
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Jeong HS, Hong S, Yoo HS, Kim J, Kim Y, Yoon C, Lee SJ, Kim SH. EPR-derived structures of flavin radical and iron-sulfur clusters from Methylosinus sporium 5 reductase. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01334j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electronic structures of two cofactors, the FAD radical and [2Fe–2S]+ of reduced MMOR from Methylosinus sporium strain 5 were investigated by advanced EPR spectroscopy. The findings provide long overdue detailed structural information of MMOR.
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Affiliation(s)
- Han Sol Jeong
- Western Seoul Center
- Korea Basic Science Institute (KBSI)
- Seoul 03759
- Rep. of Korea
- Department of Chemistry and Nano Science
| | - Sugyeong Hong
- Western Seoul Center
- Korea Basic Science Institute (KBSI)
- Seoul 03759
- Rep. of Korea
- Department of Chemistry and Nano Science
| | - Hee Seon Yoo
- Department of Chemistry and Institute of Molecular Biology and Genetics
- Jeonbuk National University
- Jeonju 54896
- Rep. of Korea
| | - Jin Kim
- Department of Chemistry
- Sunchon National University
- Suncheon 57922
- Rep. of Korea
| | - Yujeong Kim
- Western Seoul Center
- Korea Basic Science Institute (KBSI)
- Seoul 03759
- Rep. of Korea
- Department of Chemistry and Nano Science
| | - Chungwoon Yoon
- Department of Chemistry and Institute of Molecular Biology and Genetics
- Jeonbuk National University
- Jeonju 54896
- Rep. of Korea
| | - Seung Jae Lee
- Department of Chemistry and Institute of Molecular Biology and Genetics
- Jeonbuk National University
- Jeonju 54896
- Rep. of Korea
| | - Sun Hee Kim
- Western Seoul Center
- Korea Basic Science Institute (KBSI)
- Seoul 03759
- Rep. of Korea
- Department of Chemistry and Nano Science
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5
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1,2H hyperfine spectroscopy and DFT modeling unveil the demethylmenasemiquinone binding mode to E. coli nitrate reductase A (NarGHI). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148203. [PMID: 32305411 DOI: 10.1016/j.bbabio.2020.148203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 11/23/2022]
Abstract
The quinol oxidation site QD in E. coli respiratory nitrate reductase A (EcNarGHI) reacts with the three isoprenoid quinones naturally synthesized by the bacterium, i.e. ubiquinones (UQ), menaquinones (MK) and demethylmenaquinones (DMK). The binding mode of the demethylmenasemiquinone (DMSK) intermediate to the EcNarGHI QD quinol oxidation site is analyzed in detail using 1,2H hyperfine (hf) spectroscopy in combination with H2O/D2O exchange experiments and DFT modeling, and compared to the menasemiquinone one bound to the QD site (MSKD) previously studied by us. DMSKD and MSKD are shown to bind in a similar and strongly asymmetric manner through a short (~1.7 Å) H-bond. The origin of the specific hf pattern resolved on the DMSKD field-swept EPR spectrum is unambiguously ascribed to slightly inequivalent contributions from two β-methylene protons of the isoprenoid side chain. DFT calculations show that their large isotropic hf coupling constants (Aiso ~12 and 15 MHz) are consistent with both (i) a specific highly asymmetric binding mode of DMSKD and (ii) a near in-plane orientation of its isoprenyl chain at Cβ relative to the aromatic ring, which differs by ~90° to that predicted for free or NarGHI-bound MSK. Our results provide new insights into how the conformation and the redox properties of different natural quinones are selectively fine-tuned by the protein environment at a single Q site. Such a fine-tuning most likely contributes to render NarGHI as an efficient and flexible respiratory enzyme to be used upon rapid variations of the Q-pool content.
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Wright JJ, Fedor JG, Hirst J, Roessler MM. Using a chimeric respiratory chain and EPR spectroscopy to determine the origin of semiquinone species previously assigned to mitochondrial complex I. BMC Biol 2020; 18:54. [PMID: 32429970 PMCID: PMC7238650 DOI: 10.1186/s12915-020-00768-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/11/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND For decades, semiquinone intermediates have been suggested to play an essential role in catalysis by one of the most enigmatic proton-pumping enzymes, respiratory complex I, and different mechanisms have been proposed on their basis. However, the difficulty in investigating complex I semiquinones, due to the many different enzymes embedded in the inner mitochondrial membrane, has resulted in an ambiguous picture and no consensus. RESULTS In this paper, we re-examine the highly debated origin of semiquinone species in mitochondrial membranes using a novel approach. Our combination of a semi-artificial chimeric respiratory chain with pulse EPR spectroscopy (HYSCORE) has enabled us to conclude, unambiguously and for the first time, that the majority of the semiquinones observed in mitochondrial membranes originate from complex III. We also identify a minor contribution from complex II. CONCLUSIONS We are unable to attribute any semiquinone signals unambiguously to complex I and, reconciling our observations with much of the previous literature, conclude that they are likely to have been misattributed to it. We note that, for this earlier work, the tools we have relied on here to deconvolute overlapping EPR signals were not available. Proposals for the mechanism of complex I based on the EPR signals of semiquinone species observed in mitochondrial membranes should thus be treated with caution until future work has succeeded in isolating any complex I semiquinone EPR spectroscopic signatures present.
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Affiliation(s)
- John J Wright
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Justin G Fedor
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK.
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7
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Zeamari K, Gerbaud G, Grosse S, Fourmond V, Chaspoul F, Biaso F, Arnoux P, Sabaty M, Pignol D, Guigliarelli B, Burlat B. Tuning the redox properties of a [4Fe-4S] center to modulate the activity of Mo-bisPGD periplasmic nitrate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:402-413. [DOI: 10.1016/j.bbabio.2019.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 11/15/2022]
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Roessler MM, Salvadori E. Principles and applications of EPR spectroscopy in the chemical sciences. Chem Soc Rev 2018; 47:2534-2553. [PMID: 29498718 DOI: 10.1039/c6cs00565a] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Electron spins permeate every aspect of science and influence numerous chemical processes: they underpin transition metal chemistry and biochemistry, mediate photosynthesis and photovoltaics and are paramount in the field of quantum information, to name but a few. Electron paramagnetic resonance (EPR) spectroscopy detects unpaired electrons and provides detailed information on structure and bonding of paramagnetic species. In this tutorial review, aimed at non-specialists, we provide a theoretical framework and examples to illustrate the vast scope of the technique in chemical research. Case studies were chosen to exemplify systematically the different interactions that characterize a paramagnetic centre and to illustrate how EPR spectroscopy may be used to derive chemical information.
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Affiliation(s)
- Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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9
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Bando SY, Iamashita P, Guth BE, dos Santos LF, Fujita A, Abe CM, Ferreira LR, Moreira-Filho CA. A hemolytic-uremic syndrome-associated strain O113:H21 Shiga toxin-producing Escherichia coli specifically expresses a transcriptional module containing dicA and is related to gene network dysregulation in Caco-2 cells. PLoS One 2017; 12:e0189613. [PMID: 29253906 PMCID: PMC5734773 DOI: 10.1371/journal.pone.0189613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/29/2017] [Indexed: 01/22/2023] Open
Abstract
Shiga toxin-producing (Stx) Escherichia coli (STEC) O113:H21 strains are associated with human diarrhea and some of these strains may cause hemolytic uremic syndrome (HUS). The molecular mechanism underlying this capacity and the differential host cell response to HUS-causing strains are not yet completely understood. In Brazil O113:H21 strains are commonly found in cattle but, so far, were not isolated from HUS patients. Here we conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from HUS patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. Conversely, global gene expression comparison of both strains cultured in conditioned medium revealed a gene set exclusively expressed in EH41, which includes the dicA putative virulence factor regulator. Network analysis showed that this set of genes constitutes an EH41 specific transcriptional module. PCR analysis in Ec472/01 and in other 10 Brazilian cattle-isolated STEC strains revealed absence of dicA in all these strains. The GCNs of Caco-2 cells exposed to EH41 or to Ec472/01 presented a major transcriptional module containing many hubs related to inflammatory response that was not found in the GCN of control cells. Moreover, EH41 seems to cause gene network dysregulation in Caco-2 as evidenced by the large number of genes with high positive and negative covariance interactions. EH41 grows slowly than Ec472/01 when cultured in Caco-2 conditioned medium and fitness-related genes are hypoexpressed in that strain. Therefore, EH41 virulence may be derived from its capacity for dysregulating enterocyte genome functioning and its enhanced enteric survival due to slow growth.
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Affiliation(s)
- Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Beatriz E. Guth
- Departament of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, SP, Brazil
| | - Luis F. dos Santos
- Departament of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, SP, Brazil
| | - André Fujita
- Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cecilia M. Abe
- Laboratory of Bacteriology, Butantan Institute, São Paulo, SP, Brazil
| | - Leandro R. Ferreira
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
- * E-mail:
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Seif Eddine M, Biaso F, Arias‐Cartin R, Pilet E, Rendon J, Lyubenova S, Seduk F, Guigliarelli B, Magalon A, Grimaldi S. Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective2H and15N Labeling, HYSCORE Spectroscopy, and DFT Modeling. Chemphyschem 2017; 18:2704-2714. [DOI: 10.1002/cphc.201700571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/04/2017] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - Eric Pilet
- Aix Marseille University, CNRS, BIP Marseille France
- Faculté de Biologie, University Pierre et Marie Curie Paris France
| | - Julia Rendon
- Aix Marseille University, CNRS, BIP Marseille France
| | | | - Farida Seduk
- Aix Marseille University, CNRS, LCB Marseille France
| | | | - Axel Magalon
- Aix Marseille University, CNRS, LCB Marseille France
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11
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Rendon J, Biaso F, Ceccaldi P, Toci R, Seduk F, Magalon A, Guigliarelli B, Grimaldi S. Elucidating the Structures of the Low- and High-pH Mo(V) Species in Respiratory Nitrate Reductase: A Combined EPR, 14,15N HYSCORE, and DFT Study. Inorg Chem 2017; 56:4423-4435. [DOI: 10.1021/acs.inorgchem.6b03129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julia Rendon
- Aix Marseille Univ, CNRS, BIP, Marseille, France
| | | | - Pierre Ceccaldi
- Aix Marseille Univ, CNRS, BIP, Marseille, France
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - René Toci
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Farida Seduk
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB, Marseille, France
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Hirst J, Roessler MM. Energy conversion, redox catalysis and generation of reactive oxygen species by respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:872-83. [PMID: 26721206 PMCID: PMC4893023 DOI: 10.1016/j.bbabio.2015.12.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 12/30/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is critical for respiration in mammalian mitochondria. It oxidizes NADH produced by the Krebs' tricarboxylic acid cycle and β-oxidation of fatty acids, reduces ubiquinone, and transports protons to contribute to the proton-motive force across the inner membrane. Complex I is also a significant contributor to cellular oxidative stress. In complex I, NADH oxidation by a flavin mononucleotide, followed by intramolecular electron transfer along a chain of iron–sulfur clusters, delivers electrons and energy to bound ubiquinone. Either at cluster N2 (the terminal cluster in the chain) or upon the binding/reduction/dissociation of ubiquinone/ubiquinol, energy from the redox process is captured to initiate long-range energy transfer through the complex and drive proton translocation. This review focuses on current knowledge of how the redox reaction and proton transfer are coupled, with particular emphasis on the formation and role of semiquinone intermediates in both energy transduction and reactive oxygen species production. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. Current knowledge of the redox reactions catalyzed by complex I is reviewed. Possible quinone reduction pathways are presented. The presence and number of semiquinone intermediates are deliberated. The involvement of cluster N2/semiquinones in coupled proton transfer is discussed. Evidence for reactive oxygen species production by semiquinones is examined.
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Affiliation(s)
- Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
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13
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Magalon A, Alberge F. Distribution and dynamics of OXPHOS complexes in the bacterial cytoplasmic membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:198-213. [PMID: 26545610 DOI: 10.1016/j.bbabio.2015.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/23/2022]
Abstract
Oxidative phosphorylation (OXPHOS) is an essential process for most living organisms mostly sustained by protein complexes embedded in the cell membrane. In order to thrive, cells need to quickly respond to changes in the metabolic demand or in their environment. An overview of the strategies that can be employed by bacterial cells to adjust the OXPHOS outcome is provided. Regulation at the level of gene expression can only provide a means to adjust the OXPHOS outcome to long-term trends in the environment. In addition, the actual view is that bioenergetic membranes are highly compartmentalized structures. This review discusses what is known about the spatial organization of OXPHOS complexes and the timescales at which they occur. As exemplified with the commensal gut bacterium Escherichia coli, three levels of spatial organization are at play: supercomplexes, membrane microdomains and polar assemblies. This review provides a particular focus on whether dynamic spatial organization can fine-tune the OXPHOS through the definition of specialized functional membrane microdomains. Putative mechanisms responsible for spatio-temporal regulation of the OXPHOS complexes are discussed. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
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Affiliation(s)
- Axel Magalon
- CNRS, Laboratoire de Chimie Bactérienne (UMR 7283), Institut de Microbiologie de la Méditerranée, 13009 Marseille, France; Aix-Marseille University, UMR 7283, 13009 Marseille, France.
| | - François Alberge
- CNRS, Laboratoire de Chimie Bactérienne (UMR 7283), Institut de Microbiologie de la Méditerranée, 13009 Marseille, France; Aix-Marseille University, UMR 7283, 13009 Marseille, France
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14
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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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Demethylmenaquinol is a substrate of Escherichia coli nitrate reductase A (NarGHI) and forms a stable semiquinone intermediate at the NarGHI quinol oxidation site. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:739-47. [DOI: 10.1016/j.bbabio.2015.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/28/2015] [Accepted: 05/01/2015] [Indexed: 11/23/2022]
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16
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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
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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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17
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Fedor JG, Rothery RA, Weiner JH. A New Paradigm for Electron Transfer through Escherichia coli Nitrate Reductase A. Biochemistry 2014; 53:4549-56. [DOI: 10.1021/bi500394m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin G. Fedor
- Membrane
Protein Disease
Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A. Rothery
- Membrane
Protein Disease
Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joel H. Weiner
- Membrane
Protein Disease
Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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18
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Fedor JG, Rothery RA, Giraldi KS, Weiner JH. Q-site occupancy defines heme heterogeneity in Escherichia coli nitrate reductase A (NarGHI). Biochemistry 2014; 53:1733-41. [PMID: 24592999 DOI: 10.1021/bi500121x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The membrane subunit (NarI) of Escherichia coli nitrate reductase A (NarGHI) contains two b-type hemes, both of which are the highly anisotropic low-spin type. Heme bD is distal to NarGH and constitutes part of the quinone binding and oxidation site (Q-site) through the axially coordinating histidine-66 residue and one of the heme bD propionate groups. Bound quinone participates in hydrogen bonds with both the imidazole of His66 and the heme propionate, rendering the EPR spectrum of the heme bD sensitive to Q-site occupancy. As such, we hypothesize that the heterogeneity in the heme bD EPR signal arises from the differential occupancy of the Q-site. In agreement with this, the heterogeneity is dependent upon growth conditions but is still apparent when NarGHI is expressed in a strain lacking cardiolipin. Furthermore, this heterogeneity is sensitive to Q-site variants, NarI-G65A and NarI-K86A, and is collapsible by the binding of inhibitors. We found that the two main gz components of heme bD exhibit differences in reduction potential and pH dependence, which we posit is due to differential Q-site occupancy. Specifically, in a quinone-bound state, heme bD exhibits an Em,8 of -35 mV and a pH dependence of -40 mV pH(-1). In the quinone-free state, however, heme bD titrates with an Em,8 of +25 mV and a pH dependence of -59 mV pH(-1). We hypothesize that quinone binding modulates the electrochemical properties of heme bD as well as its EPR properties.
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Affiliation(s)
- Justin G Fedor
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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19
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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20
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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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21
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Arias-Cartin R, Grimaldi S, Arnoux P, Guigliarelli B, Magalon A. Cardiolipin binding in bacterial respiratory complexes: structural and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1937-49. [PMID: 22561115 DOI: 10.1016/j.bbabio.2012.04.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
The structural and functional integrity of biological membranes is vital to life. The interplay of lipids and membrane proteins is crucial for numerous fundamental processes ranging from respiration, photosynthesis, signal transduction, solute transport to motility. Evidence is accumulating that specific lipids play important roles in membrane proteins, but how specific lipids interact with and enable membrane proteins to achieve their full functionality remains unclear. X-ray structures of membrane proteins have revealed tight and specific binding of lipids. For instance, cardiolipin, an anionic phospholipid, has been found to be associated to a number of eukaryotic and prokaryotic respiratory complexes. Moreover, polar and septal accumulation of cardiolipin in a number of prokaryotes may ensure proper spatial segregation and/or activity of proteins. In this review, we describe current knowledge of the functions associated with cardiolipin binding to respiratory complexes in prokaryotes as a frame to discuss how specific lipid binding may tune their reactivity towards quinone and participate to supercomplex formation of both aerobic and anaerobic respiratory chains. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Rodrigo Arias-Cartin
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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22
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Grimaldi S, Arias-Cartin R, Lanciano P, Lyubenova S, Szenes R, Endeward B, Prisner TF, Guigliarelli B, Magalon A. Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR. J Biol Chem 2011; 287:4662-70. [PMID: 22190684 DOI: 10.1074/jbc.m111.325100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q(D)) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q(D) site (MSQ(D)) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with (1)H2O/2H2O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ(D) binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in 1H2O and 2H2O samples and by selective detection of the exchanged deuterons using Q-band 2H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b(D). Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q(D) site are discussed, in light of the unusually high thermodynamic stability of MSQ(D).
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Affiliation(s)
- Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, 13009 Marseille, France.
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23
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Warren JJ, Mayer JM. Proton-coupled electron transfer reactions at a heme-propionate in an iron-protoporphyrin-IX model compound. J Am Chem Soc 2011; 133:8544-51. [PMID: 21524059 DOI: 10.1021/ja201663p] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A heme model system has been developed in which the heme-propionate is the only proton donating/accepting site, using protoporphyrin IX-monomethyl esters (PPIX(MME)) and N-methylimidazole (MeIm). Proton-coupled electron transfer (PCET) reactions of these model compounds have been examined in acetonitrile solvent. (PPIX(MME))Fe(III)(MeIm)(2)-propionate (Fe(III)~CO(2)) is readily reduced by the ascorbate derivative 5,6-isopropylidine ascorbate to give (PPIX(MME))Fe(II)(MeIm)(2)-propionic acid (Fe(II)~CO(2)H). An excess of the hydroxylamine TEMPOH or of hydroquinone similarly reduces Fe(III)~CO(2), and TEMPO and benzoquinone oxidize Fe(II)~CO(2)H to return to Fe(III)~CO(2). The measured equilibrium constants, and the determined pK(a) and E(1/2) values, indicate that Fe(II)~CO(2)H has an effective bond dissociation free energy (BDFE) of 67.8 ± 0.6 kcal mol(-1). In these PPIX models, electron transfer occurs at the iron center and proton transfer occurs at the remote heme propionate. According to thermochemical and other arguments, the TEMPOH reaction occurs by concerted proton-electron transfer (CPET), and a similar pathway is indicated for the ascorbate derivative. Based on these results, heme propionates should be considered as potential key components of PCET/CPET active sites in heme proteins.
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Affiliation(s)
- Jeffrey J Warren
- Beckman Institute, California Institute of Technology, MC 139-74, Pasadena, California 91125-0001, USA.
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24
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Migliore A. Nonorthogonality Problem and Effective Electronic Coupling Calculation: Application to Charge Transfer in π-Stacks Relevant to Biochemistry and Molecular Electronics. J Chem Theory Comput 2011; 7:1712-25. [PMID: 26596435 DOI: 10.1021/ct200192d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently proposed method for the calculation of the effective electronic coupling (or charge-transfer integral) in a two-state system is discussed and related to other methods in the literature. The theoretical expression of the coupling is exact within the two-state model and applies to the general case where the charge transfer (CT) process involves nonorthogonal initial and final diabatic (localized) states. In this work, it is shown how this effective electronic coupling is also the one to be used in a suitable extension of Rabi's formula to the nonorthogonal representation of two-state dynamical problems. The formula for the transfer integral is inspected in the regime of long-range CT and applied to CT reactions in redox molecular systems of interest to biochemistry and/or to molecular electronics: the guanine-thymine stack from regular B-DNA, the polyaromatic perylenediimide stack, and the quinol-semiquinone couple. The calculations are performed within the framework of the Density Functional Theory (DFT), using hybrid exchange-correlation (XC) density functionals, which also allowed investigation of the appropriateness of such hybrid-DFT methods for computing electronic couplings. The use of the recently developed M06-2X and M06-HF density functionals in appropriate ways is supported by the results of this work.
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25
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Magalon A, Fedor JG, Walburger A, Weiner JH. Molybdenum enzymes in bacteria and their maturation. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.12.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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26
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Abstract
Anionic lipids play a variety of key roles in membrane function, including functional and structural effects on respiratory complexes. However, little is known about the molecular basis of these lipid-protein interactions. In this study, NarGHI, an anaerobic respiratory complex of Escherichia coli, has been used to investigate the relations in between membrane-bound proteins with phospholipids. Activity of the NarGHI complex is enhanced by anionic phospholipids both in vivo and in vitro. The anionic cardiolipin tightly associates with the NarGHI complex and is the most effective phospholipid to restore functionality of a nearly inactive detergent-solubilized enzyme complex. A specific cardiolipin-binding site is identified on the basis of the available X-ray diffraction data and of site-directed mutagenesis experiment. One acyl chain of cardiolipin is in close proximity to the heme b(D) center and is responsible for structural adjustments of b(D) and of the adjacent quinol substrate binding site. Finally, cardiolipin binding tunes the interaction with the quinol substrate. Together, our results provide a molecular basis for the activation of a bacterial respiratory complex by cardiolipin.
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27
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MacMillan F, Kacprzak S, Hellwig P, Grimaldi S, Michel H, Kaupp M. Elucidating mechanisms in haemcopperoxidases: The high-affinity QHbinding site in quinol oxidase as studied by DONUT-HYSCOREspectroscopy and density functional theory. Faraday Discuss 2011; 148:315-44; discussion 421-41. [DOI: 10.1039/c005149g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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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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29
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Arias-Cartin R, Lyubenova S, Ceccaldi P, Prisner T, Magalon A, Guigliarelli B, Grimaldi S. HYSCORE Evidence That Endogenous Mena- and Ubisemiquinone Bind at the Same Q Site (QD) of Escherichia coli Nitrate Reductase A. J Am Chem Soc 2010; 132:5942-3. [DOI: 10.1021/ja1009234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo Arias-Cartin
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Sevdalina Lyubenova
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Pierre Ceccaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Thomas Prisner
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Axel Magalon
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036) and Laboratoire de Chimie Bactérienne (UPR9043), CNRS and Aix-Marseille Université, 31 chemin J. Aiguier, 13009 Marseille, France, and Institut für Physikalische und Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
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30
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Yi SM, Narasimhulu KV, Samoilova RI, Gennis RB, Dikanov SA. Characterization of the semiquinone radical stabilized by the cytochrome aa3-600 menaquinol oxidase of Bacillus subtilis. J Biol Chem 2010; 285:18241-51. [PMID: 20351111 DOI: 10.1074/jbc.m110.116186] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome aa(3)-600 is one of the principle respiratory oxidases from Bacillus subtilis and is a member of the heme-copper superfamily of oxygen reductases. This enzyme catalyzes the two-electron oxidation of menaquinol and the four-electron reduction of O(2) to 2H(2)O. Cytochrome aa(3)-600 is of interest because it is a very close homologue of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli, except that it uses menaquinol instead of ubiquinol as a substrate. One question of interest is how the proteins differ in response to the differences in structure and electrochemical properties between ubiquinol and menaquinol. Cytochrome bo(3) has a high affinity binding site for ubiquinol that stabilizes a ubi-semiquinone. This has permitted the use of pulsed EPR techniques to investigate the protein interaction with the ubiquinone. The current work initiates studies to characterize the equivalent site in cytochrome aa(3)-600. Cytochrome aa(3)-600 has been cloned and expressed in a His-tagged form in B. subtilis. After isolation of the enzyme in dodecylmaltoside, it is shown that the pure enzyme contains 1 eq of menaquinone-7 and that the enzyme stabilizes a mena-semiquinone. Pulsed EPR studies have shown that there are both similarities as well as significant differences in the interactions of the mena-semiquinone with cytochrome aa(3)-600 in comparison with the ubi-semiquinone in cytochrome bo(3). Our data indicate weaker hydrogen bonds of the menaquinone in cytochrome aa(3)-600 in comparison with ubiquinone in cytochrome bo(3). In addition, the electronic structure of the semiquinone cyt aa(3)-600 is more shifted toward the anionic form from the neutral state in cyt bo(3).
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Affiliation(s)
- Sophia M Yi
- Departments of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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