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Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI. Long-range charge transfer mechanism of the III 2IV 2 mycobacterial supercomplex. Nat Commun 2024; 15:5276. [PMID: 38902248 PMCID: PMC11189923 DOI: 10.1038/s41467-024-49628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
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Affiliation(s)
- Daniel Riepl
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sylwia M Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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2
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Tikhonov AN. The cytochrome b 6f complex: plastoquinol oxidation and regulation of electron transport in chloroplasts. PHOTOSYNTHESIS RESEARCH 2024; 159:203-227. [PMID: 37369875 DOI: 10.1007/s11120-023-01034-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
In oxygenic photosynthetic systems, the cytochrome b6f (Cytb6f) complex (plastoquinol:plastocyanin oxidoreductase) is a heart of the hub that provides connectivity between photosystems (PS) II and I. In this review, the structure and function of the Cytb6f complex are briefly outlined, being focused on the mechanisms of a bifurcated (two-electron) oxidation of plastoquinol (PQH2). In plant chloroplasts, under a wide range of experimental conditions (pH and temperature), a diffusion of PQH2 from PSII to the Cytb6f does not limit the intersystem electron transport. The overall rate of PQH2 turnover is determined mainly by the first step of the bifurcated oxidation of PQH2 at the catalytic site Qo, i.e., the reaction of electron transfer from PQH2 to the Fe2S2 cluster of the high-potential Rieske iron-sulfur protein (ISP). This point has been supported by the quantum chemical analysis of PQH2 oxidation within the framework of a model system including the Fe2S2 cluster of the ISP and surrounding amino acids, the low-potential heme b6L, Glu78 and 2,3,5-trimethylbenzoquinol (the tail-less analog of PQH2). Other structure-function relationships and mechanisms of electron transport regulation of oxygenic photosynthesis associated with the Cytb6f complex are briefly outlined: pH-dependent control of the intersystem electron transport and the regulatory balance between the operation of linear and cyclic electron transfer chains.
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Affiliation(s)
- Alexander N Tikhonov
- Department of Biophysics, Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russian Federation, 119991.
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3
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Feng X, Schut GJ, Adams MWW, Li H. Structures and Electron Transport Paths in the Four Families of Flavin-Based Electron Bifurcation Enzymes. Subcell Biochem 2024; 104:383-408. [PMID: 38963493 DOI: 10.1007/978-3-031-58843-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Oxidoreductases facilitating electron transfer between molecules are pivotal in metabolic pathways. Flavin-based electron bifurcation (FBEB), a recently discovered energy coupling mechanism in oxidoreductases, enables the reversible division of electron pairs into two acceptors, bridging exergonic and otherwise unfeasible endergonic reactions. This chapter explores the four distinct FBEB complex families and highlights a decade of structural insights into FBEB complexes. In this chapter, we discuss the architecture, electron transfer routes, and conformational changes across all FBEB families, revealing the structural foundation that facilitate these remarkable functions.
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Affiliation(s)
- Xiang Feng
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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4
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Terai K, Yuly JL, Zhang P, Beratan DN. Correlated particle transport enables biological free energy transduction. Biophys J 2023; 122:1762-1771. [PMID: 37056051 PMCID: PMC10209040 DOI: 10.1016/j.bpj.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/17/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023] Open
Abstract
Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., they use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibrium and interacting systems. We show that neglecting correlations fails to describe free energy transduction, mistakenly predicting an abundance of slippage and energy dissipation, even for networks that are near reversible and lack interactions among particle sites. Interestingly, linear charge transport chains are well described without including correlations, even for networks that are driven and include site-site interactions typical of biological electron transfer chains. We examine three specific bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a near-reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures), and a redox-coupled proton pump (as in complex IV of respiration).
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Affiliation(s)
- Kiriko Terai
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Jonathon L Yuly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersy
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina; Department of Physics, Duke University, Durham, North Carolina; Department of Biochemistry, Duke University, Durham, North Carolina.
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5
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Havens J, Su T, Wang Q, Yu CA, Yu L, Durham B, Millett F. Photoinduced electron transfer in cytochrome bc 1: Dynamics of rotation of the Iron-sulfur protein during bifurcated electron transfer from ubiquinol to cytochrome c 1 and cytochrome b L. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148957. [PMID: 36709837 DOI: 10.1016/j.bbabio.2023.148957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
The electron transfer reactions within wild-type Rhodobacter sphaeroides cytochrome bc1 (cyt bc1) were studied using a binuclear ruthenium complex to rapidly photooxidize cyt c1. When cyt c1, the iron‑sulfur center Fe2S2, and cyt bH were reduced before the reaction, photooxidation of cyt c1 led to electron transfer from Fe2S2 to cyt c1 with a rate constant of ka = 80,000 s-1, followed by bifurcated reduction of both Fe2S2 and cyt bL by QH2 in the Qo site with a rate constant of k2 = 3000 s-1. The resulting Q then traveled from the Qo site to the Qi site and oxidized one equivalent each of cyt bL and cyt bH with a rate constant of k3 = 340 s-1. The rate constant ka was decreased in a nonlinear fashion by a factor of 53 as the viscosity was increased to 13.7. A mechanism that is consistent with the effect of viscosity involves rotational diffusion of the iron‑sulfur protein from the b state with reduced Fe2S2 close to cyt bL to one or more intermediate states, followed by rotation to the final c1 state with Fe2S2 close to cyt c1, and rapid electron transfer to cyt c1.
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Affiliation(s)
- Jeffrey Havens
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America; Vaccines and Therapeutics Division, Chemical and Biological Technologies, Defense Threat Reduction Agency, Fort Belvoir, VA 22060, United States of America
| | - Ting Su
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; ABclonal Technology Woburn, MA 01801, United States of America
| | - Qiyu Wang
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; Vesigen Therapeutics Cambridge, MA 02139, United States of America
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Linda Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America.
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6
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Q-lipid-containing membranes show high in-plane conductivity using a membrane-on-a-chip setup. iScience 2022; 26:105918. [PMID: 36711244 PMCID: PMC9874011 DOI: 10.1016/j.isci.2022.105918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
The light-driven reactions of photosynthesis as well as the mitochondrial power supply are located in specialized membranes containing a high fraction of redox-active lipids. In-plane charge transfer along such cell membranes is currently thought to be facilitated by the diffusion of redox lipids and proteins. Using a membrane on-a-chip setup, we show here that redox-active model membranes can sustain surprisingly high currents (mA) in-plane at distances of 25 μm. We also show the same phenomenon in free-standing monolayers at the air-water interface once the film is compressed such that the distance between redox centers is below 1 nm. Our data suggest that charge transfer within cell walls hosting electron transfer chains could be enabled by the coupling of redox-lipids via simultaneous electron and proton in-plane hopping, similar to conductive polymers. This has major implications for our understanding of the role of lipid membranes, suggesting that Q-lipid-containing membranes may be essential for evolving the complex redox machineries of life.
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7
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Kinetic Mathematical Modeling of Oxidative Phosphorylation in Cardiomyocyte Mitochondria. Cells 2022; 11:cells11244020. [PMID: 36552784 PMCID: PMC9777548 DOI: 10.3390/cells11244020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OXPHOS) is an oxygen-dependent process that consumes catabolized nutrients to produce adenosine triphosphate (ATP) to drive energy-dependent biological processes such as excitation-contraction coupling in cardiomyocytes. In addition to in vivo and in vitro experiments, in silico models are valuable for investigating the underlying mechanisms of OXPHOS and predicting its consequences in both physiological and pathological conditions. Here, we compare several prominent kinetic models of OXPHOS in cardiomyocytes. We examine how their mathematical expressions were derived, how their parameters were obtained, the conditions of their experimental counterparts, and the predictions they generated. We aim to explore the general landscape of energy production mechanisms in cardiomyocytes for future in silico models.
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8
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Ustynyuk LY, Tikhonov AN. Plastoquinol Oxidation: Rate-Limiting Stage in the Electron Transport Chain of Chloroplasts. BIOCHEMISTRY (MOSCOW) 2022; 87:1084-1097. [DOI: 10.1134/s0006297922100029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Kayastha K, Katsyv A, Himmrich C, Welsch S, Schuller JM, Ermler U, Müller V. Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. eLife 2022; 11:77095. [PMID: 35748623 PMCID: PMC9232219 DOI: 10.7554/elife.77095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/22/2022] [Indexed: 01/22/2023] Open
Abstract
Lactate oxidation with NAD+ as electron acceptor is a highly endergonic reaction. Some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron-transferring proteins EtfA and EtfB. The electron cryo-microscopically characterized (Ldh-EtfAB)2 complex of Acetobacterium woodii at 2.43 Å resolution consists of a mobile EtfAB shuttle domain located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle domain contact each other thereby forming the D (dehydrogenation-connected) state. The intermediary Glu37 and Glu139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. By integrating Alphafold2 calculations a plausible novel B (bifurcation-connected) state was obtained allowing electron transfer between the EtfAB base and shuttle FADs. Kinetic analysis of enzyme variants suggests a correlation between NAD+ binding site and D-to-B-state transition implicating a 75° rotation of the EtfAB shuttle domain. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is assisted by the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was proposed.
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Affiliation(s)
- Kanwal Kayastha
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Christina Himmrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jan M Schuller
- SYNMICRO Research Center and Department of Chemistry, Philipps University, Marburg, Germany
| | - Ulrich Ermler
- Departments of Molecular Membrane Biology of the Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
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10
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Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy. Biochem Soc Trans 2022; 50:877-893. [PMID: 35356963 PMCID: PMC9162462 DOI: 10.1042/bst20190963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
Cytochrome (cyt) bc1, bcc and b6f complexes, collectively referred to as cyt bc complexes, are homologous isoprenoid quinol oxidising enzymes present in diverse phylogenetic lineages. Cyt bc1 and bcc complexes are constituents of the electron transport chain (ETC) of cellular respiration, and cyt b6f complex is a component of the photosynthetic ETC. Cyt bc complexes share in general the same Mitchellian Q cycle mechanism, with which they accomplish proton translocation and thus contribute to the generation of proton motive force which drives ATP synthesis. They therefore require a quinol oxidation (Qo) and a quinone reduction (Qi) site. Yet, cyt bc complexes evolved to adapt to specific electrochemical properties of different quinone species and exhibit structural diversity. This review summarises structural information on native quinones and quinone-like inhibitors bound in cyt bc complexes resolved by X-ray crystallography and cryo-EM structures. Although the Qi site architecture of cyt bc1 complex and cyt bcc complex differs considerably, quinone molecules were resolved at the respective Qi sites in very similar distance to haem bH. In contrast, more diverse positions of native quinone molecules were resolved at Qo sites, suggesting multiple quinone binding positions or captured snapshots of trajectories toward the catalytic site. A wide spectrum of inhibitors resolved at Qo or Qi site covers fungicides, antimalarial and antituberculosis medications and drug candidates. The impact of these structures for characterising the Q cycle mechanism, as well as their relevance for the development of medications and agrochemicals are discussed.
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11
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An uncharacteristically low-potential flavin governs the energy landscape of electron bifurcation. Proc Natl Acad Sci U S A 2022; 119:e2117882119. [PMID: 35290111 PMCID: PMC8944662 DOI: 10.1073/pnas.2117882119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Nature has long been an inspiration for materials design, as it exemplifies exquisite control of both matter and energy. Electron bifurcation, a mechanism employed in biological systems to drive thermodynamically unfavorable and energetically challenging chemical reactions, is one such example. A key feature of bifurcating enzymes is the ability of a single redox cofactor to distribute a pair of electrons across two spatially separated electron transfer pathways. Here, we report on the empirical determination of both the one-electron potential and two-electron potential of the bifurcating flavin cofactor in the NADH-dependent ferredoxin-NADP+ oxidoreductase I (NfnSL) enzyme. Insights arising from the defined energy landscape of this bifurcation site may underlie the design of synthetic catalysts capable of generating high-energy intermediates. Electron bifurcation, an energy-conserving process utilized extensively throughout all domains of life, represents an elegant means of generating high-energy products from substrates with less reducing potential. The coordinated coupling of exergonic and endergonic reactions has been shown to operate over an electrochemical potential of ∼1.3 V through the activity of a unique flavin cofactor in the enzyme NADH-dependent ferredoxin-NADP+ oxidoreductase I. The inferred energy landscape has features unprecedented in biochemistry and presents novel energetic challenges, the most intriguing being a large thermodynamically uphill step for the first electron transfer of the bifurcation reaction. However, ambiguities in the energy landscape at the bifurcating site deriving from overlapping flavin spectral signatures have impeded a comprehensive understanding of the specific mechanistic contributions afforded by thermodynamic and kinetic factors. Here, we elucidate an uncharacteristically low two-electron potential of the bifurcating flavin, resolving the energetic challenge of the first bifurcation event.
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Nitschke W, Schoepp‐Cothenet B, Duval S, Zuchan K, Farr O, Baymann F, Panico F, Minguzzi A, Branscomb E, Russell MJ. Aqueous electrochemistry: The toolbox for life's emergence from redox disequilibria. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | | | - Simon Duval
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Kilian Zuchan
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Orion Farr
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
- Aix Marseille Univ CINaM (UMR 7325) Luminy France
| | - Frauke Baymann
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Francesco Panico
- Dipartimento di Chimica Università degli Studi di Milano Milan Italy
| | | | - Elbert Branscomb
- Department of Physics Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana Illinois USA
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Yuly JL, Zhang P, Ru X, Terai K, Singh N, Beratan DN. Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor. Chem 2021. [DOI: 10.1016/j.chempr.2021.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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14
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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15
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Vershubskii AV, Tikhonov AN. Structural and Functional Aspects of Electron Transport Thermoregulation and ATP Synthesis in Chloroplasts. BIOCHEMISTRY (MOSCOW) 2021; 86:92-104. [PMID: 33705285 DOI: 10.1134/s0006297921010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is focused on analysis of the mechanisms of temperature-dependent regulation of electron transport and ATP synthesis in chloroplasts of higher plants. Importance of photosynthesis thermoregulation is determined by the fact that plants are ectothermic organisms, whose own temperature depends on the ambient temperature. The review discusses the effects of temperature on the following processes in thylakoid membranes: (i) photosystem 2 activity and plastoquinone reduction; (ii) electron transfer from plastoquinol (via the cytochrome b6f complex and plastocyanin) to photosystem 1; (iii) transmembrane proton transfer; and (iv) ATP synthesis. The data on the relationship between the functional properties of chloroplasts (photosynthetic transfer of electrons and protons, functioning of ATP synthase) and structural characteristics of membrane lipids (fluidity) obtained by electron paramagnetic resonance studies are presented.
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16
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Sarewicz M, Pintscher S, Bujnowicz Ł, Wolska M, Artur Osyczka. The High-Spin Heme b L Mutant Exposes Dominant Reaction Leading to the Formation of the Semiquinone Spin-Coupled to the [2Fe-2S] + Cluster at the Q o Site of Rhodobacter capsulatus Cytochrome bc 1. Front Chem 2021; 9:658877. [PMID: 34026724 PMCID: PMC8138165 DOI: 10.3389/fchem.2021.658877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Cytochrome bc 1 (mitochondrial complex III) catalyzes electron transfer from quinols to cytochrome c and couples this reaction with proton translocation across lipid membrane; thus, it contributes to the generation of protonmotive force used for the synthesis of ATP. The energetic efficiency of the enzyme relies on a bifurcation reaction taking place at the Qo site which upon oxidation of ubiquinol directs one electron to the Rieske 2Fe2S cluster and the other to heme b L. The molecular mechanism of this reaction remains unclear. A semiquinone spin-coupled to the reduced 2Fe2S cluster (SQo-2Fe2S) was identified as a state associated with the operation of the Qo site. To get insights into the mechanism of the formation of this state, we first constructed a mutant in which one of the histidine ligands of the iron ion of heme b L Rhodobacter capsulatus cytochrome bc 1 was replaced by asparagine (H198N). This converted the low-spin, low-potential heme into the high-spin, high-potential species which is unable to support enzymatic turnover. We performed a comparative analysis of redox titrations of antimycin-supplemented bacterial photosynthetic membranes containing native enzyme and the mutant. The titrations revealed that H198N failed to generate detectable amounts of SQo-2Fe2S under neither equilibrium (in dark) nor nonequilibrium (in light), whereas the native enzyme generated clearly detectable SQo-2Fe2S in light. This provided further support for the mechanism in which the back electron transfer from heme b L to a ubiquinone bound at the Qo site is mainly responsible for the formation of semiquinone trapped in the SQo-2Fe2S state in R. capusulatus cytochrome bc 1.
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Affiliation(s)
- Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Pintscher
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Łukasz Bujnowicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Małgorzata Wolska
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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17
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Tassone G, Kola A, Valensin D, Pozzi C. Dynamic Interplay between Copper Toxicity and Mitochondrial Dysfunction in Alzheimer's Disease. Life (Basel) 2021; 11:life11050386. [PMID: 33923275 PMCID: PMC8146034 DOI: 10.3390/life11050386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder, affecting millions of people worldwide, a number expected to exponentially increase in the future since no effective treatments are available so far. AD is characterized by severe cognitive dysfunctions associated with neuronal loss and connection disruption, mainly occurring in specific brain areas such as the hippocampus, cerebral cortex, and amygdala, compromising memory, language, reasoning, and social behavior. Proteomics and redox proteomics are powerful techniques used to identify altered proteins and pathways in AD, providing relevant insights on cellular pathways altered in the disease and defining novel targets exploitable for drug development. Here, we review the main results achieved by both -omics techniques, focusing on the changes occurring in AD mitochondria under oxidative stress and upon copper exposure. Relevant information arises by the comparative analysis of these results, evidencing alterations of common mitochondrial proteins, metabolic cycles, and cascades. Our analysis leads to three shared mitochondrial proteins, playing key roles in metabolism, ATP generation, oxidative stress, and apoptosis. Their potential as targets for development of innovative AD treatments is thus suggested. Despite the relevant efforts, no effective drugs against AD have been reported so far; nonetheless, various compounds targeting mitochondria have been proposed and investigated, reporting promising results.
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Affiliation(s)
| | | | - Daniela Valensin
- Correspondence: (D.V.); (C.P.); Tel.: +39-0577-232428 (D.V.); +39-0577-232132 (C.P.)
| | - Cecilia Pozzi
- Correspondence: (D.V.); (C.P.); Tel.: +39-0577-232428 (D.V.); +39-0577-232132 (C.P.)
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18
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Camilo SRG, Curtolo F, Galassi VV, Arantes GM. Tunneling and Nonadiabatic Effects on a Proton-Coupled Electron Transfer Model for the Q o Site in Cytochrome bc1. J Chem Inf Model 2021; 61:1840-1849. [PMID: 33793213 DOI: 10.1021/acs.jcim.1c00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytochrome bc1 is a fundamental enzyme for cellular respiration and photosynthesis. This dimeric protein complex catalyzes a proton-coupled electron transfer (PCET) from the reduced coenzyme-Q substrate (Q) to a bimetallic iron-sulfur cluster in the Qo active site. Herein, we combine molecular dynamics simulations of the complete cytochrome bc1 protein with electronic-structure calculations of truncated models and a semiclassical tunneling theory to investigate the electron-proton adiabaticity of the initial reaction catalyzed in the Qo site. After sampling possible orientations between the Q substrate and a histidine side chain that functions as hydrogen acceptor, we find that a truncated model composed by ubiquinol-methyl and imidazole-iron(III)-sulfide captures the expected changes in oxidation and spin states of the electron donor and acceptor. Diabatic electronic surfaces obtained for this model with multiconfigurational wave function calculations demonstrate that this reaction is electronic nonadiabatic, and proton tunneling is faster than mixing of electronic configurations. These results indicate the formalism that should be used to calculate vibronic couplings and kinetic parameters for the initial reaction in the Qo site of cytochrome bc1. This framework for molecular simulation may also be applied to investigate other PCET reactions in the Q-cycle or in various metalloproteins that catalyze proton translocation coupled to redox processes.
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Affiliation(s)
- Sofia R G Camilo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Vanesa V Galassi
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
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19
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Crofts AR. The modified Q-cycle: A look back at its development and forward to a functional model. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148417. [PMID: 33745972 DOI: 10.1016/j.bbabio.2021.148417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 11/25/2022]
Abstract
On looking back at a lifetime of research, it is interesting to see, in the light of current progress, how things came to be, and to speculate on how things might be. I am delighted in the context of the Mitchell prize to have that excuse to present this necessarily personal view of developments in areas of my interests. I have focused on the Q-cycle and a few examples showing wider ramifications, since that had been the main interest of the lab in the 20 years since structures became available, - a watershed event in determining our molecular perspective. I have reviewed the evidence for our model for the mechanism of the first electron transfer of the bifurcated reaction at the Qo-site, which I think is compelling. In reviewing progress in understanding the second electron transfer, I have revisited some controversies to justify important conclusions which appear, from the literature, not to have been taken seriously. I hope this does not come over as nitpicking. The conclusions are important to the final section in which I develop an internally consistent mechanism for turnovers of the complex leading to a state similar to that observed in recent rapid-mix/freeze-quench experiments, reported three years ago. The final model is necessarily speculative but is open to test.
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Affiliation(s)
- Antony R Crofts
- Department of Biochemistry, 417 Roger Adams Laboratory, 600 South Mathews Avenue, Urbana, IL 61801, United States of America
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20
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Zuchan K, Baymann F, Baffert C, Brugna M, Nitschke W. The dyad of the Y-junction- and a flavin module unites diverse redox enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148401. [PMID: 33684340 DOI: 10.1016/j.bbabio.2021.148401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/26/2022]
Abstract
The concomitant presence of two distinctive polypeptide modules, which we have chosen to denominate as the "Y-junction" and the "flavin" module, is observed in 3D structures of enzymes as functionally diverse as complex I, NAD(P)-dependent [NiFe]-hydrogenases and NAD(P)-dependent formate dehydrogenases. Amino acid sequence conservation furthermore suggests that both modules are also part of NAD(P)-dependent [FeFe]-hydrogenases for which no 3D structure model is available yet. The flavin module harbours the site of interaction with the substrate NAD(P) which exchanges two electrons with a strictly conserved flavin moiety. The Y-junction module typically contains four iron-sulphur centres arranged to form a Y-shaped electron transfer conduit and mediates electron transfer between the flavin module and the catalytic units of the respective enzymes. The Y-junction module represents an electron transfer hub with three potential electron entry/exit sites. The pattern of specific redox centres present both in the Y-junction and the flavin module is correlated to present knowledge of these enzymes' functional properties. We have searched publicly accessible genomes for gene clusters containing both the Y-junction and the flavin module to assemble a comprehensive picture of the diversity of enzymes harbouring this dyad of modules and to reconstruct their phylogenetic relationships. These analyses indicate the presence of the dyad already in the last universal common ancestor and the emergence of complex I's EFG-module out of a subgroup of NAD(P)- dependent formate dehydrogenases.
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Affiliation(s)
- Kilian Zuchan
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Frauke Baymann
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Carole Baffert
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Myriam Brugna
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France.
| | - Wolfgang Nitschke
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
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21
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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22
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Kayastha K, Vitt S, Buckel W, Ermler U. Flavins in the electron bifurcation process. Arch Biochem Biophys 2021; 701:108796. [PMID: 33609536 DOI: 10.1016/j.abb.2021.108796] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/18/2022]
Abstract
The discovery of a new energy-coupling mechanism termed flavin-based electron bifurcation (FBEB) in 2008 revealed a novel field of application for flavins in biology. The key component is the bifurcating flavin endowed with strongly inverted one-electron reduction potentials (FAD/FAD•- ≪ FAD•-/FADH-) that cooperatively transfers in its reduced state one low and one high-energy electron into different directions and thereby drives an endergonic with an exergonic reduction reaction. As energy splitting at the bifurcating flavin apparently implicates one-electron chemistry, the FBEB machinery has to incorporate prior to and behind the central bifurcating flavin 2e-to-1e and 1e-to-2e switches, frequently also flavins, for oxidizing variable medium-potential two-electron donating substrates and for reducing high-potential two-electron accepting substrates. The one-electron carriers ferredoxin or flavodoxin serve as low-potential (high-energy) electron acceptors, which power endergonic processes almost exclusively in obligate anaerobic microorganisms to increase the efficiency of their energy metabolism. In this review, we outline the global organization of FBEB enzymes, the functions of the flavins therein and the surrounding of the isoalloxazine rings by which their reduction potentials are specifically adjusted in a finely tuned energy landscape.
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Affiliation(s)
- Kanwal Kayastha
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stella Vitt
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany; Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany; Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
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23
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Pagacz J, Broniec A, Wolska M, Osyczka A, Borek A. ROS signaling capacity of cytochrome bc 1: Opposing effects of adaptive and pathogenic mitochondrial mutations. Free Radic Biol Med 2021; 163:243-254. [PMID: 33352219 DOI: 10.1016/j.freeradbiomed.2020.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 01/06/2023]
Abstract
Cytochrome bc1, also known as mitochondrial complex III, is considered to be one of the important producers of reactive oxygen species (ROS) in living organisms. Under physiological conditions, a certain level of ROS produced by mitochondrial electron transport chain (ETC) might be beneficial and take part in cellular signaling. However, elevated levels of ROS might exhibit negative effects, resulting in cellular damage. It is well known that inhibiting the electron flow within mitochondrial complex III leads to high production of ROS. However, superoxide production by cytochrome bc1 in a non-inhibited system remained controversial. Here, we propose a novel method for ROS detection in ETC hybrid system in solution comprising bacterial cytochrome bc1 and mitochondrial complex IV. We clearly show that non-inhibited cytochrome bc1 generates ROS and that adaptive and pathogenic mitochondrial mutations suppress and enhance ROS production, respectively. We also noted that cytochrome bc1 produces ROS in a rate-dependent manner and that the mechanism of ROS generation changes according to the rate of operation of the enzyme. This dependency has not yet been reported, but seems to be crucial when discussing ROS signaling originating from mitochondria.
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Affiliation(s)
- Jakub Pagacz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Agnieszka Broniec
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Małgorzata Wolska
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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24
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Wise CE, Ledinina AE, Yuly JL, Artz JH, Lubner CE. The role of thermodynamic features on the functional activity of electron bifurcating enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148377. [PMID: 33453185 DOI: 10.1016/j.bbabio.2021.148377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 11/25/2022]
Abstract
Electron bifurcation is a biological mechanism to drive a thermodynamically unfavorable redox reaction through direct coupling with an exergonic reaction. This process allows microorganisms to generate high energy reducing equivalents in order to sustain life and is often found in anaerobic metabolism, where the energy economy of the cell is poor. Recent work has revealed details of the redox energy landscapes for a variety of electron bifurcating enzymes, greatly expanding the understanding of how energy is transformed by this unique mechanism. Here we highlight the plasticity of these emerging landscapes, what is known regarding their mechanistic underpinnings, and provide a context for interpreting their biochemical activity within the physiological framework. We conclude with an outlook for propelling the field toward an integrative understanding of the impact of electron bifurcation.
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Affiliation(s)
| | | | | | - Jacob H Artz
- National Renewable Energy Laboratory, Golden, CO, USA
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25
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Barragan AM, Soudackov AV, Luthey-Schulten Z, Hammes-Schiffer S, Schulten K, Solov'yov IA. Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex. J Am Chem Soc 2021; 143:715-723. [PMID: 33397104 DOI: 10.1021/jacs.0c07799] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The cytochrome bc1 complex is a transmembrane enzymatic protein complex that plays a central role in cellular energy production and is present in both photosynthetic and respiratory chain organelles. Its reaction mechanism is initiated by the binding of a quinol molecule to an active site, followed by a series of charge transfer reactions between the quinol and protein subunits. Previous work hypothesized that the primary reaction was a concerted proton-coupled electron transfer (PCET) reaction because of the apparent absence of intermediate states associated with single proton or electron transfer reactions. In the present study, the kinetics of the primary bc1 complex PCET reaction is investigated with a vibronically nonadiabatic PCET theory in conjunction with all-atom molecular dynamics simulations and electronic structure calculations. The computed rate constants and relatively high kinetic isotope effects are consistent with experimental measurements on related biomimetic systems. The analysis implicates a concerted PCET mechanism with significant hydrogen tunneling and nonadiabatic effects in the bc1 complex. Moreover, the employed theoretical framework is shown to serve as a general strategy for describing PCET reactions in bioenergetic systems.
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Affiliation(s)
- Angela M Barragan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Zaida Luthey-Schulten
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Klaus Schulten
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Strasse 9-11, Oldenburg 26111, Germany
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26
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Tikhonov AN, Vershubskii AV. Temperature-dependent regulation of electron transport and ATP synthesis in chloroplasts in vitro and in silico. PHOTOSYNTHESIS RESEARCH 2020; 146:299-329. [PMID: 32780309 DOI: 10.1007/s11120-020-00777-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
The significance of temperature-dependent regulation of photosynthetic apparatus (PSA) is determined by the fact that plant temperature changes with environmental temperature. In this work, we present a brief overview of temperature-dependent regulation of photosynthetic processes in class B chloroplasts (thylakoids) and analyze these processes using a computer model that takes into account the key stages of electron and proton transport coupled to ATP synthesis. The rate constants of partial reactions were parametrized on the basis of experimental temperature dependences of partial photosynthetic processes: (1) photosystem II (PSII) turnover and plastoquinone (PQ) reduction, (2) the plastoquinol (PQH2) oxidation by the cytochrome (Cyt) b6f complex, (3) the ATP synthase activity, and (4) the proton leak from the thylakoid lumen. We consider that PQH2 oxidation is the rate-limiting step in the intersystem electron transport. The parametrization of the rate constants of these processes is based on earlier experimental data demonstrating strong correlations between the functional and structural properties of thylakoid membranes that were probed with the lipid-soluble spin labels embedded into the membranes. Within the framework of our model, we could adequately describe a number of experimental temperature dependences of photosynthetic reactions in thylakoids. Computer modeling of electron and proton transport coupled to ATP synthesis supports the notion that PQH2 oxidation by the Cyt b6f complex and proton pumping into the lumen are the basic temperature-dependent processes that determine the overall electron flux from PSII to molecular oxygen and the net ATP synthesis upon variations of temperature. The model describes two branches of the temperature dependence of the post-illumination reduction of [Formula: see text] characterized by different activation energies (about 60 and ≤ 3.5 kJ mol-1). The model predicts the bell-like temperature dependence of ATP formation, which arises from the balance of several factors: (1) the thermo-induced acceleration of electron transport through the Cyt b6f complex, (2) deactivation of PSII photochemistry at sufficiently high temperatures, and (3) acceleration of the passive proton outflow from the thylakoid lumen bypassing the ATP synthase complex. The model describes the temperature dependence of experimentally measured parameter P/2e, determined as the ratio between the rates of ATP synthesis and pseudocyclic electron transport (H2O → PSII → PSI → O2).
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Affiliation(s)
- Alexander N Tikhonov
- Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russia.
- N.M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, Moscow, Russia.
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27
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Das A, Hessin C, Ren Y, Desage-El Murr M. Biological concepts for catalysis and reactivity: empowering bioinspiration. Chem Soc Rev 2020; 49:8840-8867. [PMID: 33107878 DOI: 10.1039/d0cs00914h] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological systems provide attractive reactivity blueprints for the design of challenging chemical transformations. Emulating the operating mode of natural systems may however not be so easy and direct translation of structural observations does not always afford the anticipated efficiency. Metalloenzymes rely on earth-abundant metals to perform an incredibly wide range of chemical transformations. To do so, enzymes in general have evolved tools and tricks to enable control of such reactivity. The underlying concepts related to these tools are usually well-known to enzymologists and bio(inorganic) chemists but may be a little less familiar to organometallic chemists. So far, the field of bioinspired catalysis has greatly focused on the coordination sphere and electronic effects for the design of functional enzyme models but might benefit from a paradigm shift related to recent findings in biological systems. The goal of this review is to bring these fields closer together as this could likely result in the development of a new generation of highly efficient bioinspired systems. This contribution covers the fields of redox-active ligands, entatic state reactivity, energy conservation through electron bifurcation, and quantum tunneling for C-H activation.
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Affiliation(s)
- Agnideep Das
- Université de Strasbourg, Institut de Chimie, UMR CNRS 7177, 67000 Strasbourg, France.
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28
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Fisher N, Meunier B, Biagini GA. The cytochrome bc 1 complex as an antipathogenic target. FEBS Lett 2020; 594:2935-2952. [PMID: 32573760 DOI: 10.1002/1873-3468.13868] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/31/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
The cytochrome bc1 complex is a key component of the mitochondrial respiratory chains of many eukaryotic microorganisms that are pathogenic for plants or humans, such as fungi responsible for crop diseases and Plasmodium falciparum, which causes human malaria. Cytochrome bc1 is an enzyme that contains two (ubi)quinone/quinol-binding sites, which can be exploited for the development of fungicidal and chemotherapeutic agents. Here, we review recent progress in determination of the structure and mechanism of action of cytochrome bc1 , and the associated development of antimicrobial agents (and associated resistance mechanisms) targeting its activity.
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Affiliation(s)
- Nicholas Fisher
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Brigitte Meunier
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Giancarlo A Biagini
- Parasitology Department, Research Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
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29
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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30
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Universal free-energy landscape produces efficient and reversible electron bifurcation. Proc Natl Acad Sci U S A 2020; 117:21045-21051. [PMID: 32801212 DOI: 10.1073/pnas.2010815117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For decades, it was unknown how electron-bifurcating systems in nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron-bifurcating molecular machines could not be designed and built. The underpinning free-energy landscapes for electron bifurcation were also enigmatic. We predict that a simple and universal free-energy landscape enables electron bifurcation, and we show that it enables high-efficiency bifurcation with limited short-circuiting (the EB scheme). The landscape relies on steep free-energy slopes in the two redox branches to insulate against short-circuiting using an electron occupancy blockade effect, without relying on nuanced changes in the microscopic rate constants for the short-circuiting reactions. The EB scheme thus unifies a body of observations on biological catalysis and energy conversion, and the scheme provides a blueprint to guide future campaigns to establish synthetic electron bifurcation machines.
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31
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李 文, 任 思, 龙 星, 田 雨. [Palmitoylome profiling indicates that androgens promote the palmitoylation of metabolism-related proteins in prostate cancer-derived LNCaP cells]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2020; 52:227-233. [PMID: 32306003 PMCID: PMC7433454 DOI: 10.19723/j.issn.1671-167x.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To explore potential therapeutic targets other than androgen-deprivation treatment for prostate cancer by screening the proteins induced by androgen at palmitoylation modification level in LNCaP cells. METHODS The LNCaP cells were treated with androgen (Methyltrienolone, R1881, 5 nmol/L) or dimethyl sulfoxide (DMSO) for 24 h, and then labeled with alkynyl palmitic acid Alk-C16 (100 μmol/L). After that, the cells were collected, lysed, the total protein was extracted, agarose beads labeled with azide (1 mmol/L) were added, and the click-chemistry reaction was carried out at room temperature for 1 h. The covalent bond formed by click-chemistry reaction of azide and alkynyl group was used to enrich the palmitoylated proteins on agarose beads. Label-free quantitation (LFQ) was used to compare the protein palmitoylation level of R1881 treated and untreated cells to screen the proteins induced by androgen at palmitoylation modification level. RESULTS In this experiment, 907 potential palmitoylated proteins (mascot score>2, P<0.05) were identified, among which 430 proteins had LFQ values not zero at least twice. Among the 430 proteins, the palmitoylation levels of 92 candidates were increased by androgen treatment, and their LFQ values were significantly upregulated (>1.5-fold, P<0.05) in ≥2 samples of androgen-treated vs. untreated LNCaP cells. We also used the software of cytoscape to classify the 92 proteins, and found that the known functional proteins of them could be divided into three categories: metabolism related, protein folding related and translation initiation related. Among them, metabolism related proteins included lipid metabolism (6), glucose metabolism (7) and respiratory electron transport chain (8), and a small amount of amino acid metabolism (2) and other metabolism related proteins (2). Notably, the ratio of LFQ of cytochrome b-c1 complex subunit 2 (UQCRC2) was significantly (>3-fold, P<0.05) higher in androgen-treated cells compared with untreated cells, indicating that the palmitoylation level of UQCRC2 was enhanced by androgen most significantly than that of others. The second was long-chain acyl CoA dehydrogenase (ACADVL) related to lipid metabolism and glucose 6-phosphate dehydrogenase (PGD) related to glucose metabolism, but the LFQ ratio of them was less than 3-fold. CONCLUSION The research on palmitoylation mechanism of metabolism, especially the proteins related to respiratory electron transport chain, will provide a new guidance for the diagnosis and treatment of prostate cancer and the development of targeted drugs.
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Affiliation(s)
- 文卿 李
- 北京医院 国家老年医学中心 国家卫生健康委员会北京老年医学研究所 国家卫生健康委员会北京老年医学重点实验室 中国医学科学院老年医学研究院,北京 100730The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
| | - 思楣 任
- 北京医院 国家老年医学中心 国家卫生健康委员会临床检验中心 中国医学科学院老年医学研究院,北京 100730National Center for Clinical Laboratory, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
- 中国医学科学院北京协和医学院研究生院,北京 100730Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - 星博 龙
- 中国医学科学院北京协和医学院研究生院,北京 100730Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
- 北京医院泌尿外科,北京 100730Department of Urology, Beijing Hospital, Beijing 100730, China
| | - 雨青 田
- 北京医院 国家老年医学中心 国家卫生健康委员会北京老年医学研究所 国家卫生健康委员会北京老年医学重点实验室 中国医学科学院老年医学研究院,北京 100730The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
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32
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Mazat JP, Devin A, Ransac S. Modelling mitochondrial ROS production by the respiratory chain. Cell Mol Life Sci 2020; 77:455-465. [PMID: 31748915 PMCID: PMC11104992 DOI: 10.1007/s00018-019-03381-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
Abstract
ROS (superoxide and oxygen peroxide in this paper) play a dual role as signalling molecules and strong oxidizing agents leading to oxidative stress. Their production mainly occurs in mitochondria although they may have other locations (such as NADPH oxidase in particular cell types). Mitochondrial ROS production depends in an interweaving way upon many factors such as the membrane potential, the cell type and the respiratory substrates. Moreover, it is experimentally difficult to quantitatively assess the contribution of each potential site in the respiratory chain. To overcome these difficulties, mathematical models have been developed with different degrees of complexity in order to analyse different physiological questions ranging from a simple reproduction/simulation of experimental results to a detailed model of the possible mechanisms leading to ROS production. Here, we analyse experimental results concerning ROS production including results still under discussion. We then critically review the three models of ROS production in the whole respiratory chain available in the literature and propose some direction for future modelling work.
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Affiliation(s)
- Jean-Pierre Mazat
- UMR 5095, IBGC CNRS, 1 Rue Camille Saint-Saëns 33077, Bordeaux Cedex, France.
- Université de Bordeaux, 146 Rue Léo-Saignat, 33076, Bordeaux Cedex, France.
| | - Anne Devin
- UMR 5095, IBGC CNRS, 1 Rue Camille Saint-Saëns 33077, Bordeaux Cedex, France
| | - Stéphane Ransac
- UMR 5095, IBGC CNRS, 1 Rue Camille Saint-Saëns 33077, Bordeaux Cedex, France
- Université de Bordeaux, 146 Rue Léo-Saignat, 33076, Bordeaux Cedex, France
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33
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Yuly JL, Lubner CE, Zhang P, Beratan DN, Peters JW. Electron bifurcation: progress and grand challenges. Chem Commun (Camb) 2019; 55:11823-11832. [DOI: 10.1039/c9cc05611d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors.
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Affiliation(s)
| | | | - Peng Zhang
- Department of Chemistry
- Duke University
- Durham
- USA
| | - David N. Beratan
- Department of Physics
- Duke University
- Durham
- USA
- Department of Chemistry
| | - John W. Peters
- Institute of Biological Chemistry
- Washington State University
- Pullman
- USA
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34
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Francia F, Khalfaoui-Hassani B, Lanciano P, Musiani F, Noodleman L, Venturoli G, Daldal F. The cytochrome b lysine 329 residue is critical for ubihydroquinone oxidation and proton release at the Q o site of bacterial cytochrome bc 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:167-179. [PMID: 30550726 DOI: 10.1016/j.bbabio.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/16/2022]
Abstract
The ubihydroquinone:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important enzyme for photosynthesis and respiration. In bacteria like Rhodobacter capsulatus, this membrane complex has three subunits, the iron‑sulfur protein (ISP) with its Fe2S2 cluster, cyt c1 and cyt b, forming two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the electron transfer pathways originating from QH2 oxidation are known, but their associated proton release routes are less well defined. Earlier, we demonstrated that the His291 of cyt b is important for this latter process. In this work, using the bacterial cyt bc1 and site directed mutagenesis, we show that Lys329 of cyt b is also critical for electron and proton transfer at the Qo site. Of the mutants examined, Lys329Arg was photosynthesis proficient and had quasi-wild type cyt bc1 activity. In contrast, the Lys329Ala and Lys329Asp were photosynthesis-impaired and contained defective but assembled cyt bc1. In particular, the bifurcated electron transfer and associated proton(s) release reactions occurring during QH2 oxidation were drastically impaired in Lys329Asp mutant. Furthermore, in silico docking studies showed that in this mutant the location and the H-bonding network around the Fe2S2 cluster of ISP on cyt b surface was different than the wild type enzyme. Based on these experimental findings and theoretical considerations, we propose that the presence of a positive charge at position 329 of cyt b is critical for efficient electron transfer and proton release for QH2 oxidation at the Qo site of cyt bc1.
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Affiliation(s)
- Francesco Francia
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | | | - Pascal Lanciano
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francesco Musiani
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA 92037, USA
| | - Giovanni Venturoli
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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35
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Bujnowicz Ł, Borek A, Kuleta P, Sarewicz M, Osyczka A. Suppression of superoxide production by a spin‐spin coupling between semiquinone and the Rieske cluster in cytochrome
bc
1. FEBS Lett 2018; 593:3-12. [DOI: 10.1002/1873-3468.13296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Łukasz Bujnowicz
- Department of Molecular Biophysics Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Arkadiusz Borek
- Department of Molecular Biophysics Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Patryk Kuleta
- Department of Molecular Biophysics Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Marcin Sarewicz
- Department of Molecular Biophysics Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
| | - Artur Osyczka
- Department of Molecular Biophysics Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Kraków Poland
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36
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Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations. Proc Natl Acad Sci U S A 2018; 115:E8614-E8623. [PMID: 30104376 DOI: 10.1073/pnas.1807984115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (Km = 44.6 ± 1.6 μM, kcat = 9,810 ± 220 seconds-1), and phosphate is a competitive inhibitor of arsenate reduction (Ki = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.
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37
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Stuchebrukhov AA. Redox-Driven Proton Pumps of the Respiratory Chain. Biophys J 2018; 115:830-840. [PMID: 30119834 DOI: 10.1016/j.bpj.2018.07.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/21/2018] [Accepted: 07/23/2018] [Indexed: 11/24/2022] Open
Abstract
In aerobic cells, the proton gradient that drives ATP synthesis is created by three different proton pumps-membrane enzymes of the respiratory electron transport chain known as complex I, III, and IV. Despite the striking dissimilarity of structures and apparent differences in molecular mechanisms of proton pumping, all three enzymes have much in common and employ the same universal physical principles of converting redox energy to proton pumping. In this study, we describe a simple mathematical model that illustrates the general principles of redox-driven proton pumps and discuss their implementation in complex I, III, and IV of the respiratory chain.
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38
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Baymann F, Schoepp-Cothenet B, Duval S, Guiral M, Brugna M, Baffert C, Russell MJ, Nitschke W. On the Natural History of Flavin-Based Electron Bifurcation. Front Microbiol 2018; 9:1357. [PMID: 30018596 PMCID: PMC6037941 DOI: 10.3389/fmicb.2018.01357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
Electron bifurcation is here described as a special case of the continuum of electron transfer reactions accessible to two-electron redox compounds with redox cooperativity. We argue that electron bifurcation is foremost an electrochemical phenomenon based on (a) strongly inverted redox potentials of the individual redox transitions, (b) a high endergonicity of the first redox transition, and (c) an escapement-type mechanism rendering completion of the first electron transfer contingent on occurrence of the second one. This mechanism is proposed to govern both the traditional quinone-based and the newly discovered flavin-based versions of electron bifurcation. Conserved and variable aspects of the spatial arrangement of electron transfer partners in flavoenzymes are assayed by comparing the presently available 3D structures. A wide sample of flavoenzymes is analyzed with respect to conserved structural modules and three major structural groups are identified which serve as basic frames for the evolutionary construction of a plethora of flavin-containing redox enzymes. We argue that flavin-based and other types of electron bifurcation are of primordial importance to free energy conversion, the quintessential foundation of life, and discuss a plausible evolutionary ancestry of the mechanism.
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Affiliation(s)
- Frauke Baymann
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | | | - Simon Duval
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Marianne Guiral
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Myriam Brugna
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Carole Baffert
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
| | - Michael J. Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Wolfgang Nitschke
- CNRS, BIP, UMR 7281, IMM FR3479, Aix-Marseille University, Marseille, France
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39
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The cytochrome b6f complex: DFT modeling of the first step of plastoquinol oxidation by the iron-sulfur protein. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Wilson CA, Crofts AR. Dissecting the pattern of proton release from partial process involved in ubihydroquinone oxidation in the Q-cycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:531-543. [PMID: 29625088 DOI: 10.1016/j.bbabio.2018.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/18/2018] [Accepted: 03/28/2018] [Indexed: 12/01/2022]
Abstract
A key feature of the modified Q-cycle of the cytochrome bc1 and related complexes is a bifurcation of QH2 oxidation involving electron transfer to two different acceptor chains, each coupled to proton release. We have studied the kinetics of proton release in chromatophore vesicles from Rhodobacter sphaeroides, using the pH-sensitive dye neutral red to follow pH changes inside on activation of the photosynthetic chain, focusing on the bifurcated reaction, in which 4H+are released on complete turnover of the Q-cycle (2H+/ubiquinol (QH2) oxidized). We identified different partial processes of the Qo-site reaction, isolated through use of specific inhibitors, and correlated proton release with electron transfer processes by spectrophotometric measurement of cytochromes or electrochromic response. In the presence of myxothiazol or azoxystrobin, the proton release observed reflected oxidation of the Rieske iron‑sulfur protein. In the absence of Qo-site inhibitors, the pH change measured represented the convolution of this proton release with release of protons on turnover of the Qo-site, involving formation of the ES-complex and oxidation of the semiquinone intermediate. Turnover also regenerated the reduced iron-sulfur protein, available for further oxidation on a second turnover. Proton release was well-matched with the rate limiting step on oxidation of QH2 on both turnovers. However, a minor lag in proton release found at pH 7 but not at pH 8 might suggest that a process linked to rapid proton release on oxidation of the intermediate semiquinone involves a group with a pK in that range.
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Affiliation(s)
- Charles A Wilson
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Antony R Crofts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States
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41
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Song Z, Iorga BI, Mounkoro P, Fisher N, Meunier B. The antimalarial compound
ELQ
‐400 is an unusual inhibitor of the
bc
1
complex, targeting both
Q
o
and
Q
i
sites. FEBS Lett 2018; 592:1346-1356. [DOI: 10.1002/1873-3468.13035] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Zehua Song
- Translational Research Institute Henan Provincial People's Hospital School of Medicine Henan University Zhengzhou China
- Institute for Integrative Biology of the Cell (I2BC) CEA CNRS Université Paris‐Sud Université Paris‐Saclay Gif‐sur‐Yvette France
| | - Bogdan I. Iorga
- Institut de Chimie des Substances Naturelles CNRS UPR 2301 Labex LERMIT Université Paris‐Saclay Gif‐sur‐Yvette France
| | - Pierre Mounkoro
- Institute for Integrative Biology of the Cell (I2BC) CEA CNRS Université Paris‐Sud Université Paris‐Saclay Gif‐sur‐Yvette France
| | - Nicholas Fisher
- MSU‐DOE Plant Research Laboratory Michigan State University East Lansing MI USA
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC) CEA CNRS Université Paris‐Sud Université Paris‐Saclay Gif‐sur‐Yvette France
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42
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, A New Mechanism of Biological Energy Coupling. Chem Rev 2018; 118:3862-3886. [PMID: 29561602 DOI: 10.1021/acs.chemrev.7b00707] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There are two types of electron bifurcation (EB), either quinone- or flavin-based (QBEB/FBEB), that involve reduction of a quinone or flavin by a two-electron transfer and two reoxidations by a high- and low-potential one-electron acceptor with a reactive semiquinone intermediate. In QBEB, the reduced low-potential acceptor (cytochrome b) is exclusively used to generate ΔμH+. In FBEB, the "energy-rich" low-potential reduced ferredoxin or flavodoxin has dual function. It can give rise to ΔμH+/Na+ via a ferredoxin:NAD reductase (Rnf) or ferredoxin:proton reductase (Ech) or conducts difficult reductions such as CO2 to CO. The QBEB membrane complexes are similar in structure and function and occur in all domains of life. In contrast, FBEB complexes are soluble and occur only in strictly anaerobic bacteria and archaea (FixABCX being an exception). The FBEB complexes constitute a group consisting of four unrelated families that contain (1) electron-transferring flavoproteins (EtfAB), (2) NAD(P)H dehydrogenase (NuoF homologues), (3) heterodisulfide reductase (HdrABC) or HdrABC homologues, and (4) NADH-dependent ferredoxin:NADP reductase (NfnAB). The crystal structures and electron transport of EtfAB-butyryl-CoA dehydrogenase and NfnAB are compared with those of complex III of the respiratory chain (cytochrome bc1), whereby unexpected common features have become apparent.
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Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany.,Max-Planck-Institut für Terrestrische Mikrobiologie , 35043 Marburg , Germany
| | - Rudolf K Thauer
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany.,Max-Planck-Institut für Terrestrische Mikrobiologie , 35043 Marburg , Germany
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43
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Abstract
This chapter presents an overview of structural properties of the cytochrome (Cyt) b 6 f complex and its functioning in chloroplasts. The Cyt b 6 f complex stands at the crossroad of photosynthetic electron transport pathways, providing connectivity between Photosystem (PSI) and Photosysten II (PSII) and pumping protons across the membrane into the thylakoid lumen. After a brief review of the chloroplast electron transport chain, the consideration is focused on the structural organization of the Cyt b 6 f complex and its interaction with plastoquinol (PQH2, reduced form of plastoquinone), a mediator of electron transfer from PSII to the Cyt b 6 f complex. The processes of PQH2 oxidation by the Cyt b 6 f complex have been considered within the framework of the Mitchell's Q-cycle. The overall rate of the intersystem electron transport is determined by PQH2 turnover at the quinone-binding site Qo of the Cyt b 6 f complex. The rate of PQH2 oxidation is controlled by the intrathylakoid pHin, which value determines the protonation/deprotonation events in the Qo-center. Two other regulatory mechanisms associated with the Cyt b 6 f complex are briefly overviewed: (i) redistribution of electron fluxes between alternative (linear and cyclic) pathways, and (ii) "state transitions" related to redistribution of solar energy between PSI and PSII.
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44
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Analysis of a Functional Dimer Model of Ubiquinol Cytochrome c Oxidoreductase. Biophys J 2017; 113:1599-1612. [PMID: 28978450 PMCID: PMC5627346 DOI: 10.1016/j.bpj.2017.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 11/21/2022] Open
Abstract
Ubiquinol cytochrome c oxidoreductase (bc1 complex) serves as an important electron junction in many respiratory systems. It funnels electrons coming from NADH and ubiquinol to cytochrome c, but it is also capable of producing significant amounts of the free radical superoxide. In situ and in other experimental systems, the enzyme exists as a dimer. But until recently, it was believed to operate as a functional monomer. Here we show that a functional dimer model is capable of explaining both kinetic and superoxide production rate data. The model consists of six electronic states characterized by the number of electrons deposited on the complex. It is fully reversible and strictly adheres to the thermodynamics governing the reactions. A total of nine independent data sets were used to parameterize the model. To explain the data with a consistent set of parameters, it was necessary to incorporate intramonomer Coulombic effects between hemes bL and bH and intermonomer Coulombic effects between bL hemes. The fitted repulsion energies fall within the theoretical range of electrostatic calculations. In addition, model analysis demonstrates that the Q pool is mostly oxidized under normal physiological operation but can switch to a more reduced state when reverse electron transport conditions are in place.
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Demmer JK, Pal Chowdhury N, Selmer T, Ermler U, Buckel W. The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile. Nat Commun 2017; 8:1577. [PMID: 29146947 PMCID: PMC5691135 DOI: 10.1038/s41467-017-01746-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/13/2017] [Indexed: 11/29/2022] Open
Abstract
The electron transferring flavoprotein/butyryl-CoA dehydrogenase (EtfAB/Bcd) catalyzes the reduction of one crotonyl-CoA and two ferredoxins by two NADH within a flavin-based electron-bifurcating process. Here we report on the X-ray structure of the Clostridium difficile (EtfAB/Bcd)4 complex in the dehydrogenase-conducting D-state, α-FAD (bound to domain II of EtfA) and δ-FAD (bound to Bcd) being 8 Å apart. Superimposing Acidaminococcus fermentans EtfAB onto C. difficile EtfAB/Bcd reveals a rotation of domain II of nearly 80°. Further rotation by 10° brings EtfAB into the bifurcating B-state, α-FAD and β-FAD (bound to EtfB) being 14 Å apart. This dual binding mode of domain II, substantiated by mutational studies, resembles findings in non-bifurcating EtfAB/acyl-CoA dehydrogenase complexes. In our proposed mechanism, NADH reduces β-FAD, which bifurcates. One electron goes to ferredoxin and one to α-FAD, which swings over to reduce δ-FAD to the semiquinone. Repetition affords a second reduced ferredoxin and δ-FADH−, which reduces crotonyl-CoA. The electron-transferring flavoprotein / butyryl-CoA dehydrogenase (EtfAB/Bcd) complex catalyzes the reduction of crotonyl-CoA and ferredoxins by NADH in anaerobic microbes. Here, the authors present the crystal structure of Clostridium difficile EtfAB/Bcd and discuss the bifurcation mechanism for electron flow.
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Affiliation(s)
- Julius K Demmer
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Nilanjan Pal Chowdhury
- Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany.,Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Thorsten Selmer
- Fachbereich Chemie und Biotechnologie, FH Aachen, Heinrich-Mußmann-Str. 1, 52428, Jülich, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany. .,Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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46
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Takizawa K, Minagawa J, Tamura M, Kusakabe N, Narita N. Red-edge position of habitable exoplanets around M-dwarfs. Sci Rep 2017; 7:7561. [PMID: 28790357 PMCID: PMC5548919 DOI: 10.1038/s41598-017-07948-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
One of the possible signs of life on distant habitable exoplanets is the red-edge, which is a rise in the reflectivity of planets between visible and near-infrared (NIR) wavelengths. Previous studies suggested the possibility that the red-edge position for habitable exoplanets around M-dwarfs may be shifted to a longer wavelength than that for Earth. We investigated plausible red-edge position in terms of the light environment during the course of the evolution of phototrophs. We show that phototrophs on M-dwarf habitable exoplanets may use visible light when they first evolve in the ocean and when they first colonize the land. The adaptive evolution of oxygenic photosynthesis may eventually also use NIR radiation, by one of two photochemical reaction centers, with the other center continuing to use visible light. These “two-color” reaction centers can absorb more photons, but they will encounter difficulty in adapting to drastically changing light conditions at the boundary between land and water. NIR photosynthesis can be more productive on land, though its evolution would be preceded by the Earth-type vegetation. Thus, the red-edge position caused by photosynthetic organisms on habitable M-dwarf exoplanets could initially be similar to that on Earth and later move to a longer wavelength.
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Affiliation(s)
- Kenji Takizawa
- Astrobiology Center, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan.,National Institute for Basic Biology, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Jun Minagawa
- National Institute for Basic Biology, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Motohide Tamura
- Astrobiology Center, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan.,Department of Astronomy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,National Astronomical Observatory of Japan, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan
| | - Nobuhiko Kusakabe
- Astrobiology Center, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan.,National Astronomical Observatory of Japan, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan
| | - Norio Narita
- Astrobiology Center, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan. .,Department of Astronomy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,National Astronomical Observatory of Japan, National Institutes of Natural Sciences, 2-21-1 Osawa, Mitaka, Tokyo, 181-8588, Japan.
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47
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Papa S, Capitanio G, Papa F. The mechanism of coupling between oxido-reduction and proton translocation in respiratory chain enzymes. Biol Rev Camb Philos Soc 2017. [DOI: 10.1111/brv.12347] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs (BMSNSO), Section of Medical Biochemistry; University of Bari ‘Aldo Moro’; Piazza G. Cesare 11 70124 Bari Italy
- Institute of Biomembranes and Bioenergetics; National Research Council at BMSNSO; Piazza G. Cesare 11 70124 Bari Italy
| | - Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs (BMSNSO), Section of Medical Biochemistry; University of Bari ‘Aldo Moro’; Piazza G. Cesare 11 70124 Bari Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs (BMSNSO), Section of Medical Biochemistry; University of Bari ‘Aldo Moro’; Piazza G. Cesare 11 70124 Bari Italy
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48
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Crofts AR, Rose SW, Burton RL, Desai AV, Kenis PJA, Dikanov SA. The Q-Cycle Mechanism of the bc1 Complex: A Biologist’s Perspective on Atomistic Studies. J Phys Chem B 2017; 121:3701-3717. [DOI: 10.1021/acs.jpcb.6b10524] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Antony R. Crofts
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Stuart W. Rose
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Rodney L. Burton
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Amit V. Desai
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Paul J. A. Kenis
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sergei A. Dikanov
- Department
of Veterinary Clinical Medicine, University of Illinois at Urbana−Champaign, 1008 West Hazelwood Drive, Urbana, Illinois 61801, United States
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49
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Geiss AF, Khandelwal R, Baurecht D, Bliem C, Reiner-Rozman C, Boersch M, Ullmann GM, Loew LM, Naumann RLC. pH and Potential Transients of the bc 1 Complex Co-Reconstituted in Proteo-Lipobeads with the Reaction Center from Rb. sphaeroides. J Phys Chem B 2017; 121:143-152. [PMID: 27992230 DOI: 10.1021/acs.jpcb.6b11116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
His-tag technology is employed to bind membrane proteins, such as the bc1 complex and the reaction center (RC) from Rhodobacter sphaeroides, to spherical as well as planar surfaces in a strict orientation. Subsequently, the spherical and planar surfaces are subjected to in situ dialysis to form proteo-lipobeads (PLBs) and protein-tethered bilayer membranes, respectively. PLBs based on Ni-nitrileotriacetic acid-functionalized agarose beads that have diameters ranging from 50 to 150 μm are used to assess proton release and membrane potential parameters by confocal laser-scanning microscopy. The pH and potential transients are thus obtained from bc1 activated by the RC. To assess the turnover of bc1 excited by the RC in a similar setting, we used the planar surface of an attenuated total reflection crystal modified with a thin gold layer to carry out time-resolved surface-enhanced IR absorption spectroscopy triggered by flash lamp excitation. The experiments suggest that both proteins interact in a cyclic manner in both environments. The activity of the proteins seems to be preserved in the same manner as that in chromatophores or reconstituted in liposomes.
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Affiliation(s)
- Andreas F Geiss
- Biosensor Technologies, Austrian Institute of Technology GmbH, AIT , Donau-City Street 1, 1220 Vienna, Austria.,University of Natural Resources and Life Sciences , Gregor-Mendel-Straße 33, 1180 Wien, Austria
| | - Raghav Khandelwal
- Indian Institute of Technology Kanpur , Kalyanpur, Kanpur, Uttar Pradesh 208016, India
| | - Dieter Baurecht
- Faculty of Chemistry, Department of Physical Chemistry, University of Vienna , Währinger Straße 42, 1090 Vienna, Austria
| | - Christina Bliem
- Biosensor Technologies, Austrian Institute of Technology GmbH, AIT , Donau-City Street 1, 1220 Vienna, Austria.,Center of Electrochemical Surface Technology, CEST , Viktor-Kaplan-Str. 2, 2700 Wiener Neustadt, Austria
| | - Ciril Reiner-Rozman
- Biosensor Technologies, Austrian Institute of Technology GmbH, AIT , Donau-City Street 1, 1220 Vienna, Austria.,Center of Electrochemical Surface Technology, CEST , Viktor-Kaplan-Str. 2, 2700 Wiener Neustadt, Austria
| | - Michael Boersch
- Single-Molecule Microscopy Group, Jena University Hospital , Nonnenplan 2-4, 07743 Jena, Germany
| | - G Matthias Ullmann
- Computational Biochemistry Group, University of Bayreuth , Universitätsstraße 30, NWI, 95447 Bayreuth, Germany
| | - Leslie M Loew
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - Renate L C Naumann
- Biosensor Technologies, Austrian Institute of Technology GmbH, AIT , Donau-City Street 1, 1220 Vienna, Austria
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50
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Barragan AM, Schulten K, Solov'yov IA. Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc 1 Complex. J Phys Chem B 2016; 120:11369-11380. [PMID: 27661199 DOI: 10.1021/acs.jpcb.6b07394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bc1 complex is a critical enzyme for the ATP production in photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q-cycle, which is well established and operates via quinol substrates that bind inside the protein complex. Despite decades of research, the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density functional theory calculations, to provide a complete and consistent quantitative description of the primary events that occur within the bc1 complex upon quinol binding. In particular, the electron and proton transfer reactions that trigger the Q-cycle in the bc1 complex from Rhodobacter capsulatus are studied. The coupled nature of these charge transfer reactions was revealed by obtaining the transition energy path connecting configurations of the Qo-site prior and after the transfers. The analysis of orbitals and partial charge distribution of the different states of the Qo-site has further supported the conclusion. Finally, key structural elements of the bc1 complex that trigger the charge transfer reactions were established, manifesting the importance of the environment in the process, which is furthermore evidenced by free energy calculations.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
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