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Li M, Zhang T, Shi Y, He C, Duan C. Modifying Proton Relay into Bioinspired Dye-Based Coordination Polymer for Photocatalytic Proton-Coupled Electron Transfer. Angew Chem Int Ed Engl 2024; 63:e202406161. [PMID: 38864758 DOI: 10.1002/anie.202406161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Proton-coupled electron transfer (PCET) imparts an energetic advantage over single electron transfer in activating inert substances. Natural PCET enzyme catalysis generally requires tripartite preorganization of proton relay, substrate-bound active center, and redox mediator, making the processes efficient and precluding side reactions. Inspired by this, a heterogeneous photocatalytic PCET system was established to achieve higher PCET driving forces by modifying proton relays into anthraquinone-based anionic coordination polymers. The proximally separated proton relays and photoredox-mediating anthraquinone moiety allowed pre-assembly of inert substrate between them, merging proton and electron into unsaturated bonds by photoreductive PCET, which enhanced reaction kinetics compared with the counter catalyst without proton relay. This photocatalytic PCET method was applied to a broad-scoped reduction of aryl ketones, unsaturated carbonyls, and aromatic compounds. The distinctive regioselectivities for the reduction of isoquinoline derivatives were found to occur on the carbon-ring sides. PCET-generated radical intermediate of quinoline could be trapped by alkene for proton relay-assisted Minisci addition, forming the pharmaceutical aza-acenaphthene scaffold within one step. When using heteroatom(X)-H/C-H compounds as proton-electron donors, this protocol could activate these inert bonds through photooxidative PCET to afford radicals and trap them by electron-deficient unsaturated compounds, furnishing the direct X-H/C-H functionalization.
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Affiliation(s)
- Mochen Li
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, School of Chemical Engineering, School of Chemistry, Dalian University of Technology, Dalian, 116024, P. R. China
| | - Tiexin Zhang
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, School of Chemical Engineering, School of Chemistry, Dalian University of Technology, Dalian, 116024, P. R. China
| | - Yusheng Shi
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, School of Chemical Engineering, School of Chemistry, Dalian University of Technology, Dalian, 116024, P. R. China
| | - Cheng He
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, School of Chemical Engineering, School of Chemistry, Dalian University of Technology, Dalian, 116024, P. R. China
| | - Chunying Duan
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, 210023, P. R. China
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2
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Hardy BJ, Dubiel P, Bungay EL, Rudin M, Williams C, Arthur CJ, Guberman‐Pfeffer MJ, Sofia Oliveira A, Curnow P, Anderson JLR. Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design. Protein Sci 2024; 33:e5113. [PMID: 38980168 PMCID: PMC11232281 DOI: 10.1002/pro.5113] [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: 05/17/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.
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Affiliation(s)
| | | | | | - May Rudin
- School of BiochemistryUniversity of BristolBristolUK
| | | | | | | | | | - Paul Curnow
- School of BiochemistryUniversity of BristolBristolUK
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3
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Srinivas S, Senthil Kumar A. Electrical Wiring of Malarial Parasite Intermediate Hematin on a Tailored N-Doped Carbon Nanomaterial Surface and Its Bioelectrocatalytic Hydrogen Peroxide Reduction and Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10634-10647. [PMID: 38723623 DOI: 10.1021/acs.langmuir.4c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Hematin, an iron-containing porphyrin compound, plays a crucial role in various biological processes, including oxygen transport, storage, and functionality of the malarial parasite. Specifically, hematin-Fe interacts with the nitrogen atom of antimalarial drugs, forming an intermediate step crucial for their function. The electron transfer functionality of hematin in biological systems has been scarcely investigated. In this study, we developed a biomimicking electrical wiring of hematin-Fe with a model N-drug system, represented as {hematin-Fe---N-drug}. We achieved this by immobilizing hematin on a multiwalled carbon nanotube (MWCNT)/N-graphene quantum dot (N-GQD) modified electrode (MWCNT/N-GQD@Hemat). N-GQD serves as a model molecular drug system containing nitrogen atoms to mimic the {hematin-Fe---N-drug} interaction. The prepared bioelectrode exhibited a distinct redox peak at a measured potential (E1/2) of -0.410 V vs Ag/AgCl, accompanied by a surface excess value of 3.54 × 10-9 mol cm-2. This observation contrasts significantly with the weak or electroinactive electrochemical responses documented in literature-based hematin systems. We performed a comprehensive set of physicochemical and electrochemical characterizations on the MWCNT/N-GQD@Hemat system, employing techniques including FESEM, TEM, Raman spectroscopy, IR spectroscopy, and AFM. To evaluate the biomimetic electrode's electroactivity, we investigated the selective-mediated reduction of H2O2 as a model system. As an important aspect of our research, we demonstrated the use of scanning electrochemical microscopy to visualize the in situ electron transfer reaction of the biomimicking electrode. In an independent study, we showed enzyme-less electrocatalytic reduction and selective electrocatalytic sensing of H2O2 with a detection limit of 319 nM. We achieved this using a batch injection analysis-coupled disposable screen-printed electrode system in physiological solution.
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Affiliation(s)
- Sakthivel Srinivas
- Nano and Bioelectrochemistry Research Laboratory, Carbon Dioxide Research and Green Technology Centre, Vellore 632014, India
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, India
| | - Annamalai Senthil Kumar
- Nano and Bioelectrochemistry Research Laboratory, Carbon Dioxide Research and Green Technology Centre, Vellore 632014, India
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, India
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4
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Duffus BR, Gauglitz M, Teutloff C, Leimkühler S. Redox potentials elucidate the electron transfer pathway of NAD +-dependent formate dehydrogenases. J Inorg Biochem 2024; 253:112487. [PMID: 38306887 DOI: 10.1016/j.jinorgbio.2024.112487] [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: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
Metal-dependent, nicotine adenine dinucleotide (NAD+)-dependent formate dehydrogenases (FDHs) are complex metalloenzymes coupling biochemical transformations through intricate electron transfer pathways. Rhodobacter capsulatus FDH is a model enzyme for understanding coupled catalysis, in that reversible CO2 reduction and formate oxidation are linked to a flavin mononuclotide (FMN)-bound diaphorase module via seven iron-sulfur (FeS) clusters as a dimer of heterotetramers. Catalysis occurs at a bis-metal-binding pterin (Mo) binding two molybdopterin guanine dinucleotides (bis-MGD), a protein-based Cys residue and a participatory sulfido ligand. Insights regarding the proposed electron transfer mechanism between the bis-MGD and the FMN have been complicated by the discovery that an alternative pathway might occur via intersubunit electron transfer between two [4Fe4S] clusters within electron transfer distance. To clarify this difference, the redox potentials of the bis-MGD and the FeS clusters were determined via redox titration by EPR spectroscopy. Redox potentials for the bis-MGD cofactor and five of the seven FeS clusters could be assigned. Furthermore, substitution of the active site residue Lys295 with Ala resulted in altered enzyme kinetics, primarily due to a more negative redox potential of the A1 [4Fe4S] cluster. Finally, characterization of the monomeric FdsGBAD heterotetramer exhibited slightly decreased formate oxidation activity and similar iron-sulfur clusters reduced relative to the dimeric heterotetramer. Comparison of the measured redox potentials relative to structurally defined FeS clusters support a mechanism by which electron transfer occurs within a heterotetrameric unit, with the interfacial [4Fe4S] cluster serving as a structural component toward the integrity of the heterodimeric structure to drive efficient catalysis.
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Affiliation(s)
- Benjamin R Duffus
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Marcel Gauglitz
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Teutloff
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Silke Leimkühler
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
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5
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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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6
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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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7
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He Z, Li Q, Xu Y, Zhang D, Pan X. Production of extracellular superoxide radical in microorganisms and its environmental implications: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122563. [PMID: 37717891 DOI: 10.1016/j.envpol.2023.122563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/24/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Extracellular superoxide radical (O2•-) is ubiquitous in microbial environments and has significant implications for pollutant transformation. Microbial extracellular O2•- can be produced through multiple pathways, including electron leakage from the respiratory electron transport chain (ETC), NADPH oxidation by the transmembrane NADPH oxidase (NOX), and extracellular reactions. Extracellular O2•- significantly influences the geochemical processes of various substances, including toxic metals and refractory organic pollutants. On one hand, extracellular O2•- can react with variable-valence metals and detoxify certain highly toxic metals, such as As(III), Cr(VI), and Hg(II). On the other hand, extracellular O2•- can directly or indirectly (via Bio-Fenton) degrade many organic pollutants, including a variety of emerging contaminants. In this work, we summarize the production mechanisms of microbial extracellular O2•-, review its roles in the transformation of environmental pollutants, and discuss the potential applications, limiting factors, and future research directions in this field.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qunqun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yao Xu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China.
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8
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Lavanya V, Pavithra D, Mohanapriya A, Santhakumar K, Senthil Kumar A. A π-π Bonding-Assisted Molecular-Wiring of Folded-Cytochrome c and Naphthoquinone and Its Electron-Relay-Based Bioelectrocatalytic H 2O 2 Reduction Reaction Visualized by Redox-Competitive Scanning Electrochemical Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11556-11570. [PMID: 37429831 DOI: 10.1021/acs.langmuir.3c00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The electron-transfer (ET) reaction of cytochrome c (Cytc) protein with biomolecules is a cutting-edge research area of interest in understanding the functionalities of natural systems. Several electrochemical biomimicking studies based on Cytc-protein-modified electrodes prepared via electrostatic interaction and covalent bonding approaches have been reported. Indeed, natural enzymes involve multiple types of bonding, such as hydrogen, ionic, covalent, and π-π, etc. In this work, we explore a Cytc-protein chemically modified glassy carbon electrode (GCE/CB@NQ/Cytc) prepared via π-π bonding using graphitic carbon as an underlying surface and an aromatic organic molecule, naphthoquinone (NQ), as a cofactor for an effective ET reaction. A simple drop-casting technique-based preparation of GCE/CB@NQ showed a distinct surface-confined redox peak at a standard electrode potential (E°) = -0.2 V vs Ag/AgCl (surface excess = 21.3 nmol cm-2) in pH 7 phosphate buffer solution. A control experiment of modification of NQ on an unmodified GCE failed to show any such unique feature. For the preparation of GCE/CB@NQ/Cytc, a dilute solution of Cytc-pH 7 phosphate buffer was drop-cast on the GCE/CB@NQ surface, wherein the protein folding and denaturalization-based complication and its associated ET functionalities were avoided. Molecular dynamics simulation studies show the complexation of NQ with Cytc at the protein binding sites. The protein-bound surface shows an efficient and selective bioelectrocatalytic reduction performance of H2O2, as demonstrated using cyclic voltammetry and amperometric i-t techniques. Finally, the redox-competition scanning electrochemical microscopy (RC-SECM) technique was adopted for in situ visualization of the electroactive adsorbed surface. The RC-SECM images clearly show the regions of highly bioelectrocatalytic active sites of Cytc-proteins bound to NQ molecules on a graphitic carbon surface. The binding of Cytc with NQ has significant implications for studying the biological electron transport mechanism, and the proposed method provides the requisite framework for such a study.
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Affiliation(s)
- V Lavanya
- Nano and Bioelectrochemistry Research Laboratory, Carbon Dioxide and Green Technology Research Centre, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
| | - Dhamodharan Pavithra
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
| | - Arumugam Mohanapriya
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
| | - K Santhakumar
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
| | - Annamalai Senthil Kumar
- Nano and Bioelectrochemistry Research Laboratory, Carbon Dioxide and Green Technology Research Centre, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology University, Vellore 632 014, Tamil Nadu, India
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9
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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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10
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Bozzi AS, Rocha WR. Calculation of Excited State Internal Conversion Rate Constant Using the One-Effective Mode Marcus-Jortner-Levich Theory. J Chem Theory Comput 2023; 19:2316-2326. [PMID: 37023359 DOI: 10.1021/acs.jctc.2c01288] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
In this article, the one-effective mode Marcus-Jortner-Levich (MJL) theory and the classical Marcus theory for electron transfer were applied to estimate the internal conversion rate constant, kIC, of organic molecules and a Ru-based complex, all belonging to the Marcus inverted region. For this, the reorganization energy was calculated using the minimum energy conical intersection point to account for more vibrational levels, correcting the density of states. The results showed good agreement with experimental and theoretically determined kIC, with a small overestimation by the Marcus theory. Also, molecules less dependent on the solvent effects, like benzophenone, presented better results than molecules with an expressive dependence, like 1-aminonaphthalene. Moreover, the results suggest that each molecule possesses unique normal modes leading to the excited state deactivation that does not necessarily match the X-H bond stretching, as previously suggested.
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Affiliation(s)
- Aline S Bozzi
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, 31270-901, Pampulha, Belo Horizonte, MG Brazil
| | - Willian R Rocha
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, 31270-901, Pampulha, Belo Horizonte, MG Brazil
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11
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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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12
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Sarewicz M, Szwalec M, Pintscher S, Indyka P, Rawski M, Pietras R, Mielecki B, Koziej Ł, Jaciuk M, Glatt S, Osyczka A. High-resolution cryo-EM structures of plant cytochrome b 6f at work. SCIENCE ADVANCES 2023; 9:eadd9688. [PMID: 36638176 PMCID: PMC9839326 DOI: 10.1126/sciadv.add9688] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome b6f (Cyt b6f) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Qp) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt b6f homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Qp in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt b6f in one direction, transiently exposing the redox-active ring of quinone during catalysis. Our work proposes an unprecedented one-way traffic model that explains efficient quinol oxidation during photosynthesis and respiration.
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Affiliation(s)
- Marcin Sarewicz
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mateusz Szwalec
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Pintscher
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Paulina Indyka
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Rafał Pietras
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Bohun Mielecki
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Łukasz Koziej
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Marcin Jaciuk
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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13
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Jeong T, Okanishi Y, Yotsui S, Kim IS, Yoshimitsu T. Organic redox cascade cyclization of 2-alkynylquinones by ascorbic acid in combination with a copper catalyst and its application to formal synthesis of liphagal. NEW J CHEM 2023. [DOI: 10.1039/d2nj05724g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The combination of a quinone-ascorbic acid organic redox reaction and a concomitant copper catalysis in situ enables new approach to hydroxybenzofurans with structural variations.
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Affiliation(s)
- Taejoo Jeong
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yusuke Okanishi
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Sora Yotsui
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - In Su Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Takehiko Yoshimitsu
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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14
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Wieferig JP, Kühlbrandt W. Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III 2 by cryo-EM. IUCRJ 2023; 10:27-37. [PMID: 36598500 PMCID: PMC9812224 DOI: 10.1107/s2052252522010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III2 (CIII2) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII2 from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII2 with a reduced high-potential chain increased the occupancy of the Qo site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c1 subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c1 than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd1-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
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Affiliation(s)
- Jan-Philip Wieferig
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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15
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de Carvalho JGM, Geißer K, Weishäupl SJ, Fischer RA, Pöthig A. Alkaline Earth Metal-Organic Frameworks Based on Tetratopic Anthraquinone-Based Linkers: Synthesis, Characterization, and Photochemical Applications. Inorg Chem 2022; 61:15831-15840. [PMID: 36166497 DOI: 10.1021/acs.inorgchem.2c01643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A tetratopic bis(diphenylamino)anthraquinone linker is presented, and its physicochemical properties are evaluated. The linker is shown to successfully coordinate alkaline earth metals leading to four new reported metal-organic frameworks (MOFs), which have been fully characterized, including single-crystal X-ray diffraction. The physicochemical and emissive properties of the MOF materials are investigated and compared to those of the uncoordinated ligand. Finally, the catalytic behavior of the ligand and the MOF materials toward the photooxidation of sulfides is described.
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Affiliation(s)
- João Guilherme M de Carvalho
- Chair of Inorganic and Metal-Organic Chemistry, Catalysis Research Center and Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching B. München, Germany
| | - Korbinian Geißer
- Chair of Inorganic and Metal-Organic Chemistry, Catalysis Research Center and Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching B. München, Germany
| | - Sebastian J Weishäupl
- Chair of Inorganic and Metal-Organic Chemistry, Catalysis Research Center and Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching B. München, Germany
| | - Roland A Fischer
- Chair of Inorganic and Metal-Organic Chemistry, Catalysis Research Center and Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching B. München, Germany
| | - Alexander Pöthig
- Chair of Inorganic and Metal-Organic Chemistry, Catalysis Research Center and Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching B. München, Germany
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16
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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17
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Du J, Xin J, Liu M, Zhang X, He H, Wu J, Xu X. Preparation of Photo-Bioelectrochemical Cells With the RC-LH Complex From Roseiflexus castenholzii. Front Microbiol 2022; 13:928046. [PMID: 35783423 PMCID: PMC9243436 DOI: 10.3389/fmicb.2022.928046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Roseiflexus castenholzii is an ancient green non-sulfur bacteria that absorbs the solar energy through bacteriochlorophylls (BChls) bound in the only light harvesting (LH) complex, and transfers to the reaction center (RC), wherein primary charge separation occurs and transforms the energy into electrochemical potentials. In contrast to purple bacteria, R. castenholzii RC-LH (rcRC-LH) does not contain an H subunit. Instead, a tightly bound tetraheme cytochrome c subunit is exposed on the P-side of the RC, which contains three BChls, three bacteriopheophytins (BPheos), two menaquinones, and one iron for electron transfer. These novel structural features of the rcRC-LH are advantageous for enhancing the electron transfer efficiency and subsequent photo-oxidation of the c-type hemes. However, the photochemical properties of rcRC-LH and its applications in developing the photo-bioelectrochemical cells (PBECs) have not been characterized. Here, we prepared a PBEC using overlapped fluorine-doped tin oxide (FTO) glass and Pt-coated glass as electrodes, and rcRC-LH mixed with varying mediators as the electrolyte. Absence of the H subunit allows rcRC-LH to be selectively adhered onto the hydrophilic surface of the front electrode with its Q-side. Upon illumination, the photogenerated electrons directly enter the front electrode and transfer to the counter electrode, wherein the accepted electrons pass through the exposed c-type hemes to reduce the excited P+, generating a steady-state current of up to 320 nA/cm2 when using 1-Methoxy-5-methylphenazinium methyl sulfate (PMS) as mediator. This study demonstrated the novel photoelectric properties of rcRC-LH and its advantages in preparing effective PBECs, showcasing a potential of this complex in developing new type PBECs.
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Affiliation(s)
- Jinsong Du
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
| | - Jiyu Xin
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Menghua Liu
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
| | - Xin Zhang
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
| | - Huimin He
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
| | - Jingyi Wu
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
| | - Xiaoling Xu
- Photosynthesis Research Center, Hangzhou Normal University, Hangzhou, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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18
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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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19
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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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20
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Structural basis for safe and efficient energy conversion in a respiratory supercomplex. Nat Commun 2022; 13:545. [PMID: 35087070 PMCID: PMC8795186 DOI: 10.1038/s41467-022-28179-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022] Open
Abstract
Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species during aerobic cellular respiration. Cytochrome bc complexes and cytochrome aa3 oxidases are major drivers of the proton motive force that fuels ATP generation via respiration, but how wasteful electron- and proton transfer is controlled to enhance safety and efficiency in the context of supercomplexes is not known. Here, we address this question with the 2.8 Å resolution cryo-EM structure of the cytochrome bcc-aa3 (III2-IV2) supercomplex from the actinobacterium Corynebacterium glutamicum. Menaquinone, substrate mimics, lycopene, an unexpected Qc site, dioxygen, proton transfer routes, and conformational states of key protonable residues are resolved. Our results show how safe and efficient energy conversion is achieved in a respiratory supercomplex through controlled electron and proton transfer. The structure may guide the rational design of drugs against actinobacteria that cause diphtheria and tuberculosis. Aerobic energy metabolism is driven by proton-pumping respiratory supercomplexes. The study reports the structural basis for energy conversion in such supercomplex. It may aid metabolic engineering and drug design against diphtheria and tuberculosis.
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21
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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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22
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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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23
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Megarity CF, Siritanaratkul B, Herold RA, Morello G, Armstrong FA. Electron flow between the worlds of Marcus and Warburg. J Chem Phys 2021; 153:225101. [PMID: 33317312 DOI: 10.1063/5.0024701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Living organisms are characterized by the ability to process energy (all release heat). Redox reactions play a central role in biology, from energy transduction (photosynthesis, respiratory chains) to highly selective catalyzed transformations of complex molecules. Distance and scale are important: electrons transfer on a 1 nm scale, hydrogen nuclei transfer between molecules on a 0.1 nm scale, and extended catalytic processes (cascades) operate most efficiently when the different enzymes are under nanoconfinement (10 nm-100 nm scale). Dynamic electrochemistry experiments (defined broadly within the term "protein film electrochemistry," PFE) reveal details that are usually hidden in conventional kinetic experiments. In PFE, the enzyme is attached to an electrode, often in an innovative way, and electron-transfer reactions, individual or within steady-state catalytic flow, can be analyzed in terms of precise potentials, proton coupling, cooperativity, driving-force dependence of rates, and reversibility (a mark of efficiency). The electrochemical experiments reveal subtle factors that would have played an essential role in molecular evolution. This article describes how PFE is used to visualize and analyze different aspects of biological redox chemistry, from long-range directional electron transfer to electron/hydride (NADPH) interconversion by a flavoenzyme and finally to NADPH recycling in a nanoconfined enzyme cascade.
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Affiliation(s)
- Clare F Megarity
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | | | - Ryan A Herold
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Giorgio Morello
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
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24
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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: 61] [Impact Index Per Article: 20.3] [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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25
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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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26
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Molecularly wiring of Cytochrome c with carboxylic acid functionalized hydroquinone on MWCNT surface and its bioelectrocatalytic reduction of H2O2 relevance to biomimetic electron-transport and redox signalling. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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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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Bayer U, Werner D, Berkefeld A, Maichle-Mössmer C, Anwander R. Cerium-quinone redox couples put under scrutiny. Chem Sci 2020; 12:1343-1351. [PMID: 34163897 PMCID: PMC8179043 DOI: 10.1039/d0sc04489j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Homoleptic cerous complexes Ce[N(SiMe3)2]3, [Ce{OSi(OtBu)3}3]2 and [Ce{OSiiPr3}3]2 were employed as thermally robust, weakly nucleophilic precursors to assess their reactivity towards 1,4-quinones in non-aqueous solution. The strongly oxidizing quinones 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) or tetrachloro-1,4-benzoquinone (Cl4BQ) readily form hydroquinolato-bridged ceric complexes of the composition [(CeIVL3)2(μ2-O2C6R4)]. Less oxidising quinones like 2,5-di-tert-butyl-1,4-benzoquinone (tBu2BQ) tend to engage in redox equilibria with the ceric hydroquinolato-bridged form being stable only in the solid state. Even less oxidising quinones such as tetramethyl-1,4-benzoquinone (Me4BQ) afford cerous semiquinolates of the type [(CeIIIL2(thf)2)(μ2-O2C6Me4)]2. All complexes were characterised by X-ray diffraction, 1H, 13C{1H} and 29Si NMR spectroscopy, DRIFT spectroscopy, UV-Vis spectroscopy and CV measurements. The species putatively formed during the electrochemical reduction of [CeIV{N(SiMe3)2}3]2(μ2-O2C6H4) could be mimicked by chemical reduction with CoIICp2 yielding [(CeIII{N(SiMe3)2}3)2(μ2-O2C6H4)][CoIIICp2]2.
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Affiliation(s)
- Uwe Bayer
- Institut für Anorganische Chemie, Eberhard Karls Universität Tübingen (EKUT) Auf der Morgenstelle 18 72076 Tübingen Germany [http://uni-tuebingen.de/syncat-anwander]
| | - Daniel Werner
- Institut für Anorganische Chemie, Eberhard Karls Universität Tübingen (EKUT) Auf der Morgenstelle 18 72076 Tübingen Germany [http://uni-tuebingen.de/syncat-anwander]
| | - Andreas Berkefeld
- Institut für Anorganische Chemie, Eberhard Karls Universität Tübingen (EKUT) Auf der Morgenstelle 18 72076 Tübingen Germany [http://uni-tuebingen.de/syncat-anwander]
| | - Cäcilia Maichle-Mössmer
- Institut für Anorganische Chemie, Eberhard Karls Universität Tübingen (EKUT) Auf der Morgenstelle 18 72076 Tübingen Germany [http://uni-tuebingen.de/syncat-anwander]
| | - Reiner Anwander
- Institut für Anorganische Chemie, Eberhard Karls Universität Tübingen (EKUT) Auf der Morgenstelle 18 72076 Tübingen Germany [http://uni-tuebingen.de/syncat-anwander]
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29
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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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Han T, Petersen JB, Li ZH, Zhai YQ, Kostopoulos A, Ortu F, McInnes EJL, Winpenny REP, Zheng YZ. Dimerized p-Semiquinone Radical Anions Stabilized by a Pair of Rare-Earth Metal Ions. Inorg Chem 2020; 59:7371-7375. [PMID: 32392411 DOI: 10.1021/acs.inorgchem.0c00503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report stable p-quinone-radical-bridged rare-earth complexes involving the ligand tetramethylquinone (QMe4•-). The complexes, {Y[(QMe4)•-Cl2(THF)3]}2 (1) and {Gd[(QMe4)•-Cl2(THF)3]}2 (2), where THF = tetrahydrofuran, are sufficiently stable that we can measure the single-crystal structures and perform magnetic and electron paramagnetic resonance measurements. These studies show the presence of a semiquinone form and that the magnetic interaction between the radicals in the dimer is strong and antiferromagnetic.
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Affiliation(s)
- Tian Han
- School of Science, Frontier Institute of Science and Technology, Research Institute of Xi'an Jiaotong University (Zhejiang), State Key Laboratory for Mechanical Behavior of Materials, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, and Xi'an Key Laboratory of Sustainable Energy and Materials Chemistry, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jonatan B Petersen
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Zi-Han Li
- School of Science, Frontier Institute of Science and Technology, Research Institute of Xi'an Jiaotong University (Zhejiang), State Key Laboratory for Mechanical Behavior of Materials, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, and Xi'an Key Laboratory of Sustainable Energy and Materials Chemistry, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yuan-Qi Zhai
- School of Science, Frontier Institute of Science and Technology, Research Institute of Xi'an Jiaotong University (Zhejiang), State Key Laboratory for Mechanical Behavior of Materials, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, and Xi'an Key Laboratory of Sustainable Energy and Materials Chemistry, Xi'an Jiaotong University, Xi'an 710049, China
| | - Andreas Kostopoulos
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Fabrizio Ortu
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Eric J L McInnes
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Richard E P Winpenny
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Yan-Zhen Zheng
- School of Science, Frontier Institute of Science and Technology, Research Institute of Xi'an Jiaotong University (Zhejiang), State Key Laboratory for Mechanical Behavior of Materials, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, and Xi'an Key Laboratory of Sustainable Energy and Materials Chemistry, Xi'an Jiaotong University, Xi'an 710049, China
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32
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Pintscher S, Wójcik-Augustyn A, Sarewicz M, Osyczka A. Charge polarization imposed by the binding site facilitates enzymatic redox reactions of quinone. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148216. [PMID: 32387188 DOI: 10.1016/j.bbabio.2020.148216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 11/19/2022]
Abstract
Quinone reduction site (Qi) of cytochrome bc1 represents one of the canonical sites used to explore the enzymatic redox reactions involving semiquinone (SQ) states. However, the mechanism by which Qi allows the completion of quinone reduction during the sequential transfers of two electrons from the adjacent heme bH and two protons to C1- and C4-carbonyl remains unclear. Here we established that the SQ coupled to an oxidized heme bH is a dominant intermediate of catalytic forward reaction and, contrary to the long-standing assumption, represents a significant population of SQ detected across pH 5-9. The pH dependence of its redox midpoint potential implicated proton exchange with histidine. Complementary quantum mechanical calculations revealed that the SQ anion formed after the first electron transfer undergoes charge and spin polarization imposed by the electrostatic field generated by histidine and the aspartate/lysine pair interacting with the C4- and C1-carbonyl, respectively. This favors a barrierless proton exchange between histidine and the C4-carbonyl, which continues until the second electron reaches the SQi. Inversion of charge polarization facilitates the uptake of the second proton by the C1-carbonyl. Based on these findings we developed a comprehensive scheme for electron and proton transfers at Qi featuring the equilibration between the anionic and neutral states of SQi as means for a leak-proof stabilization of the radical intermediate. The key catalytic role of the initial charge/spin polarization of the SQ anion at the active site, inherent to the proposed mechanism, may also be applicable to the other quinone oxidoreductases.
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Affiliation(s)
- Sebastian Pintscher
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 30387, Poland.
| | - Anna Wójcik-Augustyn
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 30387, Poland.
| | - Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 30387, Poland.
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 30387, Poland.
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Wu M, Gu J, Zong S, Guo R, Liu T, Yang M. Research journey of respirasome. Protein Cell 2020; 11:318-338. [PMID: 31919741 PMCID: PMC7196574 DOI: 10.1007/s13238-019-00681-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Respirasome, as a vital part of the oxidative phosphorylation system, undertakes the task of transferring electrons from the electron donors to oxygen and produces a proton concentration gradient across the inner mitochondrial membrane through the coupled translocation of protons. Copious research has been carried out on this lynchpin of respiration. From the discovery of individual respiratory complexes to the report of the high-resolution structure of mammalian respiratory supercomplex I1III2IV1, scientists have gradually uncovered the mysterious veil of the electron transport chain (ETC). With the discovery of the mammalian respiratory mega complex I2III2IV2, a new perspective emerges in the research field of the ETC. Behind these advances glitters the light of the revolution in both theory and technology. Here, we give a short review about how scientists 'see' the structure and the mechanism of respirasome from the macroscopic scale to the atomic scale during the past decades.
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Affiliation(s)
- Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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34
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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: 90] [Impact Index Per Article: 22.5] [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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35
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Thodika M, Fennimore M, Karsili TNV, Matsika S. Comparative study of methodologies for calculating metastable states of small to medium-sized molecules. J Chem Phys 2019; 151:244104. [DOI: 10.1063/1.5134700] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mushir Thodika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mark Fennimore
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Tolga N. V. Karsili
- Department of Chemistry, University of Louisiana, Lafayette, Louisiana 70504, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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36
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Malone LA, Qian P, Mayneord GE, Hitchcock A, Farmer DA, Thompson RF, Swainsbury DJK, Ranson NA, Hunter CN, Johnson MP. Cryo-EM structure of the spinach cytochrome b6 f complex at 3.6 Å resolution. Nature 2019; 575:535-539. [DOI: 10.1038/s41586-019-1746-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/08/2019] [Indexed: 12/29/2022]
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37
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Syroeshkin MA, Kuriakose F, Saverina EA, Timofeeva VA, Egorov MP, Alabugin IV. Hochkonversion von Reduktionsmitteln. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807247] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mikhail A. Syroeshkin
- N. D. Zelinsky Institute of Organic Chemistry Leninskyprosp. 47 119991 Moskau Russland
| | - Febin Kuriakose
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
| | - Evgeniya A. Saverina
- N. D. Zelinsky Institute of Organic Chemistry Leninskyprosp. 47 119991 Moskau Russland
- UMR CNRS 6226 ISCR University of Rennes 1 Rennes Frankreich
| | | | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry Leninskyprosp. 47 119991 Moskau Russland
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
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38
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Syroeshkin MA, Kuriakose F, Saverina EA, Timofeeva VA, Egorov MP, Alabugin IV. Upconversion of Reductants. Angew Chem Int Ed Engl 2019; 58:5532-5550. [DOI: 10.1002/anie.201807247] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Mikhail A. Syroeshkin
- N. D. Zelinsky Institute of Organic Chemistry Leninsky prosp. 47 119991 Moscow Russia
| | - Febin Kuriakose
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
| | - Evgeniya A. Saverina
- N. D. Zelinsky Institute of Organic Chemistry Leninsky prosp. 47 119991 Moscow Russia
- UMR CNRS 6226 ISCR University of Rennes 1 Rennes France
| | | | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry Leninsky prosp. 47 119991 Moscow Russia
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
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39
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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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40
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Hedges CP, Bishop DJ, Hickey AJR. Voluntary wheel running prevents the acidosis-induced decrease in skeletal muscle mitochondrial reactive oxygen species emission. FASEB J 2018; 33:4996-5004. [PMID: 30596520 DOI: 10.1096/fj.201801870r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Decreases in pH (acidosis) in vitro can alter skeletal muscle mitochondrial function [respiration and reactive oxygen species (ROS) emission]. However, because skeletal muscles readily adapt to exercise, the effects of acidosis may be different on sedentary vs. trained muscle. The aim of this work was to compare the effects of pH on skeletal muscle mitochondrial function between sedentary vs. exercise-trained male Sprague-Dawley rats ( n = 10 in each cohort). Rates of mitochondrial respiration and ROS emission were determined from the soleus muscle of both cohorts over a physiologic range of pH values (pH 6.2-7.1). Exercise-trained rats had 14% higher mean muscle buffering capacities; 46 and 40% greater enzyme activity of citrate synthase and lactate dehydrogenase, respectively; and greater activity of respiratory complexes I-IV. ADP-stimulated respiration with complex I and II substrates was ∼25% greater in exercise-trained rats but was unaffected by pH in either cohort. In both cohorts, lowering pH decreased respiration only in complex I- and complex II-supported nonphosphorylating (leak) state. However, as pH decreased, ROS emissions in complex I- and complex II-supported leak state decreased only in sedentary rats; in exercise-trained rats, ROS emissions in this state remained constant. We hypothesize that this effect may result from modulation at complex III, which declined 47% per unit pH in sedentary rats, in comparison to 23% in exercise-trained rats. Taken together, these data suggest that pH regulates mitochondrial respiratory complexes and that exercise training can decrease the effects of pH on skeletal muscle mitochondrial function.-Hedges, C. P., Bishop, D. J., Hickey, A. J. R. Voluntary wheel running prevents the acidosis-induced decrease in skeletal muscle mitochondrial reactive oxygen species emission.
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Affiliation(s)
- Christopher P Hedges
- Applied Surgery and Metabolism Laboratory, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia; and
| | - David J Bishop
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia; and.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Anthony J R Hickey
- Applied Surgery and Metabolism Laboratory, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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41
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Kausar S, Wang F, Cui H. The Role of Mitochondria in Reactive Oxygen Species Generation and Its Implications for Neurodegenerative Diseases. Cells 2018; 7:cells7120274. [PMID: 30563029 PMCID: PMC6316843 DOI: 10.3390/cells7120274] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 12/21/2022] Open
Abstract
Mitochondria are dynamic cellular organelles that consistently migrate, fuse, and divide to modulate their number, size, and shape. In addition, they produce ATP, reactive oxygen species, and also have a biological role in antioxidant activities and Ca2+ buffering. Mitochondria are thought to play a crucial biological role in most neurodegenerative disorders. Neurons, being high-energy-demanding cells, are closely related to the maintenance, dynamics, and functions of mitochondria. Thus, impairment of mitochondrial activities is associated with neurodegenerative diseases, pointing to the significance of mitochondrial functions in normal cell physiology. In recent years, considerable progress has been made in our knowledge of mitochondrial functions, which has raised interest in defining the involvement of mitochondrial dysfunction in neurodegenerative diseases. Here, we summarize the existing knowledge of the mitochondrial function in reactive oxygen species generation and its involvement in the development of neurodegenerative diseases.
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Affiliation(s)
- Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China.
| | - Feng Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China.
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China.
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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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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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44
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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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45
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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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46
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Kinetics teach that electronic coupling lowers the free-energy change that accompanies electron transfer. Proc Natl Acad Sci U S A 2018; 115:7248-7253. [PMID: 29941573 DOI: 10.1073/pnas.1722401115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Electron-transfer theories predict that an increase in the quantum-mechanical mixing (HDA) of electron donor and acceptor wavefunctions at the instant of electron transfer drives equilibrium constants toward unity. Kinetic and equilibrium studies of four acceptor-bridge-donor (A-B-D) compounds reported herein provide experimental validation of this prediction. The compounds have two redox-active groups that differ only by the orientation of the aromatic bridge: a phenyl-thiophene bridge (p) that supports strong electronic coupling of HDA > 1,000 cm-1; and a xylyl-thiophene bridge (x) that prevents planarization and decreases HDA < 100 cm-1 without a significant change in distance. Pulsed-light excitation allowed kinetic determination of the equilibrium constant, Keq In agreement with theory, Keq(p) were closer to unity compared to Keq(x). A van't Hoff analysis provided clear evidence of an adiabatic electron-transfer pathway for p-series and a nonadiabatic pathway for x-series. Collectively, the data show that the absolute magnitude of the thermodynamic driving force for electron transfers are decreased when adiabatic pathways are operative, a finding that should be taken into account in the design of hybrid materials for solar energy conversion.
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47
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Chen HW, Mallick S, Zou SF, Meng M, Liu CY. Mapping Bridge Conformational Effects on Electronic Coupling in Mo 2-Mo 2 Mixed-Valence Systems. Inorg Chem 2018; 57:7455-7467. [PMID: 29809000 DOI: 10.1021/acs.inorgchem.8b01056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The large bridging ligand 9,10-anthracenedicarboxylate and its thiolated derivatives have been employed to assemble two dimolybdenum complex units and develop three Mo2 dimers, [Mo2(DAniF)3]2(μ-9,10-O2CC14H8CO2), [Mo2(DAniF)3]2(μ-9,10-OSCC14H8COS), and [Mo2(DAniF)3]2(μ-9,10-S2CC14H8CS2) (DAniF = N, N'-di( p-anisyl)formamidinate), for the study of conformation dependence of the electronic coupling between the two Mo2 centers. These compounds feature a large deviation of the central anthracene ring from the plane defined by the Mo-Mo bond vectors, with the torsion angles (ϕ = 50-76°) increasing as the chelating atoms of the bridging ligand vary from O to S. Consequently, the corresponding mixed-valence complexes do not exhibit characteristic intervalence charge transfer absorptions in the near-IR spectra, in contrast to the phenylene and naphthalene analogues, from which these systems are assigned to the Class I in Robin-Day's scheme. Together with the phenylene and naphthalene series, the nine total mixed-valence complexes in three series complete a transition from the electronically uncoupled Class I to the strongly coupled Class II-III borderline via moderately coupled Class II and permit a systematic mapping of the bridge conformation effects on electronic coupling. Density functional theory calculations show that the HOMO-LUMO energy gap, corresponding to the metal (δ) to ligand (π*) transition energy, and the magnitude of HOMO-HOMO-1 splitting in energy are linearly related to cos2 ϕ. Therefore, our experimental and theoretical results concur to indicate that the coupling strength decreases in the order of the bridging units: phenylene > naphthalene > anthracene, which verifies the through-bond superexchange mechanism for electronic coupling and electron transfer.
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Affiliation(s)
- Huo Wen Chen
- Department of Chemistry , Jinan University , 601 Huang-Pu Avenue West , Guangzhou 510632 , China
| | - Suman Mallick
- Department of Chemistry , Jinan University , 601 Huang-Pu Avenue West , Guangzhou 510632 , China
| | - Shan Feng Zou
- Department of Chemistry , Jinan University , 601 Huang-Pu Avenue West , Guangzhou 510632 , China
| | - Miao Meng
- Department of Chemistry , Jinan University , 601 Huang-Pu Avenue West , Guangzhou 510632 , China
| | - Chun Y Liu
- Department of Chemistry , Jinan University , 601 Huang-Pu Avenue West , Guangzhou 510632 , China
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48
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Pintscher S, Pietras R, Sarewicz M, Osyczka A. Electron sweep across four b-hemes of cytochrome bc1 revealed by unusual paramagnetic properties of the Qi semiquinone intermediate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:459-469. [DOI: 10.1016/j.bbabio.2018.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/08/2018] [Accepted: 03/18/2018] [Indexed: 01/05/2023]
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49
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Borek A, Ekiert R, Osyczka A. Functional flexibility of electron flow between quinol oxidation Q o site of cytochrome bc 1 and cytochrome c revealed by combinatory effects of mutations in cytochrome b, iron-sulfur protein and cytochrome c 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:754-761. [PMID: 29705394 DOI: 10.1016/j.bbabio.2018.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 01/07/2023]
Abstract
Transfer of electron from quinol to cytochrome c is an integral part of catalytic cycle of cytochrome bc1. It is a multi-step reaction involving: i) electron transfer from quinol bound at the catalytic Qo site to the Rieske iron-sulfur ([2Fe-2S]) cluster, ii) large-scale movement of a domain containing [2Fe-2S] cluster (ISP-HD) towards cytochrome c1, iii) reduction of cytochrome c1 by reduced [2Fe-2S] cluster, iv) reduction of cytochrome c by cytochrome c1. In this work, to examine this multi-step reaction we introduced various types of barriers for electron transfer within the chain of [2Fe-2S] cluster, cytochrome c1 and cytochrome c. The barriers included: impediment in the motion of ISP-HD, uphill electron transfer from [2Fe-2S] cluster to heme c1 of cytochrome c1, and impediment in the catalytic quinol oxidation. The barriers were introduced separately or in various combinations and their effects on enzymatic activity of cytochrome bc1 were compared. This analysis revealed significant degree of functional flexibility allowing the cofactor chains to accommodate certain structural and/or redox potential changes without losing overall electron and proton transfers capabilities. In some cases inhibitory effects compensated one another to improve/restore the function. The results support an equilibrium model in which a random oscillation of ISP-HD between the Qo site and cytochrome c1 helps maintaining redox equilibrium between all cofactors of the chain. We propose a new concept in which independence of the dynamics of the Qo site substrate and the motion of ISP-HD is one of the elements supporting this equilibrium and also is a potential factor limiting the overall catalytic rate.
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Affiliation(s)
- Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Robert Ekiert
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
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50
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Xin Y, Shi Y, Niu T, Wang Q, Niu W, Huang X, Ding W, Yang L, Blankenship RE, Xu X, Sun F. Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote. Nat Commun 2018; 9:1568. [PMID: 29674684 PMCID: PMC5908803 DOI: 10.1038/s41467-018-03881-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/19/2018] [Indexed: 11/29/2022] Open
Abstract
Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC–LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery. Filamentous anoxygenic phototrophs (FAPs) are phylogenetically distant from other anoxygenic photosynthetic bacteria. Here the authors present the 4.1 Å cryo-EM structure of the photosynthetic core complex from the FAP Roseiflexus castenholzii and propose a model for energy and electron transfer.
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Affiliation(s)
- Yueyong Xin
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Yang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Tongxin Niu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China
| | - Qingqiang Wang
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Wanqiang Niu
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China
| | - Wei Ding
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China
| | - Lei Yang
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Xiaoling Xu
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China.
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, 100049, Beijing, China. .,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China.
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