1
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Wang Y, Lilienfeldt N, Hekimi S. Understanding coenzyme Q. Physiol Rev 2024; 104:1533-1610. [PMID: 38722242 DOI: 10.1152/physrev.00040.2023] [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: 10/16/2023] [Revised: 04/08/2024] [Accepted: 05/01/2024] [Indexed: 08/11/2024] Open
Abstract
Coenzyme Q (CoQ), also known as ubiquinone, comprises a benzoquinone head group and a long isoprenoid side chain. It is thus extremely hydrophobic and resides in membranes. It is best known for its complex function as an electron transporter in the mitochondrial electron transport chain (ETC) but is also required for several other crucial cellular processes. In fact, CoQ appears to be central to the entire redox balance of the cell. Remarkably, its structure and therefore its properties have not changed from bacteria to vertebrates. In metazoans, it is synthesized in all cells and is found in most, and maybe all, biological membranes. CoQ is also known as a nutritional supplement, mostly because of its involvement with antioxidant defenses. However, whether there is any health benefit from oral consumption of CoQ is not well established. Here we review the function of CoQ as a redox-active molecule in the ETC and other enzymatic systems, its role as a prooxidant in reactive oxygen species generation, and its separate involvement in antioxidant mechanisms. We also review CoQ biosynthesis, which is particularly complex because of its extreme hydrophobicity, as well as the biological consequences of primary and secondary CoQ deficiency, including in human patients. Primary CoQ deficiency is a rare inborn condition due to mutation in CoQ biosynthetic genes. Secondary CoQ deficiency is much more common, as it accompanies a variety of pathological conditions, including mitochondrial disorders as well as aging. In this context, we discuss the importance, but also the great difficulty, of alleviating CoQ deficiency by CoQ supplementation.
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Affiliation(s)
- Ying Wang
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Noah Lilienfeldt
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Siegfried Hekimi
- Department of Biology, McGill University, Montreal, Quebec, Canada
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2
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Borek A, Wójcik-Augustyn A, Kuleta P, Ekiert R, Osyczka A. Identification of hydrogen bonding network for proton transfer at the quinol oxidation site of Rhodobacter capsulatus cytochrome bc 1. J Biol Chem 2023; 299:105249. [PMID: 37714464 PMCID: PMC10583091 DOI: 10.1016/j.jbc.2023.105249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
Cytochrome bc1 catalyzes electron transfer from quinol (QH2) to cytochrome c in reactions coupled to proton translocation across the energy-conserving membrane. Energetic efficiency of the catalytic cycle is secured by a two-electron and two-proton bifurcation reaction leading to oxidation of QH2 and reduction of the Rieske cluster and heme bL. The proton paths associated with this reaction remain elusive. Here, we used site-directed mutagenesis and quantum mechanical calculations to analyze the contribution of protonable side chains located at the heme bL side of the QH2 oxidation site in Rhodobacter capsulatus cytochrome bc1. We observe that the proton path is effectively switched off when H276 and E295 are simultaneously mutated to the nonprotonable residues in the H276F/E295V double mutant. The two single mutants, H276F or E295V, are less efficient but still transfer protons at functionally relevant rates. Natural selection exposed two single mutations, N279S and M154T, that restored the functional proton transfers in H276F/E295V. Quantum mechanical calculations indicated that H276F/E295V traps the side chain of Y147 in a position distant from QH2, whereas either N279S or M154T induce local changes releasing Y147 from that position. This shortens the distance between the protonable groups of Y147 and D278 and/or increases mobility of the Y147 side chain, which makes Y147 efficient in transferring protons from QH2 toward D278 in H276F/E295V. Overall, our study identified an extended hydrogen bonding network, build up by E295, H276, D278, and Y147, involved in efficient proton removal from QH2 at the heme bL side of QH2 oxidation site.
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Affiliation(s)
- Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Wójcik-Augustyn
- 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
| | - Robert Ekiert
- 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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3
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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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4
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In silico investigation of cytochrome bc1 molecular inhibition mechanism against Trypanosoma cruzi. PLoS Negl Trop Dis 2023; 17:e0010545. [PMID: 36689459 PMCID: PMC9894551 DOI: 10.1371/journal.pntd.0010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/02/2023] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Chagas' disease is a neglected tropical disease caused by the kinetoplastid protozoan Trypanosoma cruzi. The only therapies are the nitroheterocyclic chemicals nifurtimox and benznidazole that cause various adverse effects. The need to create safe and effective medications to improve medical care remains critical. The lack of verified T. cruzi therapeutic targets hinders medication research for Chagas' disease. In this respect, cytochrome bc1 has been identified as a promising therapeutic target candidate for antibacterial medicines of medical and agricultural interest. Cytochrome bc1 belongs to the mitochondrial electron transport chain and transfers electrons from ubiquinol to cytochrome c1 by the action of two catalytic sites named Qi and Qo. The two binding sites are highly selective, and specific inhibitors exist for each site. Recent studies identified the Qi site of the cytochrome bc1 as a promising drug target against T. cruzi. However, a lack of knowledge of the drug mechanism of action unfortunately hinders the development of new therapies. In this context, knowing the cause of binding site selectivity and the mechanism of action of inhibitors and substrates is crucial for drug discovery and optimization processes. In this paper, we provide a detailed computational investigation of the Qi site of T. cruzi cytochrome b to shed light on the molecular mechanism of action of known inhibitors and substrates. Our study emphasizes the action of inhibitors at the Qi site on a highly unstructured portion of cytochrome b that could be related to the biological function of the electron transport chain complex.
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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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6
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Chen CL, Zhang L, Jin Z, Kasumov T, Chen YR. Mitochondrial redox regulation and myocardial ischemia-reperfusion injury. Am J Physiol Cell Physiol 2022; 322:C12-C23. [PMID: 34757853 PMCID: PMC8721908 DOI: 10.1152/ajpcell.00131.2021] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mitochondrial reactive oxygen species (ROS) have emerged as an important mechanism of disease and redox signaling in the cellular system. Under basal or pathological conditions, electron leakage for ROS production is primarily mediated by complexes I and III of the electron transport chain (ETC) and by the proton motive force (PMF), consisting of a membrane potential (ΔΨ) and a proton gradient (ΔpH). Several factors control redox status in mitochondria, including ROS, the PMF, oxidative posttranslational modifications (OPTM) of the ETC subunits, SOD2, and cytochrome c heme lyase (HCCS). In the mitochondrial PMF, increased ΔpH-supported backpressure due to diminishing electron transport and chemiosmosis promotes a more reductive mitochondrial physiological setting. OPTM by protein cysteine sulfonation in complex I and complex III has been shown to affect enzymatic catalysis, the proton gradient, redox status, and enzyme-mediated ROS production. Pathological conditions associated with oxidative or nitrosative stress, such as myocardial ischemia and reperfusion (I/R), increase mitochondrial ROS production and redox dysfunction via oxidative injury to complexes I and III, intensely enhancing protein cysteine sulfonation and impairing heme integrity. The physiological conditions of reductive stress induced by gains in SOD2 function normalize I/R-mediated ROS overproduction and redox dysfunction. Further insight into the cellular mechanisms by which HCCS, biogenesis of c-type cytochrome, and OPTM regulate PMF and ROS production in mitochondria will enrich our understanding of redox signal transduction and identify new therapeutic targets for cardiovascular diseases in which oxidative stress perturbs normal redox signaling.
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Affiliation(s)
- Chwen-Lih Chen
- 1Department of Integrative Medical Sciences, College of Medicine,
Northeast Ohio Medical University, Rootstown, Ohio
| | - Liwen Zhang
- 2Campus Chemical Instrument Center, Proteomics and Mass Spectrometry Facility, The Ohio State University, Columbus, Ohio
| | - Zhicheng Jin
- 3Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
| | - Takhar Kasumov
- 4Department of Pharmaceutical Sciences, College of Pharmacy,
Northeast Ohio Medical University, Rootstown, Ohio
| | - Yeong-Renn Chen
- 1Department of Integrative Medical Sciences, College of Medicine,
Northeast Ohio Medical University, Rootstown, Ohio
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7
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Wani MA, Dhaked DK. Targeting the cytochrome bc 1 complex for drug development in M. tuberculosis: review. Mol Divers 2021; 26:2949-2965. [PMID: 34762234 DOI: 10.1007/s11030-021-10335-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
The terminal oxidases of the oxidative phosphorylation pathway play a significant role in the survival and growth of M. tuberculosis, targeting these components lead to inhibition of M. tuberculosis. Many drug candidates targeting various components of the electron transport chain in M. tuberculosis have recently been discovered. The cytochrome bc1-aa3 supercomplex is one of the most important components of the electron transport chain in M. tuberculosis, and it has emerged as the novel target for several promising candidates. There are two cryo-electron microscopy structures (PDB IDs: 6ADQ and 6HWH) of the cytochrome bc1-aa3 supercomplex that aid in the development of effective and potent inhibitors for M. tuberculosis. In recent years, a number of potential candidates targeting the QcrB subunit of the cytochrome bc1 complex have been developed. In this review, we describe the recently identified inhibitors that target the electron transport chain's terminal oxidase enzyme in M. tuberculosis, specifically the QcrB subunit of the cytochrome bc1 complex.
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Affiliation(s)
- Mushtaq Ahmad Wani
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, West Bengal, 700054, India
| | - Devendra Kumar Dhaked
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, West Bengal, 700054, India.
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8
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Sindhu T, Debnath P. Cytochrome bc1-aa3 oxidase supercomplex as emerging and potential drug target against tuberculosis. Curr Mol Pharmacol 2021; 15:380-392. [PMID: 34602044 DOI: 10.2174/1874467214666210928152512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/26/2021] [Accepted: 06/06/2021] [Indexed: 11/22/2022]
Abstract
The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. The electron transfer from a variety of donors into oxygen through the respiratory electron transport chain is essential to pump protons across the membrane creating an electrochemical transmembrane gradient (proton motive force, PMF) that regulates the synthesis of ATP via the oxidative phosphorylation process. Cytochrome bc1-aa3 supercomplex in M. tuberculosis is, therefore, a major drug target for antibiotic action. In recent years, several respiratory chain components have been targeted for developing new candidate drugs, illustrating the therapeutic potential of obstructing energy conversion of M. tuberculosis. The recently available cryo-EM structure of mycobacterial cytochrome bc1-aa3 supercomplex with open and closed conformations has opened new avenues for understanding its structure and function for developing more effective, new therapeutics against pulmonary tuberculosis. In this review, we discuss the role and function of several components, subunits, and drug targeting elements of the supercomplex cytochrome bc1-aa3, and its potential inhibitors in detail.
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Affiliation(s)
- Thangaraj Sindhu
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
| | - Pal Debnath
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
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9
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Di Trani JM, Liu Z, Whitesell L, Brzezinski P, Cowen LE, Rubinstein JL. Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III. Structure 2021; 30:129-138.e4. [PMID: 34525326 DOI: 10.1016/j.str.2021.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 11/26/2022]
Abstract
Electron transfer between respiratory complexes drives transmembrane proton translocation, which powers ATP synthesis and membrane transport. The homodimeric respiratory complex III (CIII2) oxidizes ubiquinol to ubiquinone, transferring electrons to cytochrome c and translocating protons through a mechanism known as the Q cycle. The Q cycle involves ubiquinol oxidation and ubiquinone reduction at two different sites within each CIII monomer, as well as movement of the head domain of the Rieske subunit. We determined structures of Candida albicans CIII2 by cryoelectron microscopy (cryo-EM), revealing endogenous ubiquinone and visualizing the continuum of Rieske head domain conformations. Analysis of these conformations does not indicate cooperativity in the Rieske head domain position or ligand binding in the two CIIIs of the CIII2 dimer. Cryo-EM with the indazole derivative Inz-5, which inhibits fungal CIII2 and is fungicidal when administered with fungistatic azole drugs, showed that Inz-5 inhibition alters the equilibrium of Rieske head domain positions.
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Affiliation(s)
- Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Zhongle Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, Stockholm, Sweden.
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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10
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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11
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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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12
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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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13
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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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14
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Cheng H, Yang L, Liu HF, Zhang R, Chen C, Wu Y, Jiang W. N-(4-(2-chloro-4-(trifluoromethyl)phenoxy)phenyl)picolinamide as a new inhibitor of mitochondrial complex III: Synthesis, biological evaluation and computational simulations. Bioorg Med Chem Lett 2020; 30:127302. [DOI: 10.1016/j.bmcl.2020.127302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/15/2020] [Accepted: 05/31/2020] [Indexed: 01/23/2023]
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15
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Xiong MQ, Chen T, Wang YX, Zhu XL, Yang GF. Design and synthesis of potent inhibitors of bc 1 complex based on natural product neopeltolide. Bioorg Med Chem Lett 2020; 30:127324. [PMID: 32631529 DOI: 10.1016/j.bmcl.2020.127324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Neopeltolide, a natural product isolated from deep-water sponge specimen of the family neopeltidae, has been proven to be a novel inhibitor of cytochrome bc1. In this study, a series of neopeltolide derivatives was designed by replacing the 14-membered macrolactone with indole ring and confirmed by 1H NMR, 13C NMR, and HRMS. Based on the binding mode of 12h with bc1 complex, the IC50 values of compounds 16a-f (ranging from 0.70 to 1.46 μM) were improved significantly than the ester derivatives 12a-u by replacing the ester with amide linker. Subsequently, the molecular docking results indicated that compound 16e could form a π-π interaction with Phe274 and two H-bonds with Glu271 and His161 and the latter H-bond was found to account for its high activity. The present work accelerates the discovery of novel bc1 complex inhibitors to deal with the resistance that the existing bc1 complex inhibitors are facing and provides a valuable idea for the design of new fungicides.
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Affiliation(s)
- Mao-Qian Xiong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China
| | - Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China
| | - Yu-Xia Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, PR China.
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16
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Li Y, Lin J, Yao W, Gao G, Jing D, Wu Y. Discovery of a new fungicide by screening triazole sulfonylhydrazone derivatives and its downy mildew inhibition in cucumber. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yitao Li
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Jian Lin
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Wenqiang Yao
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Guoliang Gao
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Dewang Jing
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Yang Wu
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
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17
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Cheng H, Liu HF, Yang L, Zhang R, Chen C, Wu Y, Jiang W. N-(3,5-Dichloro-4-(2,4,6-trichlorophenoxy)phenyl)benzenesulfonamide: A new dual-target inhibitor of mitochondrial complex II and complex III via structural simplification. Bioorg Med Chem 2020; 28:115299. [DOI: 10.1016/j.bmc.2019.115299] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/19/2019] [Accepted: 12/26/2019] [Indexed: 12/22/2022]
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18
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Zhu G, Zeng H, Zhang S, Juli J, Pang X, Hoffmann J, Zhang Y, Morgner N, Zhu Y, Peng G, Michel H, Sun F. A 3.3 Å‐Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guoliang Zhu
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100101 China
| | - Hui Zeng
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Shuangbo Zhang
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Jana Juli
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | | | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry Goethe University Max-von Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Yan Zhang
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry Goethe University Max-von Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Yun Zhu
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Guohong Peng
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Fei Sun
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100101 China
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19
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Zhu G, Zeng H, Zhang S, Juli J, Pang X, Hoffmann J, Zhang Y, Morgner N, Zhu Y, Peng G, Michel H, Sun F. A 3.3 Å-Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability. Angew Chem Int Ed Engl 2020; 59:343-351. [PMID: 31778296 PMCID: PMC7004027 DOI: 10.1002/anie.201911554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/06/2019] [Indexed: 01/01/2023]
Abstract
Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc1 complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc1 complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c1 was found to greatly enhance the interaction between cyt. b and cyt. c1 , and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc1 complex in an extreme thermal environment.
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Affiliation(s)
- Guoliang Zhu
- National Laboratory of BiomacromoleculesInstitute of Biophysics (IBP)Chinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Hui Zeng
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Strasse 360438Frankfurt am MainGermany
| | - Shuangbo Zhang
- National Laboratory of BiomacromoleculesInstitute of Biophysics (IBP)Chinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Jana Juli
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Strasse 360438Frankfurt am MainGermany
| | | | - Jan Hoffmann
- Institute of Physical and Theoretical ChemistryGoethe UniversityMax-von Laue-Strasse 760438Frankfurt am MainGermany
| | - Yan Zhang
- National Laboratory of BiomacromoleculesInstitute of Biophysics (IBP)Chinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Nina Morgner
- Institute of Physical and Theoretical ChemistryGoethe UniversityMax-von Laue-Strasse 760438Frankfurt am MainGermany
| | - Yun Zhu
- National Laboratory of BiomacromoleculesInstitute of Biophysics (IBP)Chinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Guohong Peng
- National Laboratory of BiomacromoleculesInstitute of Biophysics (IBP)Chinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Strasse 360438Frankfurt am MainGermany
| | - Hartmut Michel
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Strasse 360438Frankfurt am MainGermany
| | - Fei Sun
- National Laboratory of BiomacromoleculesInstitute of Biophysics (IBP)Chinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
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20
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Li Y, Yao W, Lin J, Li F, Wu Y, Xu J. Design, Synthesis, and Biological Activity of Novel Triazole Sulfonamide Derivatives Containing a Benzylamine Moiety. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yitao Li
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Wenqiang Yao
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Jian Lin
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Falin Li
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Yang Wu
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Junxing Xu
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
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21
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Esser L, Zhou F, Yu CA, Xia D. Crystal structure of bacterial cytochrome bc 1 in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit. J Biol Chem 2019; 294:12007-12019. [PMID: 31182483 DOI: 10.1074/jbc.ra119.008381] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/06/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochrome bc 1 complexes (cyt bc 1), also known as complex III in mitochondria, are components of the cellular respiratory chain and of the photosynthetic apparatus of non-oxygenic photosynthetic bacteria. They catalyze electron transfer (ET) from ubiquinol to cytochrome c and concomitantly translocate protons across the membrane, contributing to the cross-membrane potential essential for a myriad of cellular activities. This ET-coupled proton translocation reaction requires a gating mechanism that ensures bifurcated electron flow. Here, we report the observation of the Rieske iron-sulfur protein (ISP) in a mobile state, as revealed by the crystal structure of cyt bc 1 from the photosynthetic bacterium Rhodobacter sphaeroides in complex with the fungicide azoxystrobin. Unlike cyt bc 1 inhibitors stigmatellin and famoxadone that immobilize the ISP, azoxystrobin causes the ISP-ED to separate from the cyt b subunit and to remain in a mobile state. Analysis of anomalous scattering signals from the iron-sulfur cluster of the ISP suggests the existence of a trajectory for electron delivery. This work supports and solidifies the hypothesis that the bimodal conformation switch of the ISP provides a gating mechanism for bifurcated ET, which is essential to the Q-cycle mechanism of cyt bc 1 function.
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Affiliation(s)
- Lothar Esser
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Fei Zhou
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.
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22
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Zhu XL, Zhang R, Wu QY, Song YJ, Wang YX, Yang JF, Yang GF. Natural Product Neopeltolide as a Cytochrome bc 1 Complex Inhibitor: Mechanism of Action and Structural Modification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:2774-2781. [PMID: 30794394 DOI: 10.1021/acs.jafc.8b06195] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The marine natural product neopeltolide was isolated from a deep-water sponge specimen of the family Neopeltidae. Neopeltolide has been proven to be a new type of inhibitor of the cytochrome bc1 complex in the mitochondrial respiration chain. However, its detailed inhibition mechanism has remained unknown. In addition, neopeltolide is difficult to synthesize because of its very complex chemical structure. In the present work, the binding mode of neopeltolide was determined for the first time by integrating molecular docking, molecular dynamics simulations, and molecular mechanics Poisson-Boltzmann surface area calculations, which showed that neopeltolide is a Qo site inhibitor of the bc1 complex. Then, according to guidance via inhibitor-protein interaction analysis, structural modification was carried out with the aim to simplify the chemical structure of neopeltolide, leading to the synthesis of a series of new neopeltolide derivatives with much simpler chemical structures. The calculated binding energies (Δ Gcal) of the newly synthesized analogues correlated very well ( R2 = 0.90) with their experimental binding free energies (Δ Gexp), which confirmed that the computational protocol was reliable. Compound 45, bearing a diphenyl ether fragment, was successfully designed and synthesized as the most potent candidate (IC50 = 12 nM) against porcine succinate cytochrome c reductase. The molecular modeling results indicate that compound 45 formed a π-π interaction with Phe274 and two hydrogen bonds with Glu271 and His161. The present work provides a new starting point for future fungicide discovery to overcome the resistance that the existing bc1 complex inhibitors are facing.
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Affiliation(s)
- Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
| | - Rui Zhang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
| | - Qiong-You Wu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
| | - Yong-Jun Song
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
| | - Yu-Xia Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology , Central China Normal University , Wuhan , Hubei 430079 , People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , People's Republic of China
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23
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Synthesis, biochemical evaluation and computational simulations of new cytochrome bc1 complex inhibitors based on N-(4-aryloxyphenyl) phthalimides. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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24
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Dreinert A, Wolf A, Mentzel T, Meunier B, Fehr M. The cytochrome bc complex inhibitor Ametoctradin has an unusual binding mode. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:567-576. [DOI: 10.1016/j.bbabio.2018.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/11/2018] [Accepted: 04/23/2018] [Indexed: 11/27/2022]
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25
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Cheng H, Song W, Nie R, Wang YX, Li HL, Jiang XS, Wu JJ, Chen C, Wu QY. Synthesis of new 4-aryloxy- N -arylanilines and their inhibitory activities against succinate-cytochrome c reductase. Bioorg Med Chem Lett 2018; 28:1330-1335. [DOI: 10.1016/j.bmcl.2018.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/23/2018] [Accepted: 03/05/2018] [Indexed: 11/26/2022]
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26
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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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27
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Abstract
This chapter presents an overview of structural properties of the cytochrome (Cyt) b 6 f complex and its functioning in chloroplasts. The Cyt b 6 f complex stands at the crossroad of photosynthetic electron transport pathways, providing connectivity between Photosystem (PSI) and Photosysten II (PSII) and pumping protons across the membrane into the thylakoid lumen. After a brief review of the chloroplast electron transport chain, the consideration is focused on the structural organization of the Cyt b 6 f complex and its interaction with plastoquinol (PQH2, reduced form of plastoquinone), a mediator of electron transfer from PSII to the Cyt b 6 f complex. The processes of PQH2 oxidation by the Cyt b 6 f complex have been considered within the framework of the Mitchell's Q-cycle. The overall rate of the intersystem electron transport is determined by PQH2 turnover at the quinone-binding site Qo of the Cyt b 6 f complex. The rate of PQH2 oxidation is controlled by the intrathylakoid pHin, which value determines the protonation/deprotonation events in the Qo-center. Two other regulatory mechanisms associated with the Cyt b 6 f complex are briefly overviewed: (i) redistribution of electron fluxes between alternative (linear and cyclic) pathways, and (ii) "state transitions" related to redistribution of solar energy between PSI and PSII.
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28
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Crofts AR, Rose SW, Burton RL, Desai AV, Kenis PJA, Dikanov SA. The Q-Cycle Mechanism of the bc1 Complex: A Biologist’s Perspective on Atomistic Studies. J Phys Chem B 2017; 121:3701-3717. [DOI: 10.1021/acs.jpcb.6b10524] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Antony R. Crofts
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Stuart W. Rose
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Rodney L. Burton
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Amit V. Desai
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Paul J. A. Kenis
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sergei A. Dikanov
- Department
of Veterinary Clinical Medicine, University of Illinois at Urbana−Champaign, 1008 West Hazelwood Drive, Urbana, Illinois 61801, United States
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29
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Zhang R, Wu QY, Tao J, Pan JH, Yang GF. An ionic liquid promoted approach to bitriazolyl compounds as succinate–ubiquinone oxidoreductase inhibitors. NEW J CHEM 2017. [DOI: 10.1039/c6nj02454h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bitriazolyl compounds, a novel skeleton that is totally different from existing commercialized SQR-inhibiting fungicides, could provide a new lead for further development of SQR inhibitors.
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Affiliation(s)
- Rui Zhang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Qiong-You Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Jun Tao
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Jin-Huan Pan
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
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30
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Francia F, Malferrari M, Lanciano P, Steimle S, Daldal F, Venturoli G. The cytochrome b Zn binding amino acid residue histidine 291 is essential for ubihydroquinone oxidation at the Q o site of bacterial cytochrome bc 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1796-1806. [PMID: 27550309 DOI: 10.1016/j.bbabio.2016.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/27/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022]
Abstract
The ubiquinol:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important membrane protein complex in photosynthetic and respiratory energy transduction. In bacteria such as Rhodobacter capsulatus it is constituted of three subunits: the iron-sulfur protein, cyt b and cyt c1, which form two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the pathways of bifurcated electron transfers emanating from QH2 oxidation are known, but the associated proton release routes are not well defined. In energy transducing complexes, Zn2+ binding amino acid residues often correlate with proton uptake or release pathways. Earlier, using combined EXAFS and structural studies, we identified Zn coordinating residues of mitochondrial and bacterial cyt bc1. In this work, using the genetically tractable bacterial cyt bc1, we substituted each of the proposed Zn binding residues with non-protonatable side chains. Among these mutants, only the His291Leu substitution destroyed almost completely the Qo site catalysis without perturbing significantly the redox properties of the cofactors or the assembly of the complex. In this mutant, which is unable to support photosynthetic growth, the bifurcated electron transfer reactions that result from QH2 oxidation at the Qo site, as well as the associated proton(s) release, were dramatically impaired. Based on these findings, on the putative role of His291 in liganding Zn, and on its solvent exposed and highly conserved position, we propose that His291 of cyt b is critical for proton release associated to QH2 oxidation at the Qo site of cyt bc1.
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Affiliation(s)
- Francesco Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Pascal Lanciano
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefan Steimle
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, 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
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31
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Ekiert R, Borek A, Kuleta P, Czernek J, Osyczka A. Mitochondrial disease-related mutations at the cytochrome b-iron-sulfur protein (ISP) interface: Molecular effects on the large-scale motion of ISP and superoxide generation studied in Rhodobacter capsulatus cytochrome bc1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1102-1110. [PMID: 27032290 PMCID: PMC4906154 DOI: 10.1016/j.bbabio.2016.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 01/06/2023]
Abstract
One of the important elements of operation of cytochrome bc1 (mitochondrial respiratory complex III) is a large scale movement of the head domain of iron–sulfur protein (ISP-HD), which connects the quinol oxidation site (Qo) located within the cytochrome b, with the outermost heme c1 of cytochrome c1. Several mitochondrial disease-related mutations in cytochrome b are located at the cytochrome b-ISP-HD interface, thus their molecular effects can be associated with altered motion of ISP-HD. Using purple bacterial model, we recently showed that one of such mutations — G167P shifts the equilibrium position of ISP-HD towards positions remote from the Qo site as compared to the native enzyme [Borek et al., J. Biol. Chem. 290 (2015) 23781-23792]. This resulted in the enhanced propensity of the mutant to generate reactive oxygen species (ROS) which was explained on the basis of the model evoking “semireverse” electron transfer from heme bL to quinone. Here we examine another mutation from that group — G332D (G290D in human), finding that it also shifts the equilibrium position of ISP-HD in the same direction, however displays less of the enhancement in ROS production. We provide spectroscopic indication that G332D might affect the electrostatics of interaction between cytochrome b and ISP-HD. This effect, in light of the measured enzymatic activities and electron transfer rates, appears to be less severe than structural distortion caused by proline in G167P mutant. Comparative analysis of the effects of G332D and G167P confirms a general prediction that mutations located at the cytochrome b-ISP-HD interface influence the motion of ISP-HD and indicates that “pushing” ISP-HD away from the Qo site is the most likely outcome of this influence. It can also be predicted that an increase in ROS production associated with the “pushing” effect is quite sensitive to overall severity of this change with more active mutants being generally more protected against elevated ROS. This article is part of a Special Issue entitled ‘EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2–6, 2016’, edited by Prof. Paolo Bernardi. Several mitochondrial mutations are located at the cytochrome b-ISP interface. We compare molecular effects of two mutations from that group. In both mutants ISP is shifted away from the Qo catalytic site. This effect is generally associated with increased ROS production. More active mutants are more protected against elevated ROS.
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Affiliation(s)
- Robert Ekiert
- 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
| | - Patryk Kuleta
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Justyna Czernek
- 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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Fehr M, Wolf A, Stammler G. Binding of the respiratory chain inhibitor ametoctradin to the mitochondrial bc1 complex. PEST MANAGEMENT SCIENCE 2016; 72:591-602. [PMID: 25914236 DOI: 10.1002/ps.4031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Ametoctradin is an agricultural fungicide that inhibits the mitochondrial bc1 complex of oomycetes. The bc1 complex has two quinone binding sites that can be addressed by inhibitors. Depending on their binding sites and binding modes, the inhibitors show different degrees of cross-resistance that need to be considered when designing spray programmes for agricultural fungicides. The binding site of ametoctradin was unknown. RESULTS Cross-resistance analyses, the reduction of isolated Pythium sp. bc1 complex in the presence of different inhibitors and molecular modelling studies were used to analyse the binding site and binding mode of ametoctradin. All three approaches provide data supporting the argument that ametoctradin binds to the Pythium bc1 complex similarly to stigmatellin. CONCLUSION The binding mode of ametoctradin differs from other agricultural fungicides such as cyazofamid and the strobilurins. This explains the lack of cross-resistance with strobilurins and related inhibitors, where resistance is mainly caused by G143A amino acid exchange. Accordingly, mixtures or alternating applications of these fungicides and ametoctradin can help to minimise the risk of the emergence of new resistant isolates.
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Affiliation(s)
- Marcus Fehr
- BASF SE, Crop Protection, Limburgerhof, Germany
| | - Antje Wolf
- BASF SE, Biological and Effect Systems Research, Ludwigshafen, Germany
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Chen C, Wu QY, Shan LY, Zhang B, Verpoort F, Yang GF. Discovery of cytochrome bc1 complex inhibitors inspired by the natural product karrikinolide. RSC Adv 2016. [DOI: 10.1039/c6ra19424a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Novel and potent inhibitors targeting the cytochrome bc1 complex were discovered from the natural product karrikinolide for the first time.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Qiong-You Wu
- Key Laboratory of Pesticide & Chemical Biology
- College of Chemistry
- Central China Normal University
- Wuhan 430079
- P. R. China
| | - Lian-Ying Shan
- Key Laboratory of Pesticide & Chemical Biology
- College of Chemistry
- Central China Normal University
- Wuhan 430079
- P. R. China
| | - Bei Zhang
- Key Laboratory of Pesticide & Chemical Biology
- College of Chemistry
- Central China Normal University
- Wuhan 430079
- P. R. China
| | - Francis Verpoort
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology
- College of Chemistry
- Central China Normal University
- Wuhan 430079
- P. R. China
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34
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Borek A, Kuleta P, Ekiert R, Pietras R, Sarewicz M, Osyczka A. Mitochondrial Disease-related Mutation G167P in Cytochrome b of Rhodobacter capsulatus Cytochrome bc1 (S151P in Human) Affects the Equilibrium Distribution of [2Fe-2S] Cluster and Generation of Superoxide. J Biol Chem 2015; 290:23781-92. [PMID: 26245902 PMCID: PMC4583038 DOI: 10.1074/jbc.m115.661314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Indexed: 12/04/2022] Open
Abstract
Cytochrome bc1 is one of the key enzymes of many bioenergetic systems. Its operation involves a large scale movement of a head domain of iron-sulfur protein (ISP-HD), which functionally connects the catalytic quinol oxidation Qo site in cytochrome b with cytochrome c1. The Qo site under certain conditions can generate reactive oxygen species in the reaction scheme depending on the actual position of ISP-HD in respect to the Qo site. Here, using a bacterial system, we show that mutation G167P in cytochrome b shifts the equilibrium distribution of ISP-HD toward positions remote from the Qo site. This renders cytochrome bc1 non-functional in vivo. This effect is remediated by addition of alanine insertions (1Ala and 2Ala) in the neck region of the ISP subunit. These insertions, which on their own shift the equilibrium distribution of ISP-HD in the opposite direction (i.e. toward the Qo site), also act in this manner in the presence of G167P. Changes in the equilibrium distribution of ISP-HD in G167P lead to an increased propensity of cytochrome bc1 to generate superoxide, which becomes evident when the concentration of quinone increases. This result corroborates the recently proposed model in which “semireverse” electron transfer back to the Qo site, occurring when ISP-HD is remote from the site, favors reactive oxygen species production. G167P suggests possible molecular effects of S151P (corresponding in sequence to G167P) identified as a mitochondrial disease-related mutation in human cytochrome b. These effects may be valid for other human mutations that change the equilibrium distribution of ISP-HD in a manner similar to G167P.
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Affiliation(s)
- Arkadiusz Borek
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Patryk Kuleta
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Robert Ekiert
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Marcin Sarewicz
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Artur Osyczka
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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35
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Vladkova R. Chlorophyllais the crucial redox sensor and transmembrane signal transmitter in the cytochromeb6fcomplex. Components and mechanisms of state transitions from the hydrophobic mismatch viewpoint. J Biomol Struct Dyn 2015; 34:824-54. [DOI: 10.1080/07391102.2015.1056551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Markevich NI, Hoek JB. Computational modeling analysis of mitochondrial superoxide production under varying substrate conditions and upon inhibition of different segments of the electron transport chain. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1847:656-79. [PMID: 25868872 PMCID: PMC4426091 DOI: 10.1016/j.bbabio.2015.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 03/24/2015] [Accepted: 04/06/2015] [Indexed: 12/13/2022]
Abstract
A computational mechanistic model of superoxide (O2•-) formation in the mitochondrial electron transport chain (ETC) was developed to facilitate the quantitative analysis of factors controlling mitochondrial O2•- production and assist in the interpretation of experimental studies. The model takes into account all individual electron transfer reactions in Complexes I and III. The model accounts for multiple, often seemingly contradictory observations on the effects of ΔΨ and ΔpH, and for the effects of multiple substrate and inhibitor conditions, including differential effects of Complex III inhibitors antimycin A, myxothiazol and stigmatellin. Simulation results confirm that, in addition to O2•- formation in Complex III and at the flavin site of Complex I, the quinone binding site of Complex I is an additional superoxide generating site that accounts for experimental observations on O2•- production during reverse electron transfer. However, our simulation results predict that, when cytochrome c oxidase is inhibited during oxidation of succinate, ROS production at this site is eliminated and almost all superoxide in Complex I is generated by reduced FMN, even when the redox pressure for reverse electron transfer from succinate is strong. In addition, the model indicates that conflicting literature data on the kinetics of electron transfer in Complex III involving the iron-sulfur protein-cytochrome bL complex can be resolved in favor of a dissociation of the protein only after electron transfer to cytochrome bH. The model predictions can be helpful in understanding factors driving mitochondrial superoxide formation in intact cells and tissues.
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Affiliation(s)
- Nikolai I Markevich
- MitoCare Center for Mitochondrial Research, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 14290, Russia.
| | - Jan B Hoek
- MitoCare Center for Mitochondrial Research, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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37
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Zhu X, Zhang M, Liu J, Ge J, Yang G. Ametoctradin is a potent Qo site inhibitor of the mitochondrial respiration complex III. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3377-3386. [PMID: 25784492 DOI: 10.1021/acs.jafc.5b00228] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ametoctradin is a new Oomycete-specific fungicide under development by BASF. It is a potent inhibitor of the bc1 complex in mitochondrial respiration. However, its detailed action mechanism remains unknown. In the present work, the binding mode of ametoctradin was first uncovered by integrating molecular docking, MD simulations, and MM/PBSA calculations, which showed that ametoctradin should be a Q(o) site inhibitor of bc1 complex. Subsequently, a series of new 1,2,4-triazolo[1,5-a]pyrimidine derivatives were designed and synthesized to further understand the substituent effects on the 5- and 6-position of 1,2,4-triazolo[1,5-a]pyrimidine. The calculated binding free energies (ΔG(cal)) of newly synthesized analogues as Qo site inhibitors correlated very well (R(2) = 0.96) with their experimental binding free energies (ΔG(exp)). Two compounds (4a and 4c) with higher inhibitory activity against porcine SQR than ametoctradin were successfully identified. The structural and mechanistic insights obtained from the present study will provide a valuable clue for future designing of a new promising bc1 inhibitor.
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Affiliation(s)
- Xiaolei Zhu
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Mengmeng Zhang
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Jingjing Liu
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Jingming Ge
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Guangfu Yang
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
- ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 30071, P.R.China
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38
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Qu Y, Dong F. New methods for determining proton pumping ability and electron transfer activity of the cytochrome bc1 complex. Acta Biochim Biophys Sin (Shanghai) 2015; 47:114-20. [PMID: 25543120 DOI: 10.1093/abbs/gmu126] [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: 11/13/2022] Open
Abstract
It is important to determine the electron transfer activity and proton pumping ability of the cytochrome bc1 complex for better understanding its structure and function. In this study, several methods for determining the electron transfer and proton pumping of the bc1 complex, including the traditional and the new methods, are presented and evaluated. For determining the proton pumping ability of the bc1 complex, the new stopped-flow method has a higher accuracy than the traditional pH meter method, and the new spectrophotometer method is more convenient than the traditional pH meter method. In measuring the electron transfer activity of the bc1 complex, the new stopped-flow method is more accurate and has a higher separating capacity than the traditional spectrophotometer method.
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Affiliation(s)
- Yuangang Qu
- College of Life Sciences, Linyi University, Linyi 276000, China Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater 74078, USA
| | - Fang Dong
- College of Life Sciences, Linyi University, Linyi 276000, China
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39
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Cheng H, Shen YQ, Pan XY, Hou YP, Wu QY, Yang GF. Discovery of 1,2,4-triazole-1,3-disulfonamides as dual inhibitors of mitochondrial complex II and complex III. NEW J CHEM 2015. [DOI: 10.1039/c5nj00215j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1,2,4-Triazole-1,3-disulfonamide derivatives as dual function inhibitors of mitochondrial complex II (SQR) and complex III (cyt bc1) were discovered.
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Affiliation(s)
- Hua Cheng
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Yan-Qing Shen
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Xia-Yan Pan
- Department of Pesticide Science
- College of Plant Protection
- Nanjing Agricultural University
- Nanjing 210095
- P. R. China
| | - Yi-Ping Hou
- Department of Pesticide Science
- College of Plant Protection
- Nanjing Agricultural University
- Nanjing 210095
- P. R. China
| | - Qiong-You Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
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40
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Tikhonov AN. The cytochrome b6f complex at the crossroad of photosynthetic electron transport pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:163-83. [PMID: 24485217 DOI: 10.1016/j.plaphy.2013.12.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/11/2013] [Indexed: 05/03/2023]
Abstract
Regulation of photosynthetic electron transport at the level of the cytochrome b6f complex provides efficient performance of the chloroplast electron transport chain (ETC). In this review, after brief overview of the structural organization of the chloroplast ETC, the consideration of the problem of electron transport control is focused on the plastoquinone (PQ) turnover and its interaction with the b6f complex. The data available show that the rates of plastoquinol (PQH2) formation in PSII and its diffusion to the b6f complex do not limit the overall rate of electron transfer between photosystem II (PSII) and photosystem I (PSI). Analysis of experimental and theoretical data demonstrates that the rate-limiting step in the intersystem chain of electron transport is determined by PQH2 oxidation at the Qo-site of the b6f complex, which is accompanied by the proton release into the thylakoid lumen. The acidification of the lumen causes deceleration of PQH2 oxidation, thus impeding the intersystem electron transport. Two other mechanisms of regulation of the intersystem electron transport have been considered: (i) "state transitions" associated with the light-induced redistribution of solar energy between PSI and PSII, and (ii) redistribution of electron fluxes between alternative pathways (noncyclic electron transport and cyclic electron flow around PSI).
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41
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Esser L, Yu CA, Xia D. Structural basis of resistance to anti-cytochrome bc₁ complex inhibitors: implication for drug improvement. Curr Pharm Des 2014; 20:704-24. [PMID: 23688079 PMCID: PMC4788501 DOI: 10.2174/138161282005140214163327] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 05/09/2013] [Indexed: 11/22/2022]
Abstract
The emergence of drug resistance has devastating economic and social consequences, a testimonial of which is the rise and fall of inhibitors against the respiratory component cytochrome bc₁ complex, a time tested and highly effective target for disease control. Unfortunately, the mechanism of resistance is a multivariate problem, including primarily mutations in the gene of the cytochrome b subunit but also activation of alternative pathways of ubiquinol oxidation and pharmacokinetic effects. There is a considerable interest in designing new bc₁ inhibitors with novel modes of binding and lower propensity to induce the development of resistance. The accumulation of crystallographic data of bc₁ complexes with and without inhibitors bound provides the structural basis for rational drug design. In particular, the cytochrome b subunit offers two distinct active sites that can be targeted for inhibition - the quinol oxidation site and the quinone reduction site. This review brings together available structural information of inhibited bc₁ by various quinol oxidation- and reductionsite inhibitors, the inhibitor binding modes, conformational changes upon inhibitor binding of side chains in the active site and large scale domain movements of the iron-sulfur protein subunit. Structural data analysis provides a clear understanding of where and why existing inhibitors fail and points towards promising alternatives.
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Affiliation(s)
| | | | - Di Xia
- Laboratory of Cell Biology, NCI, NIH, 37 Convent Dr., Building 37, Room 2122C, Bethesda MD 20892.
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42
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Dibrova DV, Cherepanov DA, Galperin MY, Skulachev VP, Mulkidjanian AY. Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1407-27. [PMID: 23871937 PMCID: PMC3839093 DOI: 10.1016/j.bbabio.2013.07.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/30/2022]
Abstract
This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On the one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Daria V Dibrova
- School of Physics, University of Osnabrueck, D-49069 Osnabrueck, Germany; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia; Institute of Mitoengineering, Lomonosov Moscow State University, Moscow 119992, Russia
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Xia D, Esser L, Tang WK, Zhou F, Zhou Y, Yu L, Yu CA. Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1278-94. [PMID: 23201476 PMCID: PMC3593749 DOI: 10.1016/j.bbabio.2012.11.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/13/2012] [Accepted: 11/19/2012] [Indexed: 01/18/2023]
Abstract
The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Tikhonov AN. pH-dependent regulation of electron transport and ATP synthesis in chloroplasts. PHOTOSYNTHESIS RESEARCH 2013; 116:511-34. [PMID: 23695653 DOI: 10.1007/s11120-013-9845-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 04/25/2013] [Indexed: 05/02/2023]
Abstract
This review is focused on pH-dependent mechanisms of regulation of photosynthetic electron transport and ATP synthesis in chloroplasts. The light-induced acidification of the thylakoid lumen is known to decelerate the plastoquinol oxidation by the cytochrome b 6 f complex, thus impeding the electron flow between photosystem II and photosystem I. Acidification of the lumen also triggers the dissipation of excess energy in the light-harvesting antenna of photosystem II, thereby protecting the photosynthetic apparatus against a solar stress. After brief description of structural and functional organization of the chloroplast electron transport chain, our attention is focused on the nature of the rate-limiting step of electron transfer between photosystem II and photosystem I. In the context of pH-dependent mechanism of photosynthetic control in chloroplasts, the mechanisms of plastoquinol oxidation by the cytochrome b 6 f complex have been considered. The light-induced alkalization of stroma is another factor of pH-dependent regulation of electron transport in chloroplasts. Alkalization of stroma induces activation of the Bassham-Benson-Calvin cycle reactions, thereby promoting efflux of electrons from photosystem I to NADP(+). The mechanisms of the light-induced activation of ATP synthase are briefly considered.
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Affiliation(s)
- Alexander N Tikhonov
- Department of Biophysics, Faculty of Physics, M. V. Lomonosov, Moscow State University, Moscow, Russia,
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Vennam PR, Fisher N, Krzyaniak MD, Kramer DM, Bowman MK. A caged, destabilized, free radical intermediate in the q-cycle. Chembiochem 2013; 14:1745-53. [PMID: 24009094 PMCID: PMC3951126 DOI: 10.1002/cbic.201300265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 11/12/2022]
Abstract
The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase (Qo ) sites, in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models have been proposed. In previous work, we trapped a Q-cycle semiquinone anion intermediate, termed SQo , in bacterial cytochrome bc1 by rapid freeze-quenching. In this work, we apply pulsed-EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and can even be destabilized with respect to solution. It is trapped in Qo at a site that is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analyses show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves "stripping" of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL while minimizing certain Q-cycle bypass reactions, including oxidation of prereduced cytochrome b and reduction of O2 .
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Affiliation(s)
- Preethi R. Vennam
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - Nicholas Fisher
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Matthew D. Krzyaniak
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - David M. Kramer
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Michael K. Bowman
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
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Li H, Zhu XL, Yang WC, Yang GF. Comparative Kinetics ofQiSite Inhibitors of Cytochromebc1Complex: Picomolar Antimycin and Micromolar Cyazofamid. Chem Biol Drug Des 2013; 83:71-80. [DOI: 10.1111/cbdd.12199] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/17/2013] [Accepted: 07/26/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Li
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
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Berry EA, De Bari H, Huang LS. Unanswered questions about the structure of cytochrome bc1 complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1258-77. [PMID: 23624176 DOI: 10.1016/j.bbabio.2013.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/13/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
Abstract
X-ray crystal structures of bc1 complexes obtained over the last 15 years have provided a firm structural basis for our understanding of the complex. For the most part there is good agreement between structures from different species, different crystal forms, and with different inhibitors bound. In this review we focus on some of the remaining unexplained differences, either between the structures themselves or the interpretations of the structural observations. These include the structural basis for the motion of the Rieske iron-sulfur protein in response to inhibitors, a possible conformational change involving tyrosine132 of cytochrome (cyt) b, the presence of cis-peptides at the beginnings of transmembrane helices C, E, and H, the structural insight into the function of the so-called "Core proteins", different modelings of the retained signal peptide, orientation of the low-potential heme b, and chirality of the Met ligand to heme c1. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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Al-Attar S, de Vries S. Energy transduction by respiratory metallo-enzymes: From molecular mechanism to cell physiology. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Bleier L, Dröse S. Superoxide generation by complex III: from mechanistic rationales to functional consequences. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1320-31. [PMID: 23269318 DOI: 10.1016/j.bbabio.2012.12.002] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/05/2012] [Accepted: 12/12/2012] [Indexed: 01/21/2023]
Abstract
Apart from complex I (NADH:ubiquinone oxidoreductase) the mitochondrial cytochrome bc1 complex (complex III; ubiquinol:cytochrome c oxidoreductase) has been identified as the main producer of superoxide and derived reactive oxygen species (ROS) within the mitochondrial respiratory chain. Mitochondrial ROS are generally linked to oxidative stress, aging and other pathophysiological settings like in neurodegenerative diseases. However, ROS produced at the ubiquinol oxidation center (center P, Qo site) of complex III seem to have additional physiological functions as signaling molecules during cellular processes like the adaptation to hypoxia. The molecular mechanism of superoxide production that is mechanistically linked to the electron bifurcation during ubiquinol oxidation is still a matter of debate. Some insight comes from extensive kinetic studies with mutated complexes from yeast and bacterial cytochrome bc1 complexes. This review is intended to bridge the gap between those mechanistic studies and investigations on complex III ROS in cellular signal transduction and highlights factors that impact superoxide generation. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Lea Bleier
- Molecular Bioenergetics Group, Medical School, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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Victoria D, Burton R, Crofts AR. Role of the -PEWY-glutamate in catalysis at the Q(o)-site of the Cyt bc(1) complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:365-86. [PMID: 23123515 DOI: 10.1016/j.bbabio.2012.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 01/09/2023]
Abstract
We re-examine the pH dependence of partial processes of ubihydroquinone (QH(2)) turnover in Glu-295 mutants in Rhodobacter sphaeroides to clarify the mechanistic role. In more crippled mutants, the bell-shaped pH profile of wildtype was replaced by dependence on a single pK at ~8.5 favoring electron transfer. Loss of the pK at 6.5 reflects a change in the rate-limiting step from the first to the second electron transfer. Over the range of pH 6-8, no major pH dependence of formation of the initial reaction complex was seen, and the rates of bypass reactions were similar to the wildtype. Occupancy of the Q(o)-site by semiquinone (SQ) was similar in the wildtype and the Glu→Trp mutant. Since heme b(L) is initially oxidized in the latter, the bifurcated reaction can still occur, allowing estimation of an empirical rate constant <10(3)s(-1) for reduction of heme b(L) by SQ from the domain distal from heme b(L), a value 1000-fold smaller than that expected from distance. If the pK ~8.5 in mutant strains is due to deprotonation of the neutral semiquinone, with Q(•-) as electron donor to heme b(L), then in wildtype this low value would preclude mechanisms for normal flux in which semiquinone is constrained to this domain. A kinetic model in which Glu-295 catalyzes H(+) transfer from QH•, and delivery of the H(+) to exit channel(s) by rotational displacement, and facilitates rapid electron transfer from SQ to heme b(L) by allowing Q(•-) to move closer to the heme, accounts well for the observations.
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Affiliation(s)
- Doreen Victoria
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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