1
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Carlström A, Ott M. Insights into conformational changes in cytochrome b during the early steps of its maturation. FEBS Lett 2024; 598:1438-1448. [PMID: 38664235 DOI: 10.1002/1873-3468.14888] [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: 12/12/2023] [Revised: 03/18/2024] [Accepted: 04/03/2024] [Indexed: 06/12/2024]
Abstract
Membrane proteins carrying redox cofactors are key subunits of respiratory chain complexes, yet the exact path of their folding and maturation remains poorly understood. Here, using cryo-EM and structure prediction via Alphafold2, we generated models of early assembly intermediates of cytochrome b (Cytb), a central subunit of complex III. The predicted structure of the first assembly intermediate suggests how the binding of Cytb to the assembly factor Cbp3-Cbp6 imposes an open configuration to facilitate the acquisition of its heme cofactors. Moreover, structure predictions of the second intermediate indicate how hemes get stabilized by binding of the assembly factor Cbp4, with a concomitant weakening of the contact between Cbp3-Cbp6 and Cytb, preparing for the release of the fully hemylated protein from the assembly factors.
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Affiliation(s)
- Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
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2
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Müh F, Bothe A, Zouni A. Towards understanding the crystallization of photosystem II: influence of poly(ethylene glycol) of various molecular sizes on the micelle formation of alkyl maltosides. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01079-5. [PMID: 38488943 DOI: 10.1007/s11120-024-01079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
The influence of poly(ethylene glycol) (PEG) polymers H-(O-CH2-CH2)p-OH with different average molecular sizes p on the micelle formation of n-alkyl-β-D-maltoside detergents with the number of carbon atoms in the alkyl chain ranging from 10 to 12 is investigated with the aim to learn more about the detergent behavior under conditions suitable for the crystallization of the photosynthetic pigment-protein complex photosystem II. PEG is shown to increase the critical micelle concentration (CMC) of all three detergents in the crystallization buffer in a way that the free energy of micelle formation increases linearly with the concentration of oxyethylene units (O-CH2-CH2) irrespective of the actual molecular weight of the polymer. The CMC shift is modeled by assuming for simplicity that it is dominated by the interaction between PEG and detergent monomers and is interpreted in terms of an increase of the transfer free energy of a methylene group of the alkyl chain by 0.2 kJ mol-1 per 1 mol L-1 increase of the concentration of oxyethylene units at 298 K. Implications of this effect for the solubilization and crystallization of protein-detergent complexes as well as detergent extraction from crystals are discussed.
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Affiliation(s)
- Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Strasse 69, 4040, Linz, Austria.
| | - Adrian Bothe
- Institut für Molekularbiologie und Biophysik, ETH Zürich, HPK, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Athina Zouni
- Institut für Biologie, Humboldt Universität zu Berlin, Leonor-Michaelis-Haus, Philippstrasse 13, 10095, Berlin, Germany
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3
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Saha S, Singh P, Dutta A, Vaidya H, Negi PC, Sengupta S, Seth S, Basak T. A Comprehensive Insight and Mechanistic Understanding of the Lipidomic Alterations Associated With DCM. JACC. ASIA 2023; 3:539-555. [PMID: 37614533 PMCID: PMC10442885 DOI: 10.1016/j.jacasi.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 06/03/2023] [Indexed: 08/25/2023]
Abstract
Dilated cardiomyopathy (DCM) is one of the major causes of heart failure characterized by the enlargement of the left ventricular cavity and contractile dysfunction of the myocardium. Lipids are the major sources of energy for the myocardium. Impairment of lipid homeostasis has a potential role in the pathogenesis of DCM. In this review, we have summarized the role of different lipids in the progression of DCM that can be considered as potential biomarkers. Further, we have also explained the mechanistic pathways followed by the lipid molecules in disease progression along with the cardioprotective role of certain lipids. As the global epidemiological status of DCM is alarming, it is high time to define some disease-specific biomarkers with greater prognostic value. We are proposing an adaptation of a system lipidomics-based approach to profile DCM patients in order to achieve a better diagnosis and prognosis of the disease.
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Affiliation(s)
- Shubham Saha
- School of Biosciences and Bioengineering. IIT-Mandi, Mandi, India
- BioX Center, Indian Institute of Technology-Mandi, Mandi, India
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Abhi Dutta
- School of Biosciences and Bioengineering. IIT-Mandi, Mandi, India
- BioX Center, Indian Institute of Technology-Mandi, Mandi, India
| | - Hiteshi Vaidya
- Department of Cardiology, Indira Gandhi Medical College & Hospital, Shimla, India
| | - Prakash Chand Negi
- Department of Cardiology, Indira Gandhi Medical College & Hospital, Shimla, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sandeep Seth
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering. IIT-Mandi, Mandi, India
- BioX Center, Indian Institute of Technology-Mandi, Mandi, India
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4
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Klusch N, Dreimann M, Senkler J, Rugen N, Kühlbrandt W, Braun HP. Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 Å resolution. NATURE PLANTS 2023; 9:142-156. [PMID: 36585502 PMCID: PMC9873573 DOI: 10.1038/s41477-022-01308-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/08/2022] [Indexed: 05/15/2023]
Abstract
Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III2 with a co-purified ubiquinone in the QO site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
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Affiliation(s)
- Niklas Klusch
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany.
| | - Maximilian Dreimann
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Nils Rugen
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany.
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5
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Corey RA, Harrison N, Stansfeld PJ, Sansom MSP, Duncan AL. Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of complexes III and IV. Chem Sci 2022; 13:13489-13498. [PMID: 36507170 PMCID: PMC9682889 DOI: 10.1039/d2sc04072g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
The mitochondrial electron transport chain comprises a series of protein complexes embedded in the inner mitochondrial membrane that generate a proton motive force via oxidative phosphorylation, ultimately generating ATP. These protein complexes can oligomerize to form larger structures called supercomplexes. Cardiolipin (CL), a conical lipid, unique within eukaryotes to the inner mitochondrial membrane, has proven essential in maintaining the stability and function of supercomplexes. Monolysocardiolipin (MLCL) is a CL variant that accumulates in people with Barth syndrome (BTHS). BTHS is caused by defects in CL biosynthesis and characterised by abnormal mitochondrial bioenergetics and destabilised supercomplexes. However, the mechanisms by which MLCL causes pathogenesis remain unclear. Here, multiscale molecular dynamics characterise the interactions of CL and MLCL with yeast and mammalian mitochondrial supercomplexes containing complex III (CIII) and complex IV (CIV). Coarse-grained simulations reveal that both CL and MLCL bind to sites at the interface between CIII and CIV of the supercomplex. Free energy perturbation calculations show that MLCL interaction is weaker than that of CL and suggest that interaction with CIV drives this difference. Atomistic contact analyses show that, although interaction with CIII is similar for CL and MLCL, CIV makes more contacts with CL than MLCL, demonstrating that CL is a more successful "glue" between the two complexes. Simulations of the human CIII2CIV supercomplex show that this interface site is maintained between species. Our study suggests that MLCL accumulation in people with BTHS disrupts supercomplex stability by formation of relatively weak interactions at the interface lipid binding site.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Noah Harrison
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Philllp J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
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6
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Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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7
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Prince RC, Dutton PL, Gunner MR. The aprotic electrochemistry of quinones. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148558. [PMID: 35413248 DOI: 10.1016/j.bbabio.2022.148558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/26/2022] [Accepted: 04/05/2022] [Indexed: 05/09/2023]
Abstract
Quinones play important roles in biological electron transfer reactions in almost all organisms, with specific roles in many physiological processes and chemotherapy. Quinones participate in two-electron, two-proton reactions in aqueous solution at equilibrium near neutral pH, but protons often lag behind the electron transfers. The relevant reactions in proteins are often sequential one electron redox processes without involving protons. Here we report the aprotic electrochemistry of the two half-couples, Q/Q.- and Q.-/Q=, of 11 parent quinones and 118 substituted 1,4-benzoquinones, 91 1,4-naphthoquinones, and 107 9,10-anthraquinones. The measured redox potentials are fit quite well with the Hammett para sigma (σpara) parameter. Occasional exceptions can involve important groups, such as methoxy substituents in ubiquinone and hydroxy substituents in therapeutics. These can generally be explained by reasonable conjectures involving steric clashes and internal hydrogen bonds. We also provide data for 25 other quinones, 2 double quinones and 15 non-quinones, all measured under similar conditions.
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Affiliation(s)
| | - P Leslie Dutton
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 10104, USA
| | - M R Gunner
- Physics Department City College of New York in the City University of New York, NY 10031, USA.
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8
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Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy. Biochem Soc Trans 2022; 50:877-893. [PMID: 35356963 PMCID: PMC9162462 DOI: 10.1042/bst20190963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
Cytochrome (cyt) bc1, bcc and b6f complexes, collectively referred to as cyt bc complexes, are homologous isoprenoid quinol oxidising enzymes present in diverse phylogenetic lineages. Cyt bc1 and bcc complexes are constituents of the electron transport chain (ETC) of cellular respiration, and cyt b6f complex is a component of the photosynthetic ETC. Cyt bc complexes share in general the same Mitchellian Q cycle mechanism, with which they accomplish proton translocation and thus contribute to the generation of proton motive force which drives ATP synthesis. They therefore require a quinol oxidation (Qo) and a quinone reduction (Qi) site. Yet, cyt bc complexes evolved to adapt to specific electrochemical properties of different quinone species and exhibit structural diversity. This review summarises structural information on native quinones and quinone-like inhibitors bound in cyt bc complexes resolved by X-ray crystallography and cryo-EM structures. Although the Qi site architecture of cyt bc1 complex and cyt bcc complex differs considerably, quinone molecules were resolved at the respective Qi sites in very similar distance to haem bH. In contrast, more diverse positions of native quinone molecules were resolved at Qo sites, suggesting multiple quinone binding positions or captured snapshots of trajectories toward the catalytic site. A wide spectrum of inhibitors resolved at Qo or Qi site covers fungicides, antimalarial and antituberculosis medications and drug candidates. The impact of these structures for characterising the Q cycle mechanism, as well as their relevance for the development of medications and agrochemicals are discussed.
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9
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Dudek J, Maack C. Mechano-energetic aspects of Barth syndrome. J Inherit Metab Dis 2022; 45:82-98. [PMID: 34423473 DOI: 10.1002/jimd.12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022]
Abstract
Energy-demanding organs like the heart are strongly dependent on oxidative phosphorylation in mitochondria. Oxidative phosphorylation is governed by the respiratory chain located in the inner mitochondrial membrane. The inner mitochondrial membrane is the only cellular membrane with significant amounts of the phospholipid cardiolipin, and cardiolipin was found to directly interact with a number of essential protein complexes, including respiratory chain complexes I to V. An inherited defect in the biogenesis of cardiolipin causes Barth syndrome, which is associated with cardiomyopathy, skeletal myopathy, neutropenia and growth retardation. Energy conversion is dependent on reducing equivalents, which are replenished by oxidative metabolism in the Krebs cycle. Cardiolipin deficiency in Barth syndrome also affects Krebs cycle activity, metabolite transport and mitochondrial morphology. During excitation-contraction coupling, calcium (Ca2+ ) released from the sarcoplasmic reticulum drives sarcomeric contraction. At the same time, Ca2+ influx into mitochondria drives the activation of Krebs cycle dehydrogenases and the regeneration of reducing equivalents. Reducing equivalents are essential not only for energy conversion, but also for maintaining a redox buffer, which is required to detoxify reactive oxygen species (ROS). Defects in CL may also affect Ca2+ uptake into mitochondria and thereby hamper energy supply and demand matching, but also detoxification of ROS. Here, we review the impact of cardiolipin deficiency on mitochondrial function in Barth syndrome and discuss potential therapeutic strategies.
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Affiliation(s)
- Jan Dudek
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Christoph Maack
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
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10
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Insights into the Role of Membrane Lipids in the Structure, Function and Regulation of Integral Membrane Proteins. Int J Mol Sci 2021; 22:ijms22169026. [PMID: 34445730 PMCID: PMC8396450 DOI: 10.3390/ijms22169026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins exist within the highly hydrophobic membranes surrounding cells and organelles, playing key roles in cellular function. It is becoming increasingly clear that the membrane does not just act as an appropriate environment for these proteins, but that the lipids that make up these membranes are essential for membrane protein structure and function. Recent technological advances in cryogenic electron microscopy and in advanced mass spectrometry methods, as well as the development of alternative membrane mimetic systems, have allowed experimental study of membrane protein–lipid complexes. These have been complemented by computational approaches, exploiting the ability of Molecular Dynamics simulations to allow exploration of membrane protein conformational changes in membranes with a defined lipid content. These studies have revealed the importance of lipids in stabilising the oligomeric forms of membrane proteins, mediating protein–protein interactions, maintaining a specific conformational state of a membrane protein and activity. Here we review some of the key recent advances in the field of membrane protein–lipid studies, with major emphasis on respiratory complexes, transporters, channels and G-protein coupled receptors.
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11
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Mitochondrion as a Target of Astaxanthin Therapy in Heart Failure. Int J Mol Sci 2021; 22:ijms22157964. [PMID: 34360729 PMCID: PMC8347622 DOI: 10.3390/ijms22157964] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022] Open
Abstract
Mitochondria are considered to be important organelles in the cell and play a key role in the physiological function of the heart, as well as in the pathogenesis and development of various heart diseases. Under certain pathological conditions, such as cardiovascular diseases, stroke, traumatic brain injury, neurodegenerative diseases, muscular dystrophy, etc., mitochondrial permeability transition pore (mPTP) is formed and opened, which can lead to dysfunction of mitochondria and subsequently to cell death. This review summarizes the results of studies carried out by our group of the effect of astaxanthin (AST) on the functional state of rat heart mitochondria upon direct addition of AST to isolated mitochondria and upon chronic administration of AST under conditions of mPTP opening. It was shown that AST exerted a protective effect under all conditions. In addition, AST treatment was found to prevent isoproterenol-induced oxidative damage to mitochondria and increase mitochondrial efficiency. AST, a ketocarotenoid, may be a potential mitochondrial target in therapy for pathological conditions associated with oxidative damage and mitochondrial dysfunction, and may be a potential mitochondrial target in therapy for pathological conditions.
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12
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Structural Investigation and Molecular Modeling Studies of Strobilurin-Based Fungicides Active against the Rice Blast Pathogen Pyricularia oryzae. Int J Mol Sci 2021; 22:ijms22073731. [PMID: 33918510 PMCID: PMC8038316 DOI: 10.3390/ijms22073731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
The increasing emergence of fungicide-resistant pathogens requires urgent solutions for crop disease management. Here, we describe a structural investigation of new fungicides obtained by combining strobilurin and succinate dehydrogenase inhibitor pharmacophores. We identified compounds endowed with very good activity against wild-type Pyricularia oryzae, combined in some cases with promising activity against strobilurin-resistant strains. The first three-dimensional model of P. oryzae cytochrome bc1 complex containing azoxystrobin as a ligand was developed. The model was validated with a set of commercially available strobilurins, and it well explains both the resistance mechanism to strobilurins mediated by the mutation G143A and the activity of metyltetraprole against strobilurin-resistant strains. The obtained results shed light on the key recognition determinants of strobilurin-like derivatives in the cytochrome bc1 active site and will guide the further rational design of new fungicides able to overcome resistance caused by G143A mutation in the rice blast pathogen.
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13
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Crofts AR. The modified Q-cycle: A look back at its development and forward to a functional model. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148417. [PMID: 33745972 DOI: 10.1016/j.bbabio.2021.148417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 11/25/2022]
Abstract
On looking back at a lifetime of research, it is interesting to see, in the light of current progress, how things came to be, and to speculate on how things might be. I am delighted in the context of the Mitchell prize to have that excuse to present this necessarily personal view of developments in areas of my interests. I have focused on the Q-cycle and a few examples showing wider ramifications, since that had been the main interest of the lab in the 20 years since structures became available, - a watershed event in determining our molecular perspective. I have reviewed the evidence for our model for the mechanism of the first electron transfer of the bifurcated reaction at the Qo-site, which I think is compelling. In reviewing progress in understanding the second electron transfer, I have revisited some controversies to justify important conclusions which appear, from the literature, not to have been taken seriously. I hope this does not come over as nitpicking. The conclusions are important to the final section in which I develop an internally consistent mechanism for turnovers of the complex leading to a state similar to that observed in recent rapid-mix/freeze-quench experiments, reported three years ago. The final model is necessarily speculative but is open to test.
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Affiliation(s)
- Antony R Crofts
- Department of Biochemistry, 417 Roger Adams Laboratory, 600 South Mathews Avenue, Urbana, IL 61801, United States of America
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14
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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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15
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Maldonado M, Guo F, Letts JA. Atomic structures of respiratory complex III 2, complex IV, and supercomplex III 2-IV from vascular plants. eLife 2021; 10:e62047. [PMID: 33463523 PMCID: PMC7815315 DOI: 10.7554/elife.62047] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial complex III (CIII2) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III2+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV, and SC III2+IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII2's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
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Affiliation(s)
- Maria Maldonado
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
| | - Fei Guo
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
- BIOEM Facility, University of California DavisDavisUnited States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
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16
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Han Z, Angerer H, Bischoff I, Qin Y, Stegmann D, Tuz K, Fritz G, Juarez O, Fürst R, Lashley D, Nasiri HR. Concise Synthesis of 1,4-Benzoquinone-Based Natural Products as Mitochondrial Complex I Substrates and Substrate-Based Inhibitors. ChemMedChem 2020; 15:2491-2499. [PMID: 32730688 DOI: 10.1002/cmdc.202000307] [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: 05/08/2020] [Revised: 07/22/2020] [Indexed: 11/06/2022]
Abstract
A short, efficient one-step synthesis of 2-methyl-5-(3-methyl-2-butenyl)-1,4-benzoquinone, a natural product from Pyrola media is described. The synthesis is based on a direct late C-H functionalization of the quinone scaffold. The formation of the natural product was confirmed by means of 2D-NMR spectroscopy. Additional derivatives were synthesized and tested alongside the natural product as potential substrate and substrate-based inhibitors of mitochondrial complex I (MCI). The structure-activity relationship study led to the discovery of 3-methylbuteneoxide-1,4-anthraquinone (1 i), an inhibitor with an IC50 of 5 μM against MCI. The identified molecule showed high selectivity for MCI when tested against other quinone-converting enzymes, including succinate dehydrogenase, and the Na (+)-translocating NADH:quinone oxidoreductase. Moreover, the identified inhibitor was also active in cell-based proliferation assays. Therefore, 1 i can be considered as a novel chemical probe for MCI.
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Affiliation(s)
- Zhenyu Han
- Department of Chemistry, William & Mary, Williamsburg, VA, 23185, USA
| | - Heike Angerer
- Medical School, Institute of Biochemistry II Structural Bioenergetics Group, Goethe University, 60590, Frankfurt am Main, Germany.,Centre for Biomolecular Magnetic Resonance Institute for Biophysical Chemistry, Goethe University, 60438, Frankfurt am Main, Germany
| | - Iris Bischoff
- Institute of Pharmaceutical Biology, Goethe University, 60438, Frankfurt am Main, Germany
| | - Yihan Qin
- Department of Chemistry, William & Mary, Williamsburg, VA, 23185, USA
| | - Dennis Stegmann
- Department of Cellular Microbiology, University Hohenheim, 70599, Stuttgart, Germany
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Günter Fritz
- Department of Cellular Microbiology, University Hohenheim, 70599, Stuttgart, Germany
| | - Oscar Juarez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Robert Fürst
- Institute of Pharmaceutical Biology, Goethe University, 60438, Frankfurt am Main, Germany
| | - Dana Lashley
- Department of Chemistry, William & Mary, Williamsburg, VA, 23185, USA
| | - Hamid R Nasiri
- Department of Cellular Microbiology, University Hohenheim, 70599, Stuttgart, Germany
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17
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Krestinin R, Baburina Y, Odinokova I, Kruglov A, Fadeeva I, Zvyagina A, Sotnikova L, Krestinina O. Isoproterenol-Induced Permeability Transition Pore-Related Dysfunction of Heart Mitochondria Is Attenuated by Astaxanthin. Biomedicines 2020; 8:biomedicines8100437. [PMID: 33092172 PMCID: PMC7589423 DOI: 10.3390/biomedicines8100437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are key organelles of the cell because their main function is the capture of energy-rich substrates from the cytoplasm and oxidative cleavage with the generation of carbon dioxide and water, processes that are coupled with the synthesis of ATP. Mitochondria are subject to oxidative stress through the formation of the mitochondrial permeability transition pore (mPTP). Various antioxidants are used to reduce damage caused by oxidative stress and to improve the protection of the antioxidant system. Astaxanthin (AST) is considered to be a dietary antioxidant, which is able to reduce oxidative stress and enhance the antioxidant defense system. In the present investigation, the effect of AST on the functional state of rat heart mitochondria impaired by isoproterenol (ISO) under mPTP functioning was examined. It was found that AST raised mitochondrial respiration, the Ca2+ retention capacity (CRC), and the rate of TPP+ influx in rat heart mitochondria (RHM) isolated from ISO-injected rats. However, the level of reactive oxygen species (ROS) production increased. In addition, the concentrations of cardiolipin (CL), Mn-SOD2, and the proteins regulating mPTP rose after the injection of ISO in RHM pretreated with AST. Based on the data obtained, we suggest that AST has a protective effect in rat heart mitochondria.
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18
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Fisher N, Meunier B, Biagini GA. The cytochrome bc 1 complex as an antipathogenic target. FEBS Lett 2020; 594:2935-2952. [PMID: 32573760 DOI: 10.1002/1873-3468.13868] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/31/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
The cytochrome bc1 complex is a key component of the mitochondrial respiratory chains of many eukaryotic microorganisms that are pathogenic for plants or humans, such as fungi responsible for crop diseases and Plasmodium falciparum, which causes human malaria. Cytochrome bc1 is an enzyme that contains two (ubi)quinone/quinol-binding sites, which can be exploited for the development of fungicidal and chemotherapeutic agents. Here, we review recent progress in determination of the structure and mechanism of action of cytochrome bc1 , and the associated development of antimicrobial agents (and associated resistance mechanisms) targeting its activity.
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Affiliation(s)
- Nicholas Fisher
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Brigitte Meunier
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Giancarlo A Biagini
- Parasitology Department, Research Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
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19
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Monolysocardiolipin (MLCL) interactions with mitochondrial membrane proteins. Biochem Soc Trans 2020; 48:993-1004. [PMID: 32453413 PMCID: PMC7329354 DOI: 10.1042/bst20190932] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022]
Abstract
Monolysocardiolipin (MLCL) is a three-tailed variant of cardiolipin (CL), the signature lipid of mitochondria. MLCL is not normally found in healthy tissue but accumulates in mitochondria of people with Barth syndrome (BTHS), with an overall increase in the MLCL:CL ratio. The reason for MLCL accumulation remains to be fully understood. The effect of MLCL build-up and decreased CL content in causing the characteristics of BTHS are also unclear. In both cases, an understanding of the nature of MLCL interaction with mitochondrial proteins will be key. Recent work has shown that MLCL associates less tightly than CL with proteins in the mitochondrial inner membrane, suggesting that MLCL accumulation is a result of CL degradation, and that the lack of MLCL–protein interactions compromises the stability of the protein-dense mitochondrial inner membrane, leading to a decrease in optimal respiration. There is some data on MLCL–protein interactions for proteins involved in the respiratory chain and in apoptosis, but there remains much to be understood regarding the nature of MLCL–protein interactions. Recent developments in structural, analytical and computational approaches mean that these investigations are now possible. Such an understanding will be key to further insights into how MLCL accumulation impacts mitochondrial membranes. In turn, these insights will help to support the development of therapies for people with BTHS and give a broader understanding of other diseases involving defective CL content.
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20
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Lynes MD, Shamsi F, Sustarsic EG, Leiria LO, Wang CH, Su SC, Huang TL, Gao F, Narain NR, Chen EY, Cypess AM, Schulz TJ, Gerhart-Hines Z, Kiebish MA, Tseng YH. Cold-Activated Lipid Dynamics in Adipose Tissue Highlights a Role for Cardiolipin in Thermogenic Metabolism. Cell Rep 2019; 24:781-790. [PMID: 30021173 DOI: 10.1016/j.celrep.2018.06.073] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/07/2018] [Accepted: 06/15/2018] [Indexed: 12/20/2022] Open
Abstract
Thermogenic fat expends energy during cold for temperature homeostasis, and its activity regulates nutrient metabolism and insulin sensitivity. We measured cold-activated lipid landscapes in circulation and in adipose tissue by MS/MSALL shotgun lipidomics. We created an interactive online viewer to visualize the changes of specific lipid species in response to cold. In adipose tissue, among the approximately 1,600 lipid species profiled, we identified the biosynthetic pathway of the mitochondrial phospholipid cardiolipin as coordinately activated in brown and beige fat by cold in wild-type and transgenic mice with enhanced browning of white fat. Together, these data provide a comprehensive lipid bio-signature of thermogenic fat activation in circulation and tissue and suggest pathways regulated by cold exposure.
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Affiliation(s)
- Matthew D Lynes
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Elahu Gosney Sustarsic
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Luiz O Leiria
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Chih-Hao Wang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Sheng-Chiang Su
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Tian Lian Huang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Fei Gao
- BERG, Framingham, MA 01701, USA
| | | | | | | | - Tim J Schulz
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; German Institute of Human Nutrition, Potsdam-Rehbrücke, Germany
| | - Zachary Gerhart-Hines
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
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21
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Salnikov ES, Aisenbrey C, Pokrandt B, Brügger B, Bechinger B. Structure, Topology, and Dynamics of Membrane-Inserted Polypeptides and Lipids by Solid-State NMR Spectroscopy: Investigations of the Transmembrane Domains of the DQ Beta-1 Subunit of the MHC II Receptor and of the COP I Protein p24. Front Mol Biosci 2019; 6:83. [PMID: 31608287 PMCID: PMC6769064 DOI: 10.3389/fmolb.2019.00083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/23/2019] [Indexed: 01/04/2023] Open
Abstract
MHC class II receptors carry important function in adaptive immunity and their malfunctioning is associated with diabetes type I, chronic inflammatory diseases and other autoimmune diseases. The protein assembles from the DQ alpha-1 and DQ beta-1 subunits where the transmembrane domains of these type I membrane proteins have been shown to be involved in homo- and heterodimer formation. Furthermore, the DQ alpha 1 chain carries a sequence motif that has been first identified in the context of p24, a protein involved in the formation of COPI vesicles of the intracellular transport machinery, to specifically interact with sphingomyelin-C18 (SM-C18). Here we investigated the membrane interactions and dynamics of DQ beta-1 in liquid crystalline POPC phospholipid bilayers by oriented 15N solid-state NMR spectroscopy. The 15N resonances are indicative of a helical tilt angle of the membrane anchor sequence around 20°. Two populations can be distinguished by their differential dynamics probably corresponding the DQ beta-1 mono- and homodimer. Whereas, this equilibrium is hardly affected by the addition of 5 mole% SM-C18 a single population is visible in DMPC lipid bilayers suggesting that the lipid saturation is an important parameter. Furthermore, the DQ alpha-1, DQ beta-1 and p24 transmembrane helical domains were reconstituted into POPC or POPC/SM-C18 lipid bilayers where the fatty acyl chain of either the phosphatidylcholine or of the sphingolipid have been deuterated. Interestingly in the presence of both sphingolipid and polypeptide a strong decrease in the innermost membrane order of the POPC palmitoyl chain is observed, an effect that is strongest for DQ beta-1. In contrast, for the first time the polypeptide interactions were monitored by deuteration of the stearoyl chain of SM-C18. The resulting 2H solid-state NMR spectra show an increase in order for p24 and DQ alpha-1 which both carry the SM recognition motif. Thereby the data are suggestive that SM-C18 together with the transmembrane domains form structures imposing positive curvature strain on the surrounding POPC lipids. This effect is attenuated when SM-C18 is recognized by the protein.
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Affiliation(s)
- Evgeniy S Salnikov
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
| | | | - Bianca Pokrandt
- Biochemiezentrum der Universität Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Biochemiezentrum der Universität Heidelberg, Heidelberg, Germany
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
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22
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Aisenbrey C, Salnikov ES, Bechinger B. Solid-State NMR Investigations of the MHC II Transmembrane Domains: Topological Equilibria and Lipid Interactions. J Membr Biol 2019; 252:371-384. [PMID: 31187155 DOI: 10.1007/s00232-019-00071-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/25/2019] [Indexed: 10/26/2022]
Abstract
The major histocompatibility complex class II (MHC II) membrane proteins are key players in the adaptive immune response. An aberrant function of these molecules is associated with a large number of autoimmune diseases such as diabetes type I and chronic inflammatory diseases. The MHC class II is assembled from DQ alpha 1 and DQ beta 1 which come together as a heterodimer through GXXXG-mediated protein-protein interactions and a highly specific protein-sphingomyelin-C18 interaction motif located on DQA1. This association can have important consequences in regulating the function of these membrane proteins. Here, we investigated the structure and topology of the DQA1 and DQB1 transmembrane helical domains by CD-, oriented 2H and 15N solid-state NMR spectroscopies. The spectra at peptide-to-lipid ratios of 0.5 to 2 mol% are indicative of a topological equilibrium involving a helix crossing the membrane with a tilt angle of about 20° and another transmembrane topology with around 30° tilt. The latter is probably representing a dimer. Furthermore, at the lowest peptide-to-lipid ratio, a third polypeptide population becomes obvious. Interestingly, the DQB1 and to a lesser extent the DQA1 transmembrane helical domains exhibit a strong fatty acyl chain disordering effect on the inner segments of the 2H-labelled palmitoyl chain of POPC bilayers. This phosphatidylcholine disordering requires the presence of sphingomyelin-C18 suggesting that the ensemble of transmembrane polypeptide and sphingolipid exerts positive curvature strain.
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Affiliation(s)
- Christopher Aisenbrey
- Institut de Chimie, Université de Strasbourg/CNRS, UMR7177, 4, Rue Blaise Pascal, 67070, Strasbourg, France
| | - Evgeniy S Salnikov
- Institut de Chimie, Université de Strasbourg/CNRS, UMR7177, 4, Rue Blaise Pascal, 67070, Strasbourg, France
| | - Burkhard Bechinger
- Institut de Chimie, Université de Strasbourg/CNRS, UMR7177, 4, Rue Blaise Pascal, 67070, Strasbourg, France.
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23
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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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Shimada S, Maeda S, Hikita M, Mieda-Higa K, Uene S, Nariai Y, Shinzawa-Itoh K. Solubilization conditions for bovine heart mitochondrial membranes allow selective purification of large quantities of respiratory complexes I, III, and V. Protein Expr Purif 2018; 150:33-43. [PMID: 29702187 DOI: 10.1016/j.pep.2018.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022]
Abstract
Ascertaining the structure and functions of mitochondrial respiratory chain complexes is essential to understanding the biological mechanisms of energy conversion; therefore, numerous studies have examined these complexes. A fundamental part of that research involves devising a method for purifying samples with good reproducibility; the samples obtained need to be stable and their constituents need to retain the same structure and functions they possess when in mitochondrial membranes. Submitochondrial bovine heart particles were isolated using differential centrifugation to adjust to a membrane concentration of 46.0% (w/v) or 31.5% (w/v) based on weight. After 0.7% (w/v) deoxycholic acid, 0.4% (w/v) decyl maltoside, and 7.2% (w/v) potassium chloride were added to the mitochondrial membranes, those membranes were solubilized. At a membrane concentration of 46%, complex V was selectively solubilized, whereas at a concentration of 31.5% (w/v), complexes I and III were solubilized. Two steps-sucrose density gradient centrifugation and anion-exchange chromatography on a POROS HQ 20 μm column-enabled selective purification of samples that retained their structure and functions. These two steps enabled complexes I, III, and V to be purified in two days with a high yield. Complexes I, III, and V were stabilized with n-decyl-β-D-maltoside. A total of 200 mg-300 mg of those complexes from one bovine heart (1.1 kg muscle) was purified with good reproducibility, and the complexes retained the same functions they possessed while in mitochondrial membranes.
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Affiliation(s)
- Satoru Shimada
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Shintaro Maeda
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Masahide Hikita
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Kaoru Mieda-Higa
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Shigefumi Uene
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Yukiko Nariai
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan.
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25
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Dudek J. Role of Cardiolipin in Mitochondrial Signaling Pathways. Front Cell Dev Biol 2017; 5:90. [PMID: 29034233 PMCID: PMC5626828 DOI: 10.3389/fcell.2017.00090] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023] Open
Abstract
The phospholipid cardiolipin (CL) is an essential constituent of mitochondrial membranes and plays a role in many mitochondrial processes, including respiration and energy conversion. Pathological changes in CL amount or species composition can have deleterious consequences for mitochondrial function and trigger the production of reactive oxygen species. Signaling networks monitor mitochondrial function and trigger an adequate cellular response. Here, we summarize the role of CL in cellular signaling pathways and focus on tissues with high-energy demand, like the heart. CL itself was recently identified as a precursor for the formation of lipid mediators. We highlight the concept of CL as a signaling platform. CL is exposed to the outer mitochondrial membrane upon mitochondrial stress and CL domains serve as a binding site in many cellular signaling events. During mitophagy, CL interacts with essential players of mitophagy like Beclin 1 and recruits the autophagic machinery by its interaction with LC3. Apoptotic signaling pathways require CL as a binding platform to recruit apoptotic factors such as tBid, Bax, caspase-8. CL required for the activation of the inflammasome and plays a role in inflammatory signaling. As changes in CL species composition has been observed in many diseases, the signaling pathways described here may play a general role in pathology.
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Affiliation(s)
- Jan Dudek
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
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26
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Krishnathas R, Bonke E, Dröse S, Zickermann V, Nasiri HR. Identification of 4- N-[2-(4-phenoxyphenyl)ethyl]quinazoline-4,6-diamine as a novel, highly potent and specific inhibitor of mitochondrial complex I. MEDCHEMCOMM 2017; 8:657-661. [PMID: 30108783 DOI: 10.1039/c6md00655h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022]
Abstract
By probing the quinone substrate binding site of mitochondrial complex I with a focused set of quinazoline-based compounds, we identified substitution patterns as being critical for the observed inhibition. The structure activity relationship study also resulted in the discovery of the quinazoline 4-N-[2-(4-phenoxyphenyl)ethyl]quinazoline-4,6-diamine (EVP4593) as a highly potent inhibitor of the multisubunit membrane protein. EVP4593 specifically and effectively reduces the mitochondrial complex I-dependent respiration with no effect on the respiratory chain complexes II-IV. Similar to established Q-site inhibitors, EVP4593 elicits the release of reactive oxygen species at the flavin site of mitochondrial complex I. Recently, EVP4593 was nominated as a lead compound for the treatment of Huntingtons disease. Our results challenge the postulated primary mode-of-action of EVP4593 as an inhibitor of NF-κB pathway activation and/or store-operated calcium influx.
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Affiliation(s)
- Robin Krishnathas
- Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7 , D-60438 Frankfurt am Main , Germany .
| | - Erik Bonke
- Department of Anaesthesiology , Intensive-Care Medicine and Pain Therapy , University Hospital Frankfurt , 60590 Frankfurt am Main , Germany
| | - Stefan Dröse
- Department of Anaesthesiology , Intensive-Care Medicine and Pain Therapy , University Hospital Frankfurt , 60590 Frankfurt am Main , Germany
| | - Volker Zickermann
- Structural Bioenergetics Group , Institute of Biochemistry II , Medical School , Goethe-University , 60438 Frankfurt am Main , Germany.,Cluster of Excellence Frankfurt "Macromolecular Complexes," , Goethe-University , 60438 Frankfurt am Main , Germany
| | - Hamid R Nasiri
- Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7 , D-60438 Frankfurt am Main , Germany .
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27
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Petereit J, Katayama K, Lorenz C, Ewert L, Schertl P, Kitsche A, Wada H, Frentzen M, Braun HP, Eubel H. Cardiolipin Supports Respiratory Enzymes in Plants in Different Ways. FRONTIERS IN PLANT SCIENCE 2017; 8:72. [PMID: 28228763 PMCID: PMC5296312 DOI: 10.3389/fpls.2017.00072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/12/2017] [Indexed: 05/23/2023]
Abstract
In eukaryotes the presence of the dimeric phospholipid cardiolipin (CL) is limited to the mitochondrial membranes. It resides predominantly in the inner membrane where it interacts with components of the mitochondrial electron transfer chain. CL deficiency has previously been shown to affect abundances of the plant NADH-dehydrogenase complex and its association with dimeric cyctochrome c reductase. Using an Arabidopsis thaliana knock-out mutant for the final enzyme of CL biosynthesis we here extend current knowledge on the dependence of plant respiration on CL. By correlating respiratory enzyme abundances with enzymatic capacities in mitochondria isolated from wild type, CL deficient and CL complemented heterotrophic cell culture lines a new picture of the participation of CL in plant respiration is emerging. Data indicate a loss of a general reduction of respiratory capacity in CL deficient mitochondria which cannot solely be attributed to decreased abundances or capacities of mitochondrial electron transfer protein complexes and supercomplexes. Instead, it most likely is the result of a loss of the mobile electron carrier cytochrome c. Furthermore, enzymes of the tricarboxylic acid cycle are found to have lower maximum activities in the mutant, including the succinate dehydrogenase complex. Interestingly, abundance of the latter is not altered, indicative of a direct impact of CL deficiency on the enzymatic capacity of this electron transfer chain protein complex.
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Affiliation(s)
- Jakob Petereit
- Institute of Plant Genetics, Leibniz Universität HannoverHannover, Germany
| | - Kenta Katayama
- Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
- Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | - Christin Lorenz
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V.Dortmund, Germany
| | - Linda Ewert
- Institute of Plant Genetics, Leibniz Universität HannoverHannover, Germany
| | - Peter Schertl
- Institute of Plant Genetics, Leibniz Universität HannoverHannover, Germany
| | - Andreas Kitsche
- Institute of Biostatistics, Leibniz Universität HannoverHannover, Germany
| | - Hajime Wada
- Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | | | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität HannoverHannover, Germany
| | - Holger Eubel
- Institute of Plant Genetics, Leibniz Universität HannoverHannover, Germany
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Dudek J, Maack C. Barth syndrome cardiomyopathy. Cardiovasc Res 2017; 113:399-410. [PMID: 28158532 DOI: 10.1093/cvr/cvx014] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/19/2016] [Accepted: 01/04/2017] [Indexed: 02/02/2023] Open
Abstract
Barth syndrome (BTHS) is an inherited form of cardiomyopathy, caused by a mutation within the gene encoding the mitochondrial transacylase tafazzin. Tafazzin is involved in the biosynthesis of the unique phospholipid cardiolipin (CL), which is almost exclusively found in mitochondrial membranes. CL directly interacts with a number of essential protein complexes in the mitochondrial membranes including the respiratory chain, mitochondrial metabolite carriers, and proteins, involved in shaping mitochondrial morphology. Here we describe, how in BTHS CL deficiency causes changes in the morphology of mitochondria, structural changes in the respiratory chain, decreased respiration, and increased generation of reactive oxygen species. A large number of cellular and animal models for BTHS have been established to elucidate how mitochondrial dysfunction induces sarcomere disorganization and reduced contractility, resulting in dilated cardiomyopathy in vivo.
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Affiliation(s)
- Jan Dudek
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Christoph Maack
- Klinik für Innere Medizin III, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany
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Amazing structure of respirasome: unveiling the secrets of cell respiration. Protein Cell 2016; 7:854-865. [PMID: 27743346 PMCID: PMC5205662 DOI: 10.1007/s13238-016-0329-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/28/2016] [Indexed: 11/02/2022] Open
Abstract
Respirasome, a huge molecular machine that carries out cellular respiration, has gained growing attention since its discovery, because respiration is the most indispensable biological process in almost all living creatures. The concept of respirasome has renewed our understanding of the respiratory chain organization, and most recently, the structure of respirasome solved by Yang's group from Tsinghua University (Gu et al. Nature 237(7622):639-643, 2016) firstly presented the detailed interactions within this huge molecular machine, and provided important information for drug design and screening. However, the study of cellular respiration went through a long history. Here, we briefly showed the detoured history of respiratory chain investigation, and then described the amazing structure of respirasome.
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Esser L, Zhou F, Zhou Y, Xiao Y, Tang WK, Yu CA, Qin Z, Xia D. Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J Biol Chem 2016; 291:25019-25031. [PMID: 27758861 DOI: 10.1074/jbc.m116.744391] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/05/2016] [Indexed: 11/06/2022] Open
Abstract
Complex III or the cytochrome (cyt) bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (QP) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the QP site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc1 of different species reveals a toxophore that appears to interact optimally with residues in the QP site. The effect of modifications or additions to the toxophore on the binding to cyt bc1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc1.
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Affiliation(s)
- Lothar Esser
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Fei Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Yihui Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.,the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Yumei Xiao
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.,the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Wai-Kwan Tang
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Chang-An Yu
- the Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Zhaohai Qin
- the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Di Xia
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
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Song Z, Laleve A, Vallières C, McGeehan JE, Lloyd RE, Meunier B. Human Mitochondrial Cytochrome b Variants Studied in Yeast: Not All Are Silent Polymorphisms. Hum Mutat 2016; 37:933-41. [PMID: 27291790 PMCID: PMC5094555 DOI: 10.1002/humu.23024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 11/12/2022]
Abstract
Variations in mitochondrial DNA (mtDNA) cytochrome b (mt‐cyb) are frequently found within the healthy population, but also occur within a spectrum of mitochondrial and common diseases. mt‐cyb encodes the core subunit (MT‐CYB) of complex III, a central component of the oxidative phosphorylation system that drives cellular energy production and homeostasis. Despite significant efforts, most mt‐cyb variations identified are not matched with corresponding biochemical data, so their functional and pathogenic consequences in humans remain elusive. While human mtDNA is recalcitrant to genetic manipulation, it is possible to introduce human‐associated point mutations into yeast mtDNA. Using this system, we reveal direct links between human mt‐cyb variations in key catalytic domains of MT‐CYB and significant changes to complex III activity or drug sensitivity. Strikingly, m.15257G>A (p.Asp171Asn) increased the sensitivity of yeast to the antimalarial drug atovaquone, and m.14798T>C (p.Phe18Leu) enhanced the sensitivity of yeast to the antidepressant drug clomipramine. We demonstrate that while a small number of mt‐cyb variations had no functional effect, others have the capacity to alter complex III properties, suggesting they could play a wider role in human health and disease than previously thought. This compendium of new mt‐cyb‐biochemical relationships in yeast provides a resource for future investigations in humans.
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Affiliation(s)
- Zehua Song
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - Anaïs Laleve
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - Cindy Vallières
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - John E McGeehan
- Molecular Biophysics Laboratories, Institute of Biomedical and Biomolecular Science, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Rhiannon E Lloyd
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Science, School of Pharmacy and Biomedicine, University of Portsmouth, Portsmouth, UK
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
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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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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Electron Transfer Reactions at the Qo Site of the Cytochrome bc 1 Complex: The Good, the Bad, and the Ugly. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Song Z, Clain J, Iorga BI, Vallières C, Lalève A, Fisher N, Meunier B. Interplay between the hinge region of iron sulphur protein and the Qo site in the bc1 complex - Analysis of Plasmodium-like mutations in the yeast enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1487-94. [PMID: 26301481 DOI: 10.1016/j.bbabio.2015.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/21/2015] [Accepted: 08/19/2015] [Indexed: 10/23/2022]
Abstract
The respiratory chain bc1 complex is central to mitochondrial bioenergetics and the target of antiprotozoals. We characterized a modified yeast bc1 complex that more closely resemble Plasmodium falciparum enzyme. The mutant version was generated by replacing ten cytochrome b Qo site residues by P. falciparum equivalents. The Plasmodium-like changes caused a major dysfunction of the catalytic mechanism of the bc1 complex resulting in superoxide overproduction and respiratory growth defect. The defect was corrected by substitution of the conserved residue Y279 by a phenylalanine, or by mutations in or in the vicinity of the hinge domain of the iron-sulphur protein. It thus appears that side-reactions can be prevented by the substitution Y279F or the modification of the iron-sulphur protein hinge region. Interestingly, P. falciparum - and all the apicomplexan - contains an unusual hinge region. We replaced the yeast hinge region by the Plasmodium version and combined it with the Plasmodium-like version of the Qo site. This combination restored the respiratory growth competence. It could be suggested that, in the apicomplexan, the hinge region and the cytochrome b Qo site have co-evolved to maintain catalytic efficiency of the bc1 complex Qo site.
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Affiliation(s)
- Zehua Song
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Jérôme Clain
- UMR 216, Faculté de Pharmacie de Paris, Université Paris Descartes, and Institut de Recherche pour le Développement, 75006 Paris, France
| | - Bogdan I Iorga
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Labex LERMIT, 91198 Gif-sur-Yvette, France
| | - Cindy Vallières
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Anaïs Lalève
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Nicholas Fisher
- Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA..
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France.
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Planas-Iglesias J, Dwarakanath H, Mohammadyani D, Yanamala N, Kagan VE, Klein-Seetharaman J. Cardiolipin Interactions with Proteins. Biophys J 2015; 109:1282-94. [PMID: 26300339 DOI: 10.1016/j.bpj.2015.07.034] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/18/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022] Open
Abstract
Cardiolipins (CL) represent unique phospholipids of bacteria and eukaryotic mitochondria with four acyl chains and two phosphate groups that have been implicated in numerous functions from energy metabolism to apoptosis. Many proteins are known to interact with CL, and several cocrystal structures of protein-CL complexes exist. In this work, we describe the collection of the first systematic and, to the best of our knowledge, the comprehensive gold standard data set of all known CL-binding proteins. There are 62 proteins in this data set, 21 of which have nonredundant crystal structures with bound CL molecules available. Using binding patch analysis of amino acid frequencies, secondary structures and loop supersecondary structures considering phosphate and acyl chain binding regions together and separately, we gained a detailed understanding of the general structural and dynamic features involved in CL binding to proteins. Exhaustive docking of CL to all known structures of proteins experimentally shown to interact with CL demonstrated the validity of the docking approach, and provides a rich source of information for experimentalists who may wish to validate predictions.
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Affiliation(s)
- Joan Planas-Iglesias
- Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom
| | - Himal Dwarakanath
- Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom
| | - Dariush Mohammadyani
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Naveena Yanamala
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Judith Klein-Seetharaman
- Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom; Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania.
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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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Saccharomyces cerevisiae-based mutational analysis of the bc1 complex Qo site residue 279 to study the trade-off between atovaquone resistance and function. Antimicrob Agents Chemother 2015; 59:4053-8. [PMID: 25918152 DOI: 10.1128/aac.00710-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/19/2015] [Indexed: 11/20/2022] Open
Abstract
The bc1 complex is central to mitochondrial bioenergetics and the target of the antimalarial drug atovaquone that binds in the quinol oxidation (Qo) site of the complex. Structural analysis has shown that the Qo site residue Y279 (Y268 in Plasmodium falciparum) is key for atovaquone binding. Consequently, atovaquone resistance can be acquired by mutation of that residue. In addition to the probability of amino acid substitution, the level of atovaquone resistance and the loss of bc1 complex activity that are associated with the novel amino acid would restrict the nature of resistance-driven mutations occurring on atovaquone exposure in native parasite populations. Using the yeast model, we characterized the effect of all the amino acid replacements resulting from a single nucleotide substitution at codon 279: Y279C, Y279D, Y279F, Y279H, Y279N, and Y279S (Y279C, D, F, H, N, and S). Two residue changes that required a double nucleotide substitution, Y279A and W, were added to the series. We found that mutations Y279A, C, and S conferred high atovaquone resistance but decreased the catalytic activity. Y279F had wild-type enzymatic activity and sensitivity to atovaquone, while the other substitutions caused a dramatic respiratory defect. The results obtained with the yeast model were examined in regard to atomic structure and compared to the reported data on the evolution of acquired atovaquone resistance in P. falciparum.
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Abstract
Quinol oxidation in the catalytic quinol oxidation site (Qo site) of cytochrome (cyt) bc1 complexes is the key step of the Q cycle mechanism, which laid the ground for Mitchell’s chemiosmotic theory of energy conversion. Bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels ATP synthesis in cellular respiration and photosynthesis. The Qo site architecture formed by cyt b and Rieske iron–sulfur protein (ISP) impedes harmful bypass reactions. Catalytic importance is assigned to four residues of cyt b formerly described as PEWY motif in the context of mitochondrial complexes, which we now denominate Qo motif as comprehensive evolutionary sequence analysis of cyt b shows substantial natural variance of the motif with phylogenetically specific patterns. In particular, the Qo motif is identified as PEWY in mitochondria, α- and ε-Proteobacteria, Aquificae, Chlorobi, Cyanobacteria, and chloroplasts. PDWY is present in Gram-positive bacteria, Deinococcus–Thermus and haloarchaea, and PVWY in β- and γ-Proteobacteria. PPWF only exists in Archaea. Distinct patterns for acidophilic organisms indicate environment-specific adaptations. Importantly, the presence of PDWY and PEWY is correlated with the redox potential of Rieske ISP and quinone species. We propose that during evolution from low to high potential electron-transfer systems in the emerging oxygenic atmosphere, cyt bc1 complexes with PEWY as Qo motif prevailed to efficiently use high potential ubiquinone as substrate, whereas cyt b with PDWY operate best with low potential Rieske ISP and menaquinone, with the latter being the likely composition of the ancestral cyt bc1 complex.
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Affiliation(s)
- Wei-Chun Kao
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- Faculty of Biology, University of Freiburg, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- *Corresponding author: E-mail:
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Mir SH, Escher C, Kao WC, Birth D, Wirth C, Hunte C. Generation of recombinant antibody fragments for membrane protein crystallization. Methods Enzymol 2015; 557:201-18. [PMID: 25950966 DOI: 10.1016/bs.mie.2014.12.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Membrane proteins are challenging targets for crystallization and structure determination by X-ray crystallography. Hurdles can be overcome by antibody-mediated crystallization. More than 25 unique structures of membrane protein:antibody complexes have already been determined. In the majority of cases, hybridoma-derived antibody fragments either in Fab or Fv fragment format were employed for these complexes. We will briefly introduce the background and current status of the strategy and describe in detail the current protocols of well-established methods for the immunization, the selection, and the characterization of antibodies, as well as the cloning, the production, and the purification of recombinant antibodies useful for structural analysis of membrane proteins.
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Affiliation(s)
- Syed H Mir
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Department of Clinical Biochemistry, University of Kashmir, Srinagar, India
| | - Claudia Escher
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Wei-Chun Kao
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Dominic Birth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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Lloyd RE, Keatley K, Littlewood DTJ, Meunier B, Holt WV, An Q, Higgins SC, Polyzoidis S, Stephenson KF, Ashkan K, Fillmore HL, Pilkington GJ, McGeehan JE. Identification and functional prediction of mitochondrial complex III and IV mutations associated with glioblastoma. Neuro Oncol 2015; 17:942-52. [PMID: 25731774 PMCID: PMC4474231 DOI: 10.1093/neuonc/nov020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/23/2015] [Indexed: 12/30/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common primary brain tumor in adults, with a dismal prognosis. Treatment is hampered by GBM's unique biology, including differential cell response to therapy. Although several mitochondrial abnormalities have been identified, how mitochondrial DNA (mtDNA) mutations contribute to GBM biology and therapeutic response remains poorly described. We sought to determine the spectrum of functional complex III and IV mtDNA mutations in GBM. Methods The complete mitochondrial genomes of 10 GBM cell lines were obtained using next-generation sequencing and combined with another set obtained from 32 GBM tissues. Three-dimensional structural mapping and analysis of all the nonsynonymous mutations identified in complex III and IV proteins was then performed to investigate functional importance. Results Over 200 mutations were identified in the mtDNAs, including a significant proportion with very low mutational loads. Twenty-five were nonsynonymous mutations in complex III and IV, 9 of which were predicted to be functional and affect mitochondrial respiratory chain activity. Most of the functional candidates were GBM specific and not found in the general population, and 2 were present in the germ-line. Patient-specific maps reveal that 43% of tumors carry at least one functional candidate. Conclusions We reveal that the spectrum of GBM-associated mtDNA mutations is wider than previously thought, as well as novel structural-functional links between specific mtDNA mutations, abnormal mitochondria, and the biology of GBM. These results could provide tangible new prognostic indicators as well as targets with which to guide the development of patient-specific mitochondrially mediated chemotherapeutic approaches.
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Affiliation(s)
- Rhiannon E Lloyd
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Kathleen Keatley
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - D Timothy J Littlewood
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Brigitte Meunier
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - William V Holt
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Qian An
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Samantha C Higgins
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Stavros Polyzoidis
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Katie F Stephenson
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Keyoumars Ashkan
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Helen L Fillmore
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Geoffrey J Pilkington
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - John E McGeehan
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
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42
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Müh F, DiFiore D, Zouni A. The influence of poly(ethylene glycol) on the micelle formation of alkyl maltosides used in membrane protein crystallization. Phys Chem Chem Phys 2015; 17:11678-91. [DOI: 10.1039/c5cp00431d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of poly(ethylene glycol) on the micelle formation of alkyl maltosides under conditions of membrane protein crystallization is investigated.
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Affiliation(s)
- Frank Müh
- Institut für Theoretische Physik
- Johannes Kepler Universität Linz
- A-4040 Linz
- Austria
| | - Dörte DiFiore
- Max-Volmer-Laboratorium für Biophysikalische Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Athina Zouni
- Institut für Biologie
- Humboldt Universität zu Berlin
- D-10095 Berlin
- Germany
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43
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Sarewicz M, Osyczka A. Electronic connection between the quinone and cytochrome C redox pools and its role in regulation of mitochondrial electron transport and redox signaling. Physiol Rev 2015; 95:219-43. [PMID: 25540143 PMCID: PMC4281590 DOI: 10.1152/physrev.00006.2014] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria.
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Affiliation(s)
- Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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44
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Ye C, Shen Z, Greenberg ML. Cardiolipin remodeling: a regulatory hub for modulating cardiolipin metabolism and function. J Bioenerg Biomembr 2014; 48:113-23. [PMID: 25432572 DOI: 10.1007/s10863-014-9591-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/14/2014] [Indexed: 12/11/2022]
Abstract
Cardiolipin (CL), the signature phospholipid of mitochondria, is involved in a plethora of cellular processes and is crucial for mitochondrial function and architecture. The de novo synthesis of CL in the mitochondria is followed by a unique remodeling process, in which CL undergoes cycles of deacylation and reacylation. Specific fatty acyl composition is acquired during this process, and remodeled CL contains predominantly unsaturated fatty acids. The importance of CL remodeling is underscored by the life-threatening genetic disorder Barth syndrome (BTHS), caused by mutations in tafazzin, which reacylates monolysocardiolipin (MLCL) generated from the deacylation of CL. Just as CL-deficient yeast mutants have been instrumental in elucidating functions of this lipid, the recently characterized CL-phospholipase mutant cld1Δ and the tafazzin mutant taz1Δ are powerful tools to understand the functions of CL remodeling. In this review, we discuss recent advances in understanding the role of CL in mitochondria with specific focus on the enigmatic functions of CL remodeling.
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Affiliation(s)
- Cunqi Ye
- Department of Biological Sciences, Wayne State University, Detroit, 5047 Gullen Mall, Michigan, 48202, MI, USA
| | - Zheni Shen
- Department of Biological Sciences, Wayne State University, Detroit, 5047 Gullen Mall, Michigan, 48202, MI, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, 5047 Gullen Mall, Michigan, 48202, MI, USA.
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45
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Hong S, de Almeida W, Taguchi AT, Samoilova R, Gennis RB, O’Malley PJ, Dikanov SA, Crofts AR. The semiquinone at the Qi site of the bc1 complex explored using HYSCORE spectroscopy and specific isotopic labeling of ubiquinone in Rhodobacter sphaeroides via (13)C methionine and construction of a methionine auxotroph. Biochemistry 2014; 53:6022-31. [PMID: 25184535 PMCID: PMC4179594 DOI: 10.1021/bi500654y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/02/2014] [Indexed: 11/30/2022]
Abstract
Specific isotopic labeling at the residue or substituent level extends the scope of different spectroscopic approaches to the atomistic level. Here we describe (13)C isotopic labeling of the methyl and methoxy ring substituents of ubiquinone, achieved through construction of a methionine auxotroph in Rhodobacter sphaeroides strain BC17 supplemented with l-methionine with the side chain methyl group (13)C-labeled. Two-dimensional electron spin echo envelope modulation (HYSCORE) was applied to study the (13)C methyl and methoxy hyperfine couplings in the semiquinone generated in situ at the Qi site of the bc1 complex in its membrane environment. The data were used to characterize the distribution of unpaired spin density and the conformations of the methoxy substituents based on density functional theory calculations of (13)C hyperfine tensors in the semiquinone of the geometry-optimized X-ray structure of the bc1 complex (Protein Data Bank entry 1PP9 ) with the highest available resolution. Comparison with other proteins indicates individual orientations of the methoxy groups in each particular case are always different from the methoxy conformations in the anion radical prepared in a frozen alcohol solution. The protocol used in the generation of the methionine auxotroph is more generally applicable and, because it introduces a gene deletion using a suicide plasmid, can be applied repeatedly.
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Affiliation(s)
- Sangjin Hong
- Department
of Biochemistry, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Alexander T. Taguchi
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rimma
I. Samoilova
- V.
V. Voevodsky Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Robert B. Gennis
- Department
of Biochemistry, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Sergei A. Dikanov
- Department
of Veterinary Clinical Medicine, University
of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Antony R. Crofts
- Department
of Biochemistry, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
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46
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Siregar JE, Kurisu G, Kobayashi T, Matsuzaki M, Sakamoto K, Mi-ichi F, Watanabe YI, Hirai M, Matsuoka H, Syafruddin D, Marzuki S, Kita K. Direct evidence for the atovaquone action on the Plasmodium cytochrome bc1 complex. Parasitol Int 2014; 64:295-300. [PMID: 25264100 DOI: 10.1016/j.parint.2014.09.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 11/16/2022]
Abstract
Atovaquone, a coenzyme Q analogue has been indicated to specifically target the cytochrome bc1 complex of the mitochondrial respiratory chain in the malarial parasite and other protozoan. Various mutations in the quinone binding site of the cytochrome b gene of Plasmodium spp. such as M133I, L144S, L271V, K272R, Y268C, Y268S, Y268N, and V284F are suggesting to associate with resistance to atovaquone. There is no direct evidence of relation between the mutations and resistance to atovaquone in Plasmodium parasite that has been available. Technical difficulties in isolating active assayable mitochondria in the malarial parasite hinder us to obtain direct biochemical evidence to support the relation between the mutations and drug resistance. The establishment of a mitochondrial isolation method for the malaria parasite has allowed us to test the degree of resistance of Plasmodium berghei isolates to atovaquone directly. We have tested the activity of dihydroorotate (DHO)-cytochrome c reductase in various P. berghei atovaquone resistant clones in the presence of a wide concentration range of atovaquone. Our results show the IC(50) of P. berghei atovaquone resistant clones is much higher (1.5 up to 40 nM) in comparison to the atovaquone sensitive clones (0.132-0.465 nM). The highest IC(50) was revealed in clones carrying Y268C and Y268N mutations (which play an important role in atovaquone resistance in Plasmodium falciparum), with an approximately 100-fold increase. The findings indicate the importance of the mutation in the quinone binding site of the cytochrome b gene and that provide a direct evidence for the atovaquone inhibitory mechanism in the cytochrome bc1 complex of the parasite.
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Affiliation(s)
- Josephine E Siregar
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tamaki Kobayashi
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kimitoshi Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Fumika Mi-ichi
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoh-ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Makoto Hirai
- Department of Medical Zoology, Jichi Medical School, Minami-kawachi, Tochigi 329-0498, Japan
| | - Hiroyuki Matsuoka
- Department of Medical Zoology, Jichi Medical School, Minami-kawachi, Tochigi 329-0498, Japan
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia
| | - Sangkot Marzuki
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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47
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Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action. Nat Commun 2014; 5:4029. [DOI: 10.1038/ncomms5029] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 05/02/2014] [Indexed: 11/08/2022] Open
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48
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Loo JH, Trejaut JA, Yen JC, Chen ZS, Ng WM, Huang CY, Hsu KN, Hung KH, Hsiao Y, Wei YH, Lin M. Mitochondrial DNA association study of type 2 diabetes with or without ischemic stroke in Taiwan. BMC Res Notes 2014; 7:223. [PMID: 24713204 PMCID: PMC4108081 DOI: 10.1186/1756-0500-7-223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/01/2014] [Indexed: 11/10/2022] Open
Abstract
Background The importance of mitochondrial DNA (mtDNA) polymorphism in the prediction of type 2 diabetes (T2D) in men and women is not well understood. We questioned whether mtDNA polymorphism, mitochondrial functions, age and gender influenced the occurrence of T2D with or without ischemic stroke (IS). Methods We first designed a matched case–control study of 373 T2D patients and 327 healthy unrelated individuals without history of IS. MtDNA haplogroups were determined on all participants using sequencing of the control region and relevant SNPs from the coding region. Mitochondria functional tests, systemic biochemical measurements and complete genomic mtDNA sequencing were further determined on 239 participants (73 healthy controls, 33 T2D with IS, 70 T2D only and 63 IS patients without T2D). Results MtDNA haplogroups B4a1a, and E2b1 showed significant association with T2D (P <0.05), and haplogroup D4 indicated resistance (P <0.05). Mitochondrial and systemic functional tests showed significantly less variance within groups bearing the same mtDNA haplotypes. There was a pronounced male excess among all T2D patients and prevalence of IS was seen only in the older population. Finally, nucleotide variant np 15746, a determinant of haplogroup G3 seen in Japanese and of B4a1a prevalent in Taiwanese was associated with T2D in both populations. Conclusions Men appeared more susceptible to T2D than women. Although the significant association of B4a1a and E2b1 with T2D ceased when corrected for multiple testings, these haplogroups are seen only among Taiwan Aborigines, Southeast Asian and the Pacific Ocean islanders where T2D is predominant. The data further suggested that physiological and biochemical measurements were influenced by the mtDNA genetic profile of the individual. More understanding of the function of the mitochondrion in the development of T2D might indicate ways of influencing the early course of the disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Marie Lin
- Mackay Memorial Hospital, No, 45, Mínshēng Rd, Danshui District, New Taipei City, Taiwan.
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49
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Ye C, Lou W, Li Y, Chatzispyrou IA, Hüttemann M, Lee I, Houtkooper RH, Vaz FM, Chen S, Greenberg ML. Deletion of the cardiolipin-specific phospholipase Cld1 rescues growth and life span defects in the tafazzin mutant: implications for Barth syndrome. J Biol Chem 2013; 289:3114-25. [PMID: 24318983 DOI: 10.1074/jbc.m113.529487] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cardiolipin (CL) that is synthesized de novo is deacylated to monolysocardiolipin (MLCL), which is reacylated by tafazzin. Remodeled CL contains mostly unsaturated fatty acids. In eukaryotes, loss of tafazzin leads to growth and respiration defects, and in humans, this results in the life-threatening disorder Barth syndrome. Tafazzin deficiency causes a decrease in the CL/MLCL ratio and decreased unsaturated CL species. Which of these biochemical outcomes contributes to the physiological defects is not known. Yeast cells have a single CL-specific phospholipase, Cld1, that can be exploited to distinguish between these outcomes. The cld1Δ mutant has decreased unsaturated CL, but the CL/MLCL ratio is similar to that of wild type cells. We show that cld1Δ rescues growth, life span, and respiratory defects of the taz1Δ mutant. This suggests that defective growth and respiration in tafazzin-deficient cells are caused by the decreased CL/MLCL ratio and not by a deficiency in unsaturated CL. CLD1 expression is increased during respiratory growth and regulated by the heme activator protein transcriptional activation complex. Overexpression of CLD1 leads to decreased mitochondrial respiration and growth and instability of mitochondrial DNA. However, ATP concentrations are maintained by increasing glycolysis. We conclude that transcriptional regulation of Cld1-mediated deacylation of CL influences energy metabolism by modulating the relative contribution of glycolysis and respiration.
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Affiliation(s)
- Cunqi Ye
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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50
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Baniulis D, Hasan SS, Stofleth JT, Cramer WA. Mechanism of enhanced superoxide production in the cytochrome b(6)f complex of oxygenic photosynthesis. Biochemistry 2013; 52:8975-83. [PMID: 24298890 DOI: 10.1021/bi4013534] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The specific rate of superoxide (O2(•-)) production in the purified active crystallizable cytochrome b6f complex, normalized to the rate of electron transport, has been found to be more than an order of magnitude greater than that measured in isolated yeast respiratory bc1 complex. The biochemical and structural basis for the enhanced production of O2(•-) in the cytochrome b6f complex compared to that in the bc1 complex is discussed. The higher rate of superoxide production in the b6f complex could be a consequence of an increased residence time of plastosemiquinone/plastoquinol in its binding niche near the Rieske protein iron-sulfur cluster, resulting from (i) occlusion of the quinone portal by the phytyl chain of the unique bound chlorophyll, (ii) an altered environment of the proton-accepting glutamate believed to be a proton acceptor from semiquinone, or (iii) a more negative redox potential of the heme bp on the electrochemically positive side of the complex. The enhanced rate of superoxide production in the b6f complex is physiologically significant as the chloroplast-generated reactive oxygen species (ROS) functions in the regulation of excess excitation energy, is a source of oxidative damage inflicted during photosynthetic reactions, and is a major source of ROS in plant cells. Altered levels of ROS production are believed to convey redox signaling from the organelle to the cytosol and nucleus.
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Affiliation(s)
- Danas Baniulis
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University , West Lafayette, Indiana 47907, United States
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