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Dubinin MV, Chulkov AV, Igoshkina AD, Cherepanova AA, Mikina NV. Effect of 2-aminoethoxydiphenyl borate on the functions of mouse skeletal muscle mitochondria. Biochem Biophys Res Commun 2024; 712-713:149944. [PMID: 38636302 DOI: 10.1016/j.bbrc.2024.149944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
This work examined the effect of 2-aminoethoxydiphenyl borate (2-APB) on the functioning of isolated mouse skeletal muscle mitochondria and modeled its putative interaction with mitochondrial proteins. We have shown that 2-APB is able to dose-dependently suppress mitochondrial respiration in state 3 and 3UDNP driven by substrates of complex I and II. This effect of 2-APB was accompanied by a slight dose-dependent decrease in mitochondrial membrane potential and appears to be due to inhibition of complex I and complex III of the electron transport chain (ETC) with IC50 values of 200 and 120 μM, respectively. The results of molecular docking identified putative 2-APB interaction sites in these ETC complexes. 2-APB was shown to dose-dependently inhibit both mitochondrial Ca2+ uptake and Ca2+ efflux, which seems to be caused by a decrease in the membrane potential of the organelles. We have found that 2-APB has no significant effect on mitochondrial calcium retention capacity. On the other hand, 2-APB exhibited antioxidant effect by reducing mitochondrial hydrogen peroxide production but without affecting superoxide generation. It is concluded that the effect of 2-APB on mitochondrial targets should be taken into account when interpreting the results of cell and in vivo experiments.
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Affiliation(s)
- Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El, 424001, Russia.
| | | | | | | | - Natalia V Mikina
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El, 424001, Russia
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2
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Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024; 384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
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Affiliation(s)
| | | | | | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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3
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Rigobello L, Lugli F, Caporali L, Bartocci A, Fadanni J, Zerbetto F, Iommarini L, Carelli V, Ghelli AM, Musiani F. A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory complex I. Int J Biol Macromol 2024; 273:133086. [PMID: 38871105 DOI: 10.1016/j.ijbiomac.2024.133086] [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: 03/21/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether a single or a combination of CI variants may impact oxidative phosphorylation. Here we propose a computational approach based on coarse-grained molecular dynamics simulations aimed at investigating new CI variants. One of the primary CI variants associated with the Leber hereditary optic neuropathy (m.14484T>C/MT-ND6) was used as a test case and was investigated alone or in combination with two additional rare CI variants whose role remains uncertain. We found that the primary variant positioned in the E-channel region, which is fundamental for CI function, stiffens the enzyme dynamics. Moreover, a new mechanism for the transition between π- and α-conformation in the helix carrying the primary variant is proposed. This may have implications for the E-channel opening/closing mechanism. Finally, our findings show that one of the rare variants, located next to the primary one, further worsens the stiffening, while the other rare variant does not affect CI function. This approach may be extended to other variants candidate to exert a pathogenic impact on CI dynamics, or to investigate the interaction of multiple variants.
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Affiliation(s)
- Laura Rigobello
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy
| | - Francesca Lugli
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna I-40126, Italy.
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna I-40124, Italy
| | - Alessio Bartocci
- Department of Physics, University of Trento, Trento I-38123, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento I-38123, Italy
| | - Jacopo Fadanni
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna I-40126, Italy
| | - Francesco Zerbetto
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna I-40126, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna I-40124, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna I-40123, Italy
| | - Anna Maria Ghelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy; IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna I-40124, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy.
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4
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Belosludtsev KN, Ilzorkina AI, Matveeva LA, Chulkov AV, Semenova AA, Dubinin MV, Belosludtseva NV. Effect of VBIT-4 on the functional activity of isolated mitochondria and cell viability. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184329. [PMID: 38679309 DOI: 10.1016/j.bbamem.2024.184329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
VBIT-4 is a new inhibitor of the oligomerization of VDAC proteins of the outer mitochondrial membrane preventing the development of oxidative stress, mitochondrial dysfunction, and cell death in various pathologies. However, as a VDAC inhibitor, VBIT-4 may itself cause mitochondrial dysfunction in healthy cells. The article examines the effect of VBIT-4 on the functional activity of rat liver mitochondria and cell cultures. We have demonstrated that high concentrations of VBIT-4 (15-30 μM) suppressed mitochondrial respiration in state 3 and 3UDNP driven by substrates of complex I and II. VBIT-4 induced depolarization of organelles fueled by substrates of complex I but not complex II of the respiratory chain. VBIT-4 has been found to inhibit the activity of complexes I, III, and IV of the respiratory chain. Molecular docking demonstrated that VBIT-4 interacts with the rotenone-binding site in complex I with similar affinity. 15-30 μM VBIT-4 caused an increase in H2O2 production in mitochondria, decreased the Ca2+ retention capacity, but increased the time of Ca2+-dependent mitochondrial swelling. We have found that the incubation of breast adenocarcinoma (MCF-7) with 30 μM VBIT-4 for 48 h led to the decrease of the mitochondrial membrane potential, an increase in ROS production and death of MCF-7 cells. The mechanism of action of VBIT-4 on mitochondria and cells is discussed.
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Affiliation(s)
| | - Anna I Ilzorkina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow region 142290, Russia
| | | | | | - Alena A Semenova
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia
| | - Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia
| | - Natalia V Belosludtseva
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow region 142290, Russia
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5
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024:10.1038/s41586-024-07488-9. [PMID: 38811722 DOI: 10.1038/s41586-024-07488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1-4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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6
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Djurabekova A, Lasham J, Zdorevskyi O, Zickermann V, Sharma V. Long-range electron proton coupling in respiratory complex I - insights from molecular simulations of the quinone chamber and antiporter-like subunits. Biochem J 2024; 481:499-514. [PMID: 38572757 DOI: 10.1042/bcj20240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Respiratory complex I is a redox-driven proton pump. Several high-resolution structures of complex I have been determined providing important information about the putative proton transfer paths and conformational transitions that may occur during catalysis. However, how redox energy is coupled to the pumping of protons remains unclear. In this article, we review biochemical, structural and molecular simulation data on complex I and discuss several coupling models, including the key unresolved mechanistic questions. Focusing both on the quinone-reductase domain as well as the proton-pumping membrane-bound domain of complex I, we discuss a molecular mechanism of proton pumping that satisfies most experimental and theoretical constraints. We suggest that protonation reactions play an important role not only in catalysis, but also in the physiologically-relevant active/deactive transition of complex I.
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Affiliation(s)
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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7
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Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. Nat Struct Mol Biol 2024:10.1038/s41594-024-01255-0. [PMID: 38575788 DOI: 10.1038/s41594-024-01255-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.
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Affiliation(s)
- Irene Vercellino
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
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8
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Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024; 128:2304-2316. [PMID: 38430110 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, the accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here, we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two large membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with titratable amino acids modeled in their standard protonation (charged) states, the structure diverges far from its starting conformation. In comparison, MD simulations performed with predetermined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results support the notion that it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to the launch of any conventional MD simulations. Furthermore, the combined approach of fast protonation state prediction and MD simulations can provide valuable information about the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states in proteinaceous environments currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions but also the atomic modeling of density data.
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Affiliation(s)
- Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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9
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Smith HE, Mackenzie AM, Seddon C, Mould R, Kalampouka I, Malakar P, Needham SR, Beis K, Bell JD, Nunn A, Botchway SW. The use of NADH anisotropy to investigate mitochondrial cristae alignment. Sci Rep 2024; 14:5980. [PMID: 38472304 DOI: 10.1038/s41598-024-55780-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Life may be expressed as the flow of electrons, protons, and other ions, resulting in large potential difference. It is also highly photo-sensitive, as a large proportion of the redox capable molecules it relies on are chromophoric. It is thus suggestive that a key organelle in eukaryotes, the mitochondrion, constantly adapt their morphology as part of the homeostatic process. Studying unstained in vivo nano-scale structure in live cells is technically very challenging. One option is to study a central electron carrier in metabolism, reduced nicotinamide adenine dinucleotide (NADH), which is fluorescent and mostly located within mitochondria. Using one and two-photon absorption (340-360 nm and 730 nm, respectively), fluorescence lifetime imaging and anisotropy spectroscopy of NADH in solution and in live cells, we show that mitochondria do indeed appear to be aligned and exhibit high anisotropy (asymmetric directionality). Aqueous solution of NADH showed an anisotropy of ~ 0.20 compared to fluorescein or coumarin of < 0.1 and 0.04 in water respectively and as expected for small organic molecules. The anisotropy of NADH also increased further to 0.30 in the presence of proteins and 0.42 in glycerol (restricted environment) following two-photon excitation, suggesting more ordered structures. Two-photon NADH fluorescence imaging of Michigan Cancer Foundation-7 (MCF7) also showed strong anisotropy of 0.25 to 0.45. NADH has a quantum yield of fluorescence of 2% compared to more than 40% for photoionisation (electron generation), when exposed to light at 360 nm and below. The consequence of such highly ordered and directional NADH patterns with respect to electron ejection upon ultra-violet (UV) excitation could be very informative-especially in relation to ascertaining the extent of quantum effects in biology, including electron and photonic cascade, communication and modulation of effects such as spin and tunnelling.
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Affiliation(s)
- Holly E Smith
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Alasdair M Mackenzie
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Chloe Seddon
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Rhys Mould
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Ifi Kalampouka
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Partha Malakar
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Sarah R Needham
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Jimmy D Bell
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Alistair Nunn
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Stanley W Botchway
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK.
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10
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Gisdon FJ, Zunker M, Wolf JN, Prüfer K, Ackermann J, Welsch C, Koch I. Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. Bioinformatics 2024; 40:btae112. [PMID: 38449296 DOI: 10.1093/bioinformatics/btae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
MOTIVATION The functional complexity of biochemical processes is strongly related to the interplay of proteins and their assembly into protein complexes. In recent years, the discovery and characterization of protein complexes have substantially progressed through advances in cryo-electron microscopy, proteomics, and computational structure prediction. This development results in a strong need for computational approaches to analyse the data of large protein complexes for structural and functional characterization. Here, we aim to provide a suitable approach, which processes the growing number of large protein complexes, to obtain biologically meaningful information on the hierarchical organization of the structures of protein complexes. RESULTS We modelled the quaternary structure of protein complexes as undirected, labelled graphs called complex graphs. In complex graphs, the vertices represent protein chains and the edges spatial chain-chain contacts. We hypothesized that clusters based on the complex graph correspond to functional biological modules. To compute the clusters, we applied the Leiden clustering algorithm. To evaluate our approach, we chose the human respiratory complex I, which has been extensively investigated and exhibits a known biological module structure experimentally validated. Additionally, we characterized a eukaryotic group II chaperonin TRiC/CCT and the head of the bacteriophage Φ29. The analysis of the protein complexes correlated with experimental findings and indicated known functional, biological modules. Using our approach enables not only to predict functional biological modules in large protein complexes with characteristic features but also to investigate the flexibility of specific regions and coformational changes. The predicted modules can aid in the planning and analysis of experiments. AVAILABILITY AND IMPLEMENTATION Jupyter notebooks to reproduce the examples are available on our public GitHub repository: https://github.com/MolBIFFM/PTGLtools/tree/main/PTGLmodulePrediction.
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Affiliation(s)
- Florian J Gisdon
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Mariella Zunker
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Jan Niclas Wolf
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Kai Prüfer
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Jörg Ackermann
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
| | - Christoph Welsch
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, 60590 Frankfurt am Main, Germany
| | - Ina Koch
- Goethe University Frankfurt, Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, 60325 Frankfurt am Main, Germany
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11
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Laube E, Schiller J, Zickermann V, Vonck J. Using cryo-EM to understand the assembly pathway of respiratory complex I. Acta Crystallogr D Struct Biol 2024; 80:159-173. [PMID: 38372588 PMCID: PMC10910544 DOI: 10.1107/s205979832400086x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the first component of the mitochondrial respiratory chain. In recent years, high-resolution cryo-EM studies of complex I from various species have greatly enhanced the understanding of the structure and function of this important membrane-protein complex. Less well studied is the structural basis of complex I biogenesis. The assembly of this complex of more than 40 subunits, encoded by nuclear or mitochondrial DNA, is an intricate process that requires at least 20 different assembly factors in humans. These are proteins that are transiently associated with building blocks of the complex and are involved in the assembly process, but are not part of mature complex I. Although the assembly pathways have been studied extensively, there is limited information on the structure and molecular function of the assembly factors. Here, the insights that have been gained into the assembly process using cryo-EM are reviewed.
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Affiliation(s)
- Eike Laube
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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12
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Mourokh L, Friedman J. Mitochondria at the Nanoscale: Physics Meets Biology-What Does It Mean for Medicine? Int J Mol Sci 2024; 25:2835. [PMID: 38474079 DOI: 10.3390/ijms25052835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Mitochondria are commonly perceived as "cellular power plants". Intriguingly, power conversion is not their only function. In the first part of this paper, we review the role of mitochondria in the evolution of eukaryotic organisms and in the regulation of the human body, specifically focusing on cancer and autism in relation to mitochondrial dysfunction. In the second part, we overview our previous works, revealing the physical principles of operation for proton-pumping complexes in the inner mitochondrial membrane. Our proposed simple models reveal the physical mechanisms of energy exchange. They can be further expanded to answer open questions about mitochondrial functions and the medical treatment of diseases associated with mitochondrial disorders.
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Affiliation(s)
- Lev Mourokh
- Physics Department, Queens College, The City University of New York, 65-30 Kissena Blvd. Flushing, New York, NY 11367, USA
| | - Jonathan Friedman
- Physics Department, Queens College, The City University of New York, 65-30 Kissena Blvd. Flushing, New York, NY 11367, USA
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13
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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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14
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Aleo SJ, Del Dotto V, Romagnoli M, Fiorini C, Capirossi G, Peron C, Maresca A, Caporali L, Capristo M, Tropeano CV, Zanna C, Ross-Cisneros FN, Sadun AA, Pignataro MG, Giordano C, Fasano C, Cavaliere A, Porcelli AM, Tioli G, Musiani F, Catania A, Lamperti C, Marzoli SB, De Negri A, Cascavilla ML, Battista M, Barboni P, Carbonelli M, Amore G, La Morgia C, Smirnov D, Vasilescu C, Farzeen A, Blickhaeuser B, Prokisch H, Priglinger C, Livonius B, Catarino CB, Klopstock T, Tiranti V, Carelli V, Ghelli AM. Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy. Cell Rep Med 2024; 5:101383. [PMID: 38272025 PMCID: PMC10897523 DOI: 10.1016/j.xcrm.2023.101383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 07/03/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Idebenone, the only approved treatment for Leber hereditary optic neuropathy (LHON), promotes recovery of visual function in up to 50% of patients, but we can neither predict nor understand the non-responders. Idebenone is reduced by the cytosolic NAD(P)H oxidoreductase I (NQO1) and directly shuttles electrons to respiratory complex III, bypassing complex I affected in LHON. We show here that two polymorphic variants drastically reduce NQO1 protein levels when homozygous or compound heterozygous. This hampers idebenone reduction. In its oxidized form, idebenone inhibits complex I, decreasing respiratory function in cells. By retrospectively analyzing a large cohort of idebenone-treated LHON patients, classified by their response to therapy, we show that patients with homozygous or compound heterozygous NQO1 variants have the poorest therapy response, particularly if carrying the m.3460G>A/MT-ND1 LHON mutation. These results suggest consideration of patient NQO1 genotype and mitochondrial DNA mutation in the context of idebenone therapy.
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Affiliation(s)
- Serena Jasmine Aleo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valentina Del Dotto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Giada Capirossi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Camille Peron
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Mariantonietta Capristo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | | | - Claudia Zanna
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | | | - Alfredo A Sadun
- Doheny Eye Institute, Pasadena, CA, USA; Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Maria Gemma Pignataro
- Departments of Radiology, Oncology, and Pathology, Sapienza, University of Rome, Rome, Italy
| | - Carla Giordano
- Departments of Radiology, Oncology, and Pathology, Sapienza, University of Rome, Rome, Italy
| | - Chiara Fasano
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Andrea Cavaliere
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Anna Maria Porcelli
- Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gaia Tioli
- Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Francesco Musiani
- Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Stefania Bianchi Marzoli
- Neuro-Ophthalmology Center and Ocular Electrophysiology Laboratory, IRCCS Istituto Auxologico Italiano, Capitanio Hospital, Milan, Italy
| | | | | | | | | | - Michele Carbonelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Giulia Amore
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Dmitrii Smirnov
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Catalina Vasilescu
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Aiman Farzeen
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Beryll Blickhaeuser
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany; Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Munich, Germany
| | - Claudia Priglinger
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Bettina Livonius
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Claudia B Catarino
- Department of Neurology, Friedrich Baur Institute, LMU Klinikum, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich Baur Institute, LMU Klinikum, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Valeria Tiranti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
| | - Anna Maria Ghelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy; Departments of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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15
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Moran BM, Payne CY, Powell DL, Iverson ENK, Donny AE, Banerjee SM, Langdon QK, Gunn TR, Rodriguez-Soto RA, Madero A, Baczenas JJ, Kleczko KM, Liu F, Matney R, Singhal K, Leib RD, Hernandez-Perez O, Corbett-Detig R, Frydman J, Gifford C, Schartl M, Havird JC, Schumer M. A lethal mitonuclear incompatibility in complex I of natural hybrids. Nature 2024; 626:119-127. [PMID: 38200310 PMCID: PMC10830419 DOI: 10.1038/s41586-023-06895-8] [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: 07/30/2021] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of hybrid incompatibilities, in which alleles derived from two different species no longer interact properly in hybrids1-3. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes4-6 and that incompatibilities involving multiple genes should be common7,8, but there has been sparse empirical data to evaluate these predictions. Here we describe a mitonuclear incompatibility involving three genes whose protein products are in physical contact within respiratory complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations do not complete embryonic development or die as juveniles, whereas those heterozygous for the incompatibility have reduced complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the effects of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and evidence that an incompatibility has been transferred between species via hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford University, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico.
| | - Cheyenne Y Payne
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Erik N K Iverson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | | | - Quinn K Langdon
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Theresa R Gunn
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Angel Madero
- Department of Biology, Stanford University, Stanford, CA, USA
| | - John J Baczenas
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Fang Liu
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Rowan Matney
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Kratika Singhal
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Ryan D Leib
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Osvaldo Hernandez-Perez
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Russell Corbett-Detig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Casey Gifford
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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16
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Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK. Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism. Cell 2024; 187:659-675.e18. [PMID: 38215760 PMCID: PMC10919891 DOI: 10.1016/j.cell.2023.12.010] [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: 02/20/2023] [Revised: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024]
Abstract
The electron transport chain (ETC) of mitochondria, bacteria, and archaea couples electron flow to proton pumping and is adapted to diverse oxygen environments. Remarkably, in mice, neurological disease due to ETC complex I dysfunction is rescued by hypoxia through unknown mechanisms. Here, we show that hypoxia rescue and hyperoxia sensitivity of complex I deficiency are evolutionarily conserved to C. elegans and are specific to mutants that compromise the electron-conducting matrix arm. We show that hypoxia rescue does not involve the hypoxia-inducible factor pathway or attenuation of reactive oxygen species. To discover the mechanism, we use C. elegans genetic screens to identify suppressor mutations in the complex I accessory subunit NDUFA6/nuo-3 that phenocopy hypoxia rescue. We show that NDUFA6/nuo-3(G60D) or hypoxia directly restores complex I forward activity, with downstream rescue of ETC flux and, in some cases, complex I levels. Additional screens identify residues within the ubiquinone binding pocket as being required for the rescue by NDUFA6/nuo-3(G60D) or hypoxia. This reveals oxygen-sensitive coupling between an accessory subunit and the quinone binding pocket of complex I that can restore forward activity in the same manner as hypoxia.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maria Miranda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sandra M Wellner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexis A Jourdain
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
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17
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Shin YC, Latorre-Muro P, Djurabekova A, Zdorevskyi O, Bennett CF, Burger N, Song K, Xu C, Sharma V, Liao M, Puigserver P. Structural basis of respiratory complexes adaptation to cold temperatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575914. [PMID: 38293190 PMCID: PMC10827213 DOI: 10.1101/2024.01.16.575914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain (1, 2). Yet, the structural basis of respiratory complex adaptation to cold remains elusive. Herein we combined thermoregulatory physiology and cryo-EM to study endogenous respiratory supercomplexes exposed to different temperatures. A cold-induced conformation of CI:III 2 (termed type 2) was identified with a ∼25° rotation of CIII 2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting different catalytic states which favor electron transfer. Large-scale supercomplex simulations in lipid membrane reveal how unique lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations and biochemical analyses unveil the mechanisms and dynamics of respiratory adaptation at the structural and energetic level.
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18
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Braun HP, Klusch N. Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases? TRENDS IN PLANT SCIENCE 2024; 29:64-71. [PMID: 37599162 DOI: 10.1016/j.tplants.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
The mitochondrial NADH-dehydrogenase complex of the respiratory chain, known as complex I, includes a carbonic anhydrase (CA) module attached to its membrane arm on the matrix side in protozoans, algae, and plants. Its physiological role is so far unclear. Recent electron cryo-microscopy (cryo-EM) structures show that the CA module may directly provide protons for translocation across the inner mitochondrial membrane at complex I. CAs can have a central role in adjusting the proton concentration in the mitochondrial matrix. We suggest that CA anchoring in complex I represents the original configuration to secure oxidative phosphorylation (OXPHOS) in the context of early endosymbiosis. After development of 'modern mitochondria' with pronounced cristae structures, this anchoring became dispensable, but has been retained in protozoans, algae, and plants.
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Affiliation(s)
- Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Niklas Klusch
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt, Germany.
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19
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Harada H, Moriya K, Kobuchi H, Ishihara N, Utsumi T. Protein N-myristoylation plays a critical role in the mitochondrial localization of human mitochondrial complex I accessory subunit NDUFB7. Sci Rep 2023; 13:22991. [PMID: 38151566 PMCID: PMC10752898 DOI: 10.1038/s41598-023-50390-z] [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: 09/18/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The present study examined human N-myristoylated proteins that specifically localize to mitochondria among the 1,705 human genes listed in MitoProteome, a mitochondrial protein database. We herein employed a strategy utilizing cellular metabolic labeling with a bioorthogonal myristic acid analog in transfected COS-1 cells established in our previous studies. Four proteins, DMAC1, HCCS, NDUFB7, and PLGRKT, were identified as N-myristoylated proteins that specifically localize to mitochondria. Among these proteins, DMAC1 and NDUFB7 play critical roles in the assembly of complex I of the mitochondrial respiratory chain. DMAC1 functions as an assembly factor, and NDUFB7 is an accessory subunit of complex I. An analysis of the intracellular localization of non-myristoylatable G2A mutants revealed that protein N-myristoylation occurring on NDUFB7 was important for the mitochondrial localization of this protein. Furthermore, an analysis of the role of the CHCH domain in NDUFB7 using Cys to Ser mutants revealed that it was essential for the mitochondrial localization of NDUFB7. Therefore, the present results showed that NDUFB7, a vital component of human mitochondrial complex I, was N-myristoylated, and protein N-myrisotylation and the CHCH domain were both indispensable for the specific targeting and localization of NDUFB7 to mitochondria.
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Affiliation(s)
- Haruna Harada
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Koko Moriya
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Hirotsugu Kobuchi
- Department of Cell Chemistry, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Naotada Ishihara
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Toshihiko Utsumi
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.
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20
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Han H, Zhao C, Liu M, Zhu H, Meng F, Zhang Y, Wang G, Wang L, Di L, Mingyuen Lee S, Zhang Q, Cui G. Mitochondrial complex I inhibition by homoharringtonine: A novel strategy for suppression of chronic myeloid leukemia. Biochem Pharmacol 2023; 218:115875. [PMID: 37871881 DOI: 10.1016/j.bcp.2023.115875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Chronic myeloid leukemia (CML) is a hematologic malignancy predominantly driven by the BCR-ABL fusion gene. One of the significant challenges in treating CML lies in the emergence of resistance to tyrosine kinase inhibitors (TKIs), especially those associated with the T315I mutation. Homoharringtonine (HHT) is an FDA-approved, naturally-derived drug with known anti-leukemic properties, but its precise mechanisms of action remain incompletely understood. In this study, we rigorously evaluated the anti-CML activity of HHT through both in vitro and in vivo assays, observing substantial anti-CML effects. To elucidate the molecular mechanisms underpinning these effects, we performed proteomic analysis on BCR-ABL T315I mutation-bearing cells treated with HHT. Comprehensive pathway enrichment analysis identified oxidative phosphorylation (OXPHOS) as the most significantly disrupted, suggesting a key role in the mechanism of action of HHT. Further bioinformatics exploration revealed a substantial downregulation of proteins localized within mitochondrial complex I (MCI), a critical OXPHOS component. These results were validated through Western blot analysis and were supplemented by marked reductions in MCI activity, ATP level, and oxygen consumption rate (OCR) upon HHT exposure. Collectively, our results shed light on the potent anti-CML properties of HHT, particularly its effectiveness against T315I mutant cells through MCI inhibition. Our study underscores a novel therapeutic strategy to overcome BCR-ABL T315I mutation resistance, illuminating a previously uncharted mechanism of action for HHT.
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Affiliation(s)
- Han Han
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Chen Zhao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Mengchen Liu
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Hongxuan Zhu
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Fancheng Meng
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Ying Zhang
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Guibin Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Li Wang
- Faculty of Health sciences, University of Macau, Macau SAR, China
| | - Lijun Di
- Faculty of Health sciences, University of Macau, Macau SAR, China
| | - Simon Mingyuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Qingwen Zhang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China.
| | - Guozhen Cui
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China.
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21
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Yi JT, Wang P, Stuchebrukhov AA. Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I. Sci Rep 2023; 13:20413. [PMID: 37989876 PMCID: PMC10663621 DOI: 10.1038/s41598-023-47314-2] [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: 08/13/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023] Open
Abstract
In all resolved structures of complex I, there exists a tunnel-like Q-chamber for ubiquinone binding and reduction. The entrance to the Q-chamber in ND1 subunit forms a narrow bottleneck, which is rather tight and requires thermal conformational changes for ubiquinone to get in and out of the binding chamber. The substitution of alanine with threonine at the bottleneck (AlaThr MUT), associated with 3460/ND1 mtDNA mutation in human complex I, is implicated in Leber's Hereditary Optic Neuropathy (LHON). Here, we show the AlaThr MUT further narrows the Q-chamber entrance cross-section area by almost 30%, increasing the activation free energy barrier of quinone passage by approximately 5 kJ mol-1. This severely disrupts quinone binding and reduction as quinone passage through the bottleneck is slowed down almost tenfold. Our estimate of the increase in free energy barrier is entirely due to the bottleneck narrowing, leading to a reduction of the transition state entropy between WT and MUT, and thus more difficult quinone passage. Additionally, we investigate details of possible water exchange between the Q-chamber and membrane. We find water exchange is dynamic in WT but may be severely slowed in MUT. We propose that LHON symptoms caused by 3460/ND1 mtDNA mutation are due to slowed quinone binding. This leads to an increased production of reactive oxidative species due to upstream electron backup at the FMN site of complex I, thus resulting in a mt bioenergetic defect.
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Affiliation(s)
- Jason Tae Yi
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA.
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22
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Kohler A, Barrientos A, Fontanesi F, Ott M. The functional significance of mitochondrial respiratory chain supercomplexes. EMBO Rep 2023; 24:e57092. [PMID: 37828827 PMCID: PMC10626428 DOI: 10.15252/embr.202357092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/10/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
The mitochondrial respiratory chain (MRC) is a key energy transducer in eukaryotic cells. Four respiratory chain complexes cooperate in the transfer of electrons derived from various metabolic pathways to molecular oxygen, thereby establishing an electrochemical gradient over the inner mitochondrial membrane that powers ATP synthesis. This electron transport relies on mobile electron carries that functionally connect the complexes. While the individual complexes can operate independently, they are in situ organized into large assemblies termed respiratory supercomplexes. Recent structural and functional studies have provided some answers to the question of whether the supercomplex organization confers an advantage for cellular energy conversion. However, the jury is still out, regarding the universality of these claims. In this review, we discuss the current knowledge on the functional significance of MRC supercomplexes, highlight experimental limitations, and suggest potential new strategies to overcome these obstacles.
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Affiliation(s)
- Andreas Kohler
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Antoni Barrientos
- Department of Neurology, Miller School of MedicineUniversity of MiamiMiamiFLUSA
- Department of Biochemistry and Molecular Biology, Miller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, Miller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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23
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Okoye CN, Koren SA, Wojtovich AP. Mitochondrial complex I ROS production and redox signaling in hypoxia. Redox Biol 2023; 67:102926. [PMID: 37871533 PMCID: PMC10598411 DOI: 10.1016/j.redox.2023.102926] [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: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Mitochondria are a main source of cellular energy. Oxidative phosphorylation (OXPHOS) is the major process of aerobic respiration. Enzyme complexes of the electron transport chain (ETC) pump protons to generate a protonmotive force (Δp) that drives OXPHOS. Complex I is an electron entry point into the ETC. Complex I oxidizes nicotinamide adenine dinucleotide (NADH) and transfers electrons to ubiquinone in a reaction coupled with proton pumping. Complex I also produces reactive oxygen species (ROS) under various conditions. The enzymatic activities of complex I can be regulated by metabolic conditions and serves as a regulatory node of the ETC. Complex I ROS plays diverse roles in cell metabolism ranging from physiologic to pathologic conditions. Progress in our understanding indicates that ROS release from complex I serves important signaling functions. Increasing evidence suggests that complex I ROS is important in signaling a mismatch in energy production and demand. In this article, we review the role of ROS from complex I in sensing acute hypoxia.
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Affiliation(s)
- Chidozie N Okoye
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Shon A Koren
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Wojtovich
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA; Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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24
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Tao H, Zhu P, Xia W, Chu M, Chen K, Wang Q, Gu Y, Lu X, Bai J, Geng D. The Emerging Role of the Mitochondrial Respiratory Chain in Skeletal Aging. Aging Dis 2023:AD.2023.0924. [PMID: 37815897 DOI: 10.14336/ad.2023.0924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/24/2023] [Indexed: 10/12/2023] Open
Abstract
Maintenance of mitochondrial homeostasis is crucial for ensuring healthy mitochondria and normal cellular function. This process is primarily responsible for regulating processes that include mitochondrial OXPHOS, which generates ATP, as well as mitochondrial oxidative stress, apoptosis, calcium homeostasis, and mitophagy. Bone mesenchymal stem cells express factors that aid in bone formation and vascular growth. Positive regulation of hematopoietic stem cells in the bone marrow affects the differentiation of osteoclasts. Furthermore, the metabolic regulation of cells that play fundamental roles in various regions of the bone, as well as interactions within the bone microenvironment, actively participates in regulating bone integrity and aging. The maintenance of cellular homeostasis is dependent on the regulation of intracellular organelles, thus understanding the impact of mitochondrial functional changes on overall bone metabolism is crucially important. Recent studies have revealed that mitochondrial homeostasis can lead to morphological and functional abnormalities in senescent cells, particularly in the context of bone diseases. Mitochondrial dysfunction in skeletal diseases results in abnormal metabolism of bone-associated cells and a secondary dysregulated microenvironment within bone tissue. This imbalance in the oxidative system and immune disruption in the bone microenvironment ultimately leads to bone dysplasia. In this review, we examine the latest developments in mitochondrial respiratory chain regulation and its impacts on maintenance of bone health. Specifically, we explored whether enhancing mitochondrial function can reduce the occurrence of bone cell deterioration and improve bone metabolism. These findings offer prospects for developing bone remodeling biology strategies to treat age-related degenerative diseases.
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Affiliation(s)
- Huaqiang Tao
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Pengfei Zhu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Wenyu Xia
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Miao Chu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Kai Chen
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Qiufei Wang
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Jiangsu, China
| | - Ye Gu
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Jiangsu, China
| | - Xiaomin Lu
- Department of Oncology, Affiliated Haian Hospital of Nantong University, Jiangsu, China
| | - Jiaxiang Bai
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, China
| | - Dechun Geng
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Jiangsu, China
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25
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Kim H, Saura P, Pöverlein MC, Gamiz-Hernandez AP, Kaila VRI. Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I. J Am Chem Soc 2023; 145:17075-17086. [PMID: 37490414 PMCID: PMC10416309 DOI: 10.1021/jacs.3c03086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 07/27/2023]
Abstract
Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.
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Affiliation(s)
- Hyunho Kim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | | | - Ana P. Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
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26
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Yan Q, Liu S, Sun Y, Chen C, Yang S, Lin M, Long J, Yao J, Lin Y, Yi F, Meng L, Tan Y, Ai Q, Chen N, Yang Y. Targeting oxidative stress as a preventive and therapeutic approach for cardiovascular disease. J Transl Med 2023; 21:519. [PMID: 37533007 PMCID: PMC10394930 DOI: 10.1186/s12967-023-04361-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/16/2023] [Indexed: 08/04/2023] Open
Abstract
Cardiovascular diseases (CVDs) continue to exert a significant impact on global mortality rates, encompassing conditions like pulmonary arterial hypertension (PAH), atherosclerosis (AS), and myocardial infarction (MI). Oxidative stress (OS) plays a crucial role in the pathogenesis and advancement of CVDs, highlighting its significance as a contributing factor. Maintaining an equilibrium between reactive oxygen species (ROS) and antioxidant systems not only aids in mitigating oxidative stress but also confers protective benefits on cardiac health. Herbal monomers can inhibit OS in CVDs by activating multiple signaling pathways, such as increasing the activity of endogenous antioxidant systems and decreasing the level of ROS expression. Given the actions of herbal monomers to significantly protect the normal function of the heart and reduce the damage caused by OS to the organism. Hence, it is imperative to recognize the significance of herbal monomers as prospective therapeutic interventions for mitigating oxidative damage in CVDs. This paper aims to comprehensively review the origins and mechanisms underlying OS, elucidate the intricate association between CVDs and OS, and explore the therapeutic potential of antioxidant treatment utilizing herbal monomers. Furthermore, particular emphasis will be placed on examining the cardioprotective effects of herbal monomers by evaluating their impact on cardiac signaling pathways subsequent to treatment.
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Affiliation(s)
- Qian Yan
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Shasha Liu
- Department of Pharmacy, Changsha Hospital for Matemal&Child Health Care, Changsha, People's Republic of China
| | - Yang Sun
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Chen Chen
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Songwei Yang
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Meiyu Lin
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Junpeng Long
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Jiao Yao
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yuting Lin
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Fan Yi
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, 100048, China
| | - Lei Meng
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yong Tan
- Department of Nephrology, Xiangtan Central Hospital, Xiangtan, 411100, China
| | - Qidi Ai
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China.
| | - Naihong Chen
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China.
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Yantao Yang
- Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China.
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27
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Grba DN, Chung I, Bridges HR, Agip ANA, Hirst J. Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I. SCIENCE ADVANCES 2023; 9:eadi1359. [PMID: 37531432 PMCID: PMC10396290 DOI: 10.1126/sciadv.adi1359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023]
Abstract
Respiratory complex I, a key enzyme in mammalian metabolism, captures the energy released by reduction of ubiquinone by NADH to drive protons across the inner mitochondrial membrane, generating the proton-motive force for ATP synthesis. Despite remarkable advances in structural knowledge of this complicated membrane-bound enzyme, its mechanism of catalysis remains controversial. In particular, how ubiquinone reduction is coupled to proton pumping and the pathways and mechanisms of proton translocation are contested. We present a 2.4-Å resolution cryo-EM structure of complex I from mouse heart mitochondria in the closed, active (ready-to-go) resting state, with 2945 water molecules modeled. By analyzing the networks of charged and polar residues and water molecules present, we evaluate candidate pathways for proton transfer through the enzyme, for the chemical protons for ubiquinone reduction, and for the protons transported across the membrane. Last, we compare our data to the predictions of extant mechanistic models, and identify key questions to answer in future work to test them.
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28
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Hardy RE, Chung I, Yu Y, Loh SHY, Morone N, Soleilhavoup C, Travaglio M, Serreli R, Panman L, Cain K, Hirst J, Martins LM, MacFarlane M, Pryde KR. The antipsychotic medications aripiprazole, brexpiprazole and cariprazine are off-target respiratory chain complex I inhibitors. Biol Direct 2023; 18:43. [PMID: 37528429 PMCID: PMC10391878 DOI: 10.1186/s13062-023-00375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/11/2023] [Indexed: 08/03/2023] Open
Abstract
Antipsychotic drugs are the mainstay of treatment for schizophrenia and provide adjunct therapies for other prevalent psychiatric conditions, including bipolar disorder and major depressive disorder. However, they also induce debilitating extrapyramidal syndromes (EPS), such as Parkinsonism, in a significant minority of patients. The majority of antipsychotic drugs function as dopamine receptor antagonists in the brain while the most recent 'third'-generation, such as aripiprazole, act as partial agonists. Despite showing good clinical efficacy, these newer agents are still associated with EPS in ~ 5 to 15% of patients. However, it is not fully understood how these movement disorders develop. Here, we combine clinically-relevant drug concentrations with mutliscale model systems to show that aripiprazole and its primary active metabolite induce mitochondrial toxicity inducing robust declines in cellular ATP and viability. Aripiprazole, brexpiprazole and cariprazine were shown to directly inhibit respiratory complex I through its ubiquinone-binding channel. Importantly, all three drugs induced mitochondrial toxicity in primary embryonic mouse neurons, with greater bioenergetic inhibition in ventral midbrain neurons than forebrain neurons. Finally, chronic feeding with aripiprazole resulted in structural damage to mitochondria in the brain and thoracic muscle of adult Drosophila melanogaster consistent with locomotor dysfunction. Taken together, we show that antipsychotic drugs acting as partial dopamine receptor agonists exhibit off-target mitochondrial liabilities targeting complex I.
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Affiliation(s)
- Rachel E Hardy
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Samantha H Y Loh
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nobuhiro Morone
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Clement Soleilhavoup
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Marco Travaglio
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Riccardo Serreli
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Lia Panman
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Kelvin Cain
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Luis M Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Marion MacFarlane
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Kenneth R Pryde
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK.
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29
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Ikunishi R, Otani R, Masuya T, Shinzawa-Itoh K, Shiba T, Murai M, Miyoshi H. Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones. J Biol Chem 2023; 299:105001. [PMID: 37394006 PMCID: PMC10416054 DOI: 10.1016/j.jbc.2023.105001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/04/2023] Open
Abstract
NADH-ubiquinone (UQ) oxidoreductase (complex I) couples electron transfer from NADH to UQ with proton translocation in its membrane part. The UQ reduction step is key to triggering proton translocation. Structural studies have identified a long, narrow, tunnel-like cavity within complex I, through which UQ may access a deep reaction site. To elucidate the physiological relevance of this UQ-accessing tunnel, we previously investigated whether a series of oversized UQs (OS-UQs), whose tail moiety is too large to enter and transit the narrow tunnel, can be catalytically reduced by complex I using the native enzyme in bovine heart submitochondrial particles (SMPs) and the isolated enzyme reconstituted into liposomes. Nevertheless, the physiological relevance remained unclear because some amphiphilic OS-UQs were reduced in SMPs but not in proteoliposomes, and investigation of extremely hydrophobic OS-UQs was not possible in SMPs. To uniformly assess the electron transfer activities of all OS-UQs with the native complex I, here we present a new assay system using SMPs, which were fused with liposomes incorporating OS-UQ and supplemented with a parasitic quinol oxidase to recycle reduced OS-UQ. In this system, all OS-UQs tested were reduced by the native enzyme, and the reduction was coupled with proton translocation. This finding does not support the canonical tunnel model. We propose that the UQ reaction cavity is flexibly open in the native enzyme to allow OS-UQs to access the reaction site, but their access is obstructed in the isolated enzyme as the cavity is altered by detergent-solubilizing from the mitochondrial membrane.
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Affiliation(s)
- Ryo Ikunishi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ryohei Otani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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30
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Kägi J, Sloan W, Schimpf J, Nasiri HR, Lashley D, Friedrich T. Exploring ND-011992, a quinazoline-type inhibitor targeting quinone reductases and quinol oxidases. Sci Rep 2023; 13:12226. [PMID: 37507428 PMCID: PMC10382516 DOI: 10.1038/s41598-023-39430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial energy metabolism has become a promising target for next-generation tuberculosis chemotherapy. One strategy to hamper ATP production is to inhibit the respiratory oxidases. The respiratory chain of Mycobacterium tuberculosis comprises a cytochrome bcc:aa3 and a cytochrome bd ubiquinol oxidase that require a combined approach to block their activity. A quinazoline-type compound called ND-011992 has previously been reported to ineffectively inhibit bd oxidases, but to act bactericidal in combination with inhibitors of cytochrome bcc:aa3 oxidase. Due to the structural similarity of ND-011992 to quinazoline-type inhibitors of respiratory complex I, we suspected that this compound is also capable of blocking other respiratory chain complexes. Here, we synthesized ND-011992 and a bromine derivative to study their effect on the respiratory chain complexes of Escherichia coli. And indeed, ND-011992 was found to inhibit respiratory complex I and bo3 oxidase in addition to bd-I and bd-II oxidases. The IC50 values are all in the low micromolar range, with inhibition of complex I providing the lowest value with an IC50 of 0.12 µM. Thus, ND-011992 acts on both, quinone reductases and quinol oxidases and could be very well suited to regulate the activity of the entire respiratory chain.
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Affiliation(s)
- Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willough Sloan
- Department of Chemistry, William & Mary, Williamsburg, VA, USA
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hamid R Nasiri
- Department of Cellular Microbiology, University Hohenheim, Stuttgart, Germany
| | - Dana Lashley
- Department of Chemistry, William & Mary, Williamsburg, VA, USA.
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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31
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Wang X, Wang H, Zhang M. A multi-stimuli-responsive nanochannel inspired by biological disulfide bond. Talanta 2023; 265:124785. [PMID: 37348351 DOI: 10.1016/j.talanta.2023.124785] [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: 02/02/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/24/2023]
Abstract
Disulfide bonds exist widely in channel protein and play an essential role in matter exchange and signal transduction (e.g., rhodopsin, canonical transient receptor potential 5 (TRPC5)). The research on disulfide bond in nanochannel is significant for the cognition of their biological functions. However, the fragility of biological channel limits the in-situ study and practical application. Herein, an innovative biologically-inspired artificial nanochannel based on disulfide bond (NCDS) with excellent durability, adjustable surface property is proposed. The constructed NCDS has a multi-response to UV-light, thiol (e.g., cysteine (Cys)) or pH stimulation, and can obtain reversibility after regulation by hydrogen peroxide (H2O2) or H+. The biomimetic NCDS shows great potential in biosensor and intelligent response design. This study also shines new light to channel protein based on disulfide bond that despite the nanochannel has specificity, it will be modulated by the change of nature environment, such as UV-light and chemical microenvironment (e.g., redox state and pH), which might be the reason of some disease.
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Affiliation(s)
- Xiaofang Wang
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Huiming Wang
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Meining Zhang
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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32
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Zdorevskyi O, Djurabekova A, Lasham J, Sharma V. Horizontal proton transfer across the antiporter-like subunits in mitochondrial respiratory complex I. Chem Sci 2023; 14:6309-6318. [PMID: 37325138 PMCID: PMC10266447 DOI: 10.1039/d3sc01427d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Respiratory complex I is a redox-driven proton pump contributing to about 40% of total proton motive force required for mitochondrial ATP generation. Recent high-resolution cryo-EM structural data revealed the positions of several water molecules in the membrane domain of the large enzyme complex. However, it remains unclear how protons flow in the membrane-bound antiporter-like subunits of complex I. Here, we performed multiscale computer simulations on high-resolution structural data to model explicit proton transfer processes in the ND2 subunit of complex I. Our results show protons can travel the entire width of antiporter-like subunits, including at the subunit-subunit interface, parallel to the membrane. We identify a previously unrecognized role of conserved tyrosine residues in catalyzing horizontal proton transfer, and that long-range electrostatic effects assist in reducing energetic barriers of proton transfer dynamics. Results from our simulations warrant a revision in several prevailing proton pumping models of respiratory complex I.
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Affiliation(s)
| | | | - Jonathan Lasham
- Department of Physics, University of Helsinki Helsinki Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki Helsinki Finland
- HiLIFE Institute of Biotechnology, University of Helsinki Helsinki Finland
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Ghifari AS, Saha S, Murcha MW. The biogenesis and regulation of the plant oxidative phosphorylation system. PLANT PHYSIOLOGY 2023; 192:728-747. [PMID: 36806687 DOI: 10.1093/plphys/kiad108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 06/01/2023]
Abstract
Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Saurabh Saha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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Han F, Hu Y, Wu M, He Z, Tian H, Zhou L. Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae. Nat Commun 2023; 14:2542. [PMID: 37248254 DOI: 10.1038/s41467-023-38158-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Tetrahymena thermophila, a classic ciliate model organism, has been shown to possess tubular mitochondrial cristae and highly divergent electron transport chain involving four transmembrane protein complexes (I-IV). Here we report cryo-EM structures of its ~8 MDa megacomplex IV2 + (I + III2 + II)2, as well as a ~ 10.6 MDa megacomplex (IV2 + I + III2 + II)2 at lower resolution. In megacomplex IV2 + (I + III2 + II)2, each CIV2 protomer associates one copy of supercomplex I + III2 and one copy of CII, forming a half ring-shaped architecture that adapts to the membrane curvature of mitochondrial cristae. Megacomplex (IV2 + I + III2 + II)2 defines the relative position between neighbouring half rings and maintains the proximity between CIV2 and CIII2 cytochrome c binding sites. Our findings expand the current understanding of divergence in eukaryotic electron transport chain organization and how it is related to mitochondrial morphology.
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Affiliation(s)
- Fangzhu Han
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Yiqi Hu
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Mengchen Wu
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Zhaoxiang He
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Hongtao Tian
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Long Zhou
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China.
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China.
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Rákosníková T, Kelifová S, Štufková H, Lokvencová K, Lišková P, Kousal B, Honzík T, Hansíková H, Martínek V, Tesařová M. Case report: A rare variant m.4135T>C in the MT-ND1 gene leads to Leber hereditary optic neuropathy and altered respiratory chain supercomplexes. Front Genet 2023; 14:1182288. [PMID: 37274791 PMCID: PMC10233053 DOI: 10.3389/fgene.2023.1182288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
Leber hereditary optic neuropathy is a primary mitochondrial disease characterized by acute visual loss due to the degeneration of retinal ganglion cells. In this study, we describe a patient carrying a rare missense heteroplasmic variant in MT-ND1, NC_012920.1:m.4135T>C (p.Tyr277His) manifesting with a typical bilateral painless decrease of the visual function, triggered by physical exercise or higher ambient temperature. Functional studies in muscle and fibroblasts show that amino acid substitution Tyr277 with His leads to only a negligibly decreased level of respiratory chain complex I (CI), but the formation of supercomplexes and the activity of the enzyme are disturbed noticeably. Our data indicate that although CI is successfully assembled in the patient's mitochondria, its function is hampered by the m.4135T>C variant, probably by stabilizing CI in its inactive form. We conclude that the m.4135T>C variant together with a combination of external factors is necessary to manifest the phenotype.
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Affiliation(s)
- Tereza Rákosníková
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Silvie Kelifová
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Hana Štufková
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Kateřina Lokvencová
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Petra Lišková
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Bohdan Kousal
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Tomáš Honzík
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Hana Hansíková
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Václav Martínek
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czechia
| | - Markéta Tesařová
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
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Strotmann L, Harter C, Gerasimova T, Ritter K, Jessen HJ, Wohlwend D, Friedrich T. H 2O 2 selectively damages the binuclear iron-sulfur cluster N1b of respiratory complex I. Sci Rep 2023; 13:7652. [PMID: 37169846 PMCID: PMC10175503 DOI: 10.1038/s41598-023-34821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
NADH:ubiquinone oxidoreductase, respiratory complex I, plays a major role in cellular energy metabolism by coupling electron transfer with proton translocation. Electron transfer is catalyzed by a flavin mononucleotide and a series of iron-sulfur (Fe/S) clusters. As a by-product of the reaction, the reduced flavin generates reactive oxygen species (ROS). It was suggested that the ROS generated by the respiratory chain in general could damage the Fe/S clusters of the complex. Here, we show that the binuclear Fe/S cluster N1b is specifically damaged by H2O2, however, only at high concentrations. But under the same conditions, the activity of the complex is hardly affected, since N1b can be easily bypassed during electron transfer.
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Affiliation(s)
- Lisa Strotmann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Caroline Harter
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Kevin Ritter
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Henning J Jessen
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
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37
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Minhas BF, Beck EA, Cheng CHC, Catchen J. Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Sci Rep 2023; 13:6939. [PMID: 37117267 PMCID: PMC10147917 DOI: 10.1038/s41598-023-34237-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.
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Affiliation(s)
- Bushra Fazal Minhas
- Informatics Programs, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Emily A Beck
- Data Science Initiative, University of Oregon, Eugene, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Julian Catchen
- Informatics Programs, University of Illinois at Urbana-Champaign, Urbana, USA.
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, USA.
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38
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Pereira CS, Teixeira MH, Russell DA, Hirst J, Arantes GM. Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility. Sci Rep 2023; 13:6738. [PMID: 37185607 PMCID: PMC10130173 DOI: 10.1038/s41598-023-33333-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Respiratory complex I is a major cellular energy transducer located in the inner mitochondrial membrane. Its inhibition by rotenone, a natural isoflavonoid, has been used for centuries by indigenous peoples to aid in fishing and, more recently, as a broad-spectrum pesticide or even a possible anticancer therapeutic. Unraveling the molecular mechanism of rotenone action will help to design tuned derivatives and to understand the still mysterious catalytic mechanism of complex I. Although composed of five fused rings, rotenone is a flexible molecule and populates two conformers, bent and straight. Here, a rotenone derivative locked in the straight form was synthesized and found to inhibit complex I with 600-fold less potency than natural rotenone. Large-scale molecular dynamics and free energy simulations of the pathway for ligand binding to complex I show that rotenone is more stable in the bent conformer, either free in the membrane or bound to the redox active site in the substrate-binding Q-channel. However, the straight conformer is necessary for passage from the membrane through the narrow entrance of the channel. The less potent inhibition of the synthesized derivative is therefore due to its lack of internal flexibility, and interconversion between bent and straight forms is required to enable efficient kinetics and high stability for rotenone binding. The ligand also induces reconfiguration of protein loops and side-chains inside the Q-channel similar to structural changes that occur in the open to closed conformational transition of complex I. Detailed understanding of ligand flexibility and interactions that determine rotenone binding may now be exploited to tune the properties of synthetic derivatives for specific applications.
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Affiliation(s)
- Caroline S Pereira
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-900, Brazil
| | - Murilo H Teixeira
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-900, Brazil
| | - David A Russell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-900, Brazil.
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Lettl C, Schindele F, Mehdipour AR, Steiner T, Ring D, Brack-Werner R, Stecher B, Eisenreich W, Bilitewski U, Hummer G, Witschel M, Fischer W, Haas R. Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chem Biol 2023; 30:499-512.e5. [PMID: 37100053 DOI: 10.1016/j.chembiol.2023.04.003] [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: 09/22/2022] [Revised: 02/16/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023]
Abstract
Respiratory complex I is a multicomponent enzyme conserved between eukaryotic cells and many bacteria, which couples oxidation of electron donors and quinone reduction with proton pumping. Here, we report that protein transport via the Cag type IV secretion system, a major virulence factor of the Gram-negative bacterial pathogen Helicobacter pylori, is efficiently impeded by respiratory inhibition. Mitochondrial complex I inhibitors, including well-established insecticidal compounds, selectively kill H. pylori, while other Gram-negative or Gram-positive bacteria, such as the close relative Campylobacter jejuni or representative gut microbiota species, are not affected. Using a combination of different phenotypic assays, selection of resistance-inducing mutations, and molecular modeling approaches, we demonstrate that the unique composition of the H. pylori complex I quinone-binding pocket is the basis for this hypersensitivity. Comprehensive targeted mutagenesis and compound optimization studies highlight the potential to develop complex I inhibitors as narrow-spectrum antimicrobial agents against this pathogen.
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Affiliation(s)
- Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Franziska Schindele
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ahmad Reza Mehdipour
- Center for Molecular Modeling, Ghent University, 9052 Zwijnaarde, Belgium; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Thomas Steiner
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technical University Munich, 85748 Garching, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany
| | - Ruth Brack-Werner
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany; German Research Center for Environmental Health, Institute of Virology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technical University Munich, 85748 Garching, Germany
| | - Ursula Bilitewski
- Helmholtz Center for Infection Research, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Braunschweig, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | | | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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40
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Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148951. [PMID: 36509126 DOI: 10.1016/j.bbabio.2022.148951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 Å long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.
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Gladyshev GV, Zharova TV, Kareyeva AV, Grivennikova VG. Proton-translocating NADH:ubiquinone oxidoreductase of Paracoccus denitrificans plasma membranes catalyzes FMN-independent reverse electron transfer to hexaammineruthenium (III). BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148963. [PMID: 36842539 DOI: 10.1016/j.bbabio.2023.148963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
NADH-OH, the specific inhibitor of NADH-binding site of the mammalian complex I, is shown to completely block FMN-dependent reactions of P. denitrificans enzyme in plasma membrane vesicles: NADH oxidation (in a competitive manner with Ki of 1 nM) as well as reduction of pyridine nucleotides, ferricyanide and oxygen in the reverse electron transfer. In contrast to these activities, the reverse electron transfer to hexaammineruthenium (III) catalyzed by plasma membrane vesicles is insensitive to NADH-OH. To explain these results, we hypothesize the existence of a non-FMN redox group of P. denitrificans complex I that is capable of reducing hexaammineruthenium (III), which is corroborated by the complex kinetics of NADH: hexaammineruthenium (III)-reductase activity, catalyzed by this enzyme. A new assay procedure for measuring succinate-driven reverse electron transfer catalyzed by P. denitrificans complex I to hexaammineruthenium (III) is proposed.
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Affiliation(s)
- Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russian Federation.
| | - Tatyana V Zharova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russian Federation
| | - Alexandra V Kareyeva
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russian Federation
| | - Vera G Grivennikova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russian Federation
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42
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Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Structure of mycobacterial respiratory complex I. Proc Natl Acad Sci U S A 2023; 120:e2214949120. [PMID: 36952383 PMCID: PMC10068793 DOI: 10.1073/pnas.2214949120] [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: 09/04/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
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Affiliation(s)
- Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
| | - Alicia Plourde
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, TorontoM5S 1A8, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91Stockholm, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, TorontoM5G 1L7, Canada
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43
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Sazanov LA. From the 'black box' to 'domino effect' mechanism: what have we learned from the structures of respiratory complex I. Biochem J 2023; 480:319-333. [PMID: 36920092 DOI: 10.1042/bcj20210285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 03/16/2023]
Abstract
My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant 'black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm ('domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.
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Affiliation(s)
- Leonid A Sazanov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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44
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Genetic mutations affecting mitochondrial function in cancer drug resistance. Genes Genomics 2023; 45:261-270. [PMID: 36609747 PMCID: PMC9947062 DOI: 10.1007/s13258-022-01359-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Mitochondria are organelles that serve as a central hub for physiological processes in eukaryotes, including production of ATP, regulation of calcium dependent signaling, generation of ROS, and regulation of apoptosis. Cancer cells undergo metabolic reprogramming in an effort to support their increasing requirements for cell survival, growth, and proliferation, and mitochondria have primary roles in these processes. Because of their central function in survival of cancer cells and drug resistance, mitochondria are an important target in cancer therapy and many drugs targeting mitochondria that target the TCA cycle, apoptosis, metabolic pathway, and generation of ROS have been developed. Continued use of mitochondrial-targeting drugs can lead to resistance due to development of new somatic mutations. Use of drugs is limited due to these mutations, which have been detected in mitochondrial proteins. In this review, we will focus on genetic mutations in mitochondrial target proteins and their function in induction of drug-resistance.
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45
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Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C. Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 2023; 615:541-547. [PMID: 36890228 PMCID: PMC10017518 DOI: 10.1038/s41586-023-05781-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival1. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments2,3. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2 and how the derived electrons are transferred to the respiratory chain1. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H2 at the expense of O2, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H2 in ambient air.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Moritz Senger
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Jack Badley
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Princess R Cabotaje
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Ruyu Jia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Zehui Duan
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
| | - Ping Huang
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Christopher K Barlow
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Matthew Belousoff
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ralf B Schittenhelm
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia.
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, Australia.
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46
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Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice. Nat Commun 2023; 14:1172. [PMID: 36859533 PMCID: PMC9977773 DOI: 10.1038/s41467-023-36894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The hypoxic ventilatory response (HVR) is a life-saving reflex, triggered by the activation of chemoreceptor glomus cells in the carotid body (CB) connected with the brainstem respiratory center. The molecular mechanisms underlying glomus cell acute oxygen (O2) sensing are unclear. Genetic disruption of mitochondrial complex I (MCI) selectively abolishes the HVR and glomus cell responsiveness to hypoxia. However, it is unknown what functions of MCI (metabolic, proton transport, or signaling) are essential for O2 sensing. Here we show that transgenic mitochondrial expression of NDI1, a single-molecule yeast NADH/quinone oxidoreductase that does not directly contribute to proton pumping, fully recovers the HVR and glomus cell sensitivity to hypoxia in MCI-deficient mice. Therefore, maintenance of mitochondrial NADH dehydrogenase activity and the electron transport chain are absolutely necessary for O2-dependent regulation of breathing. NDI1 expression also rescues other systemic defects caused by MCI deficiency. These data explain the role of MCI in acute O2 sensing by arterial chemoreceptors and demonstrate the optimal recovery of complex organismal functions by gene therapy.
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Zhu Q, Sun Y, Fu M, Bian M, Zhu X, Wang K, Geng H, Zeng W, Shen W, Hu Y. Ultrasensitive Small-Molecule Fluorescent Thermometer Reveals Hot Mitochondria in Surgically Resected Human Tumors. ACS Sens 2023; 8:51-60. [PMID: 36573608 DOI: 10.1021/acssensors.2c01563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Warburg effect suggests that upregulated glycolysis arising from high glucose uptake in cancer cells might be accompanied with suppressed mitochondrial respiration. However, recent studies have shown that the mitochondrial temperature in cancer cells could be relatively higher than that in normal cells, suggesting hyperactive mitochondrial respiration in cancer cells. However, hot mitochondria have not been reported in patients with cancer. Here, near-infrared small-molecule fluorescent probes TRNs are rationally designed with two ethyl amino groups as the temperature-sensitive moiety. Afterward, a mitochondrial targeting group is installed via ether bonds on TRN-8 to build MTN. To the best of our knowledge, MTN is the near-infrared probe with the highest sensitivity for mitochondrial temperature. Moreover, it also displays high photostability, wide linearity, and high specificity. Using MTN, we can monitor the ups and downs of mitochondrial temperature in cancer cells upon the perturbations of mitochondrial respiration. Furthermore, we demonstrate that the mitochondrial temperature in surgically resected human tumors is relatively higher than that in paracancerous tissues. Our results indicate that relatively hot mitochondria may exist in tumors from patients. We envisage that our study provides critical evidence for revisiting the Warburg effect and cancer metabolism.
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Affiliation(s)
- Qing Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yue Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Manlin Fu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Mianli Bian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiaomei Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kai Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Haoxing Geng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Shen
- Department of Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yi Hu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing 100730, China
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48
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Bridges HR, Blaza JN, Yin Z, Chung I, Pollak MN, Hirst J. Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides. Science 2023; 379:351-357. [PMID: 36701435 PMCID: PMC7614227 DOI: 10.1126/science.ade3332] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The molecular mode of action of biguanides, including the drug metformin, which is widely used in the treatment of diabetes, is incompletely characterized. Here, we define the inhibitory drug-target interaction(s) of a model biguanide with mammalian respiratory complex I by combining cryo-electron microscopy and enzyme kinetics. We interpret these data to explain the selectivity of biguanide binding to different enzyme states. The primary inhibitory site is in an amphipathic region of the quinone-binding channel, and an additional binding site is in a pocket on the intermembrane-space side of the enzyme. An independent local chaotropic interaction, not previously described for any drug, displaces a portion of a key helix in the membrane domain. Our data provide a structural basis for biguanide action and enable the rational design of medicinal biguanides.
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Affiliation(s)
- Hannah R. Bridges
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,Authors for correspondence: and
| | - James N. Blaza
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, The University of York, YO10 5DD, UK
| | - Zhan Yin
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Michael N. Pollak
- Lady Davis Institute of the Jewish General Hospital and Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,Authors for correspondence: and
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Agip ANA, Chung I, Sanchez-Martinez A, Whitworth AJ, Hirst J. Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster. eLife 2023; 12:e84424. [PMID: 36622099 PMCID: PMC9977279 DOI: 10.7554/elife.84424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. Drosophila melanogaster is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from Drosophila and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the Drosophila enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of Drosophila complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.
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Affiliation(s)
- Ahmed-Noor A Agip
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Injae Chung
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Alvaro Sanchez-Martinez
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Alexander J Whitworth
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
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50
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Formate hydrogenlyase, formic acid translocation and hydrogen production: dynamic membrane biology during fermentation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148919. [PMID: 36152681 DOI: 10.1016/j.bbabio.2022.148919] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Formate hydrogenlyase-1 (FHL-1) is a complex-I-like enzyme that is commonly found in gram-negative bacteria. The enzyme comprises a peripheral arm and a membrane arm but is not involved in quinone reduction. Instead, FHL-1 couples formate oxidation to the reduction of protons to molecular hydrogen (H2). Escherichia coli produces FHL-1 under fermentative conditions where it serves to detoxify formic acid in the environment. The membrane biology and bioenergetics surrounding E. coli FHL-1 have long held fascination. Here, we review recent work on understanding the molecular basis of formic acid efflux and influx. We also consider the structure and function of E. coli FHL-1, its relationship with formate transport, and pay particular attention to the molecular interface between the peripheral arm and the membrane arm. Finally, we highlight the interesting phenotype of genetic mutation of the ND1 Loop, which is located at that interface.
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