1
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Steenberge LH, Rogers S, Sung AY, Fan J, Pagliarini DJ. Coenzyme Q 4 is a functional substitute for coenzyme Q 10 and can be targeted to the mitochondria. J Biol Chem 2024; 300:107269. [PMID: 38588811 PMCID: PMC11087978 DOI: 10.1016/j.jbc.2024.107269] [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: 07/20/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Coenzyme Q10 (CoQ10) is an important cofactor and antioxidant for numerous cellular processes, and its deficiency has been linked to human disorders including mitochondrial disease, heart failure, Parkinson's disease, and hypertension. Unfortunately, treatment with exogenous CoQ10 is often ineffective, likely due to its extreme hydrophobicity and high molecular weight. Here, we show that less hydrophobic CoQ species with shorter isoprenoid tails can serve as viable substitutes for CoQ10 in human cells. We demonstrate that CoQ4 can perform multiple functions of CoQ10 in CoQ-deficient cells at markedly lower treatment concentrations, motivating further investigation of CoQ4 as a supplement for CoQ10 deficiencies. In addition, we describe the synthesis and evaluation of an initial set of compounds designed to target CoQ4 selectively to mitochondria using triphenylphosphonium. Our results indicate that select versions of these compounds can successfully be delivered to mitochondria in a cell model and be cleaved to produce CoQ4, laying the groundwork for further development.
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Affiliation(s)
- Laura H Steenberge
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Sean Rogers
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA; Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Andrew Y Sung
- University of Wisconsin Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jing Fan
- Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA; Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA.
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2
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Hu Y, Yuan M, Julian A, Tuz K, Juárez O. Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions. Front Microbiol 2024; 15:1347466. [PMID: 38468849 PMCID: PMC10926992 DOI: 10.3389/fmicb.2024.1347466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world's health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3-4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.
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Affiliation(s)
- Yuyao Hu
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Alexander Julian
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
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3
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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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4
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Ježek P, Jabůrek M, Holendová B, Engstová H, Dlasková A. Mitochondrial Cristae Morphology Reflecting Metabolism, Superoxide Formation, Redox Homeostasis, and Pathology. Antioxid Redox Signal 2023; 39:635-683. [PMID: 36793196 PMCID: PMC10615093 DOI: 10.1089/ars.2022.0173] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
Significance: Mitochondrial (mt) reticulum network in the cell possesses amazing ultramorphology of parallel lamellar cristae, formed by the invaginated inner mitochondrial membrane. Its non-invaginated part, the inner boundary membrane (IBM) forms a cylindrical sandwich with the outer mitochondrial membrane (OMM). Crista membranes (CMs) meet IBM at crista junctions (CJs) of mt cristae organizing system (MICOS) complexes connected to OMM sorting and assembly machinery (SAM). Cristae dimensions, shape, and CJs have characteristic patterns for different metabolic regimes, physiological and pathological situations. Recent Advances: Cristae-shaping proteins were characterized, namely rows of ATP-synthase dimers forming the crista lamella edges, MICOS subunits, optic atrophy 1 (OPA1) isoforms and mitochondrial genome maintenance 1 (MGM1) filaments, prohibitins, and others. Detailed cristae ultramorphology changes were imaged by focused-ion beam/scanning electron microscopy. Dynamics of crista lamellae and mobile CJs were demonstrated by nanoscopy in living cells. With tBID-induced apoptosis a single entirely fused cristae reticulum was observed in a mitochondrial spheroid. Critical Issues: The mobility and composition of MICOS, OPA1, and ATP-synthase dimeric rows regulated by post-translational modifications might be exclusively responsible for cristae morphology changes, but ion fluxes across CM and resulting osmotic forces might be also involved. Inevitably, cristae ultramorphology should reflect also mitochondrial redox homeostasis, but details are unknown. Disordered cristae typically reflect higher superoxide formation. Future Directions: To link redox homeostasis to cristae ultramorphology and define markers, recent progress will help in uncovering mechanisms involved in proton-coupled electron transfer via the respiratory chain and in regulation of cristae architecture, leading to structural determination of superoxide formation sites and cristae ultramorphology changes in diseases. Antioxid. Redox Signal. 39, 635-683.
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Affiliation(s)
- Petr Ježek
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martin Jabůrek
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Blanka Holendová
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Engstová
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrea Dlasková
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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5
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Fuller JT, Barnes S, Sadun LA, Ajmera P, Alexandrova AN, Sadun AA. Coenzyme Q10 trapping in mitochondrial complex I underlies Leber's hereditary optic neuropathy. Proc Natl Acad Sci U S A 2023; 120:e2304884120. [PMID: 37733737 PMCID: PMC10523484 DOI: 10.1073/pnas.2304884120] [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: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 09/23/2023] Open
Abstract
How does a single amino acid mutation occurring in the blinding disease, Leber's hereditary optic neuropathy (LHON), impair electron shuttling in mitochondria? We investigated changes induced by the m.3460 G>A mutation in mitochondrial protein ND1 using the tools of Molecular Dynamics and Free Energy Perturbation simulations, with the goal of determining the mechanism by which this mutation affects mitochondrial function. A recent analysis suggested that the mutation's replacement of alanine A52 with a threonine perturbs the stability of a region where binding of the electron shuttling protein, Coenzyme Q10, occurs. We found two functionally opposing changes involving the role of Coenzyme Q10. The first showed that quantum electron transfer from the terminal Fe/S complex, N2, to the Coenzyme Q10 headgroup, docked in its binding pocket, is enhanced. However, this positive adjustment is overshadowed by our finding that the mobility of Coenzyme Q10 in its oxidized and reduced states, entering and exiting its binding pocket, is disrupted by the mutation in a manner that leads to conditions promoting the generation of reactive oxygen species. An increase in reactive oxygen species caused by the LHON mutation has been proposed to be responsible for this optic neuropathy.
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Affiliation(s)
- Jack T. Fuller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Steven Barnes
- Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Doheny Eye Institute, Pasadena, CA91103
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Lorenzo A. Sadun
- Department of Mathematics, University of Texas at Austin, Austin, TX78712
| | - Pujan Ajmera
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | | | - Alfredo A. Sadun
- Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Doheny Eye Institute, Pasadena, CA91103
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6
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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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7
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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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8
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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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9
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Steenberge LH, Sung AY, Fan J, Pagliarini DJ. Coenzyme Q 4 is a functional substitute for coenzyme Q 10 and can be targeted to the mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549963. [PMID: 37503166 PMCID: PMC10370177 DOI: 10.1101/2023.07.20.549963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Coenzyme Q 10 (CoQ 10 ) is an important cofactor and antioxidant for numerous cellular processes, and its deficiency has been linked to human disorders including mitochondrial disease, heart failure, Parkinson's disease, and hypertension. Unfortunately, treatment with exogenous oral CoQ 10 is often ineffective, likely due to the extreme hydrophobicity and high molecular weight of CoQ 10 . Here, we show that less hydrophobic CoQ species with shorter isoprenoid tails can serve as viable substitutes for CoQ 10 in human cells. We demonstrate that CoQ 4 can perform multiple functions of CoQ 10 in CoQ-deficient cells at markedly lower treatment concentrations, motivating further investigation of CoQ 4 as a supplement for CoQ 10 deficiencies. In addition, we describe the synthesis and evaluation of an initial set of compounds designed to target CoQ 4 selectively to mitochondria using triphenylphosphonium (TPP). Our results indicate that select versions of these compounds can successfully be delivered to mitochondria in a cell model and be cleaved to produce CoQ 4 , laying the groundwork for further development.
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10
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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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11
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Jeffreys LN, Ardrey A, Hafiz TA, Dyer LA, Warman AJ, Mosallam N, Nixon GL, Fisher NE, Hong WD, Leung SC, Aljayyoussi G, Bibby J, Almeida DV, Converse PJ, Fotouhi N, Berry NG, Nuermberger EL, Upton AM, O'Neill PM, Ward SA, Biagini GA. Identification of 2-Aryl-Quinolone Inhibitors of Cytochrome bd and Chemical Validation of Combination Strategies for Respiratory Inhibitors against Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:221-238. [PMID: 36606559 PMCID: PMC9926492 DOI: 10.1021/acsinfecdis.2c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis cytochrome bd quinol oxidase (cyt bd), the alternative terminal oxidase of the respiratory chain, has been identified as playing a key role during chronic infection and presents a putative target for the development of novel antitubercular agents. Here, we report confirmation of successful heterologous expression of M. tuberculosis cytochrome bd. The heterologous M. tuberculosis cytochrome bd expression system was used to identify a chemical series of inhibitors based on the 2-aryl-quinolone pharmacophore. Cytochrome bd inhibitors displayed modest efficacy in M. tuberculosis growth suppression assays together with a bacteriostatic phenotype in time-kill curve assays. Significantly, however, inhibitor combinations containing our front-runner cyt bd inhibitor CK-2-63 with either cyt bcc-aa3 inhibitors (e.g., Q203) and/or adenosine triphosphate (ATP) synthase inhibitors (e.g., bedaquiline) displayed enhanced efficacy with respect to the reduction of mycobacterium oxygen consumption, growth suppression, and in vitro sterilization kinetics. In vivo combinations of Q203 and CK-2-63 resulted in a modest lowering of lung burden compared to treatment with Q203 alone. The reduced efficacy in the in vivo experiments compared to in vitro experiments was shown to be a result of high plasma protein binding and a low unbound drug exposure at the target site. While further development is required to improve the tractability of cyt bd inhibitors for clinical evaluation, these data support the approach of using small-molecule inhibitors to target multiple components of the branched respiratory chain of M. tuberculosis as a combination strategy to improve therapeutic and pharmacokinetic/pharmacodynamic (PK/PD) indices related to efficacy.
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Affiliation(s)
- Laura N Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Alison Ardrey
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Taghreed A Hafiz
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Lauri-Anne Dyer
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Ashley J Warman
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Nada Mosallam
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Gemma L Nixon
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Nicholas E Fisher
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - W David Hong
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Suet C Leung
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Ghaith Aljayyoussi
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Jaclyn Bibby
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Deepak V Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland21205, United States
| | - Paul J Converse
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland21205, United States
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, New York10005, United States
| | - Neil G Berry
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Eric L Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland21205, United States
| | - Anna M Upton
- Global Alliance for TB Drug Development, New York, New York10005, United States.,Evotec (US) Inc., 303B College Road East, Princeton, New Jersey08540, United States
| | - Paul M O'Neill
- Department of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K
| | - Stephen A Ward
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
| | - Giancarlo A Biagini
- Centre for Drugs and Diagnostics, Department of Tropical Infectious Diseases, Liverpool School of Tropical Medicine, Pembroke Place, LiverpoolL3 5QA, U.K
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12
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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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13
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Stuchebrukhov AA, Hayashi T. Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping. FEBS Lett 2023; 597:237-245. [PMID: 36251339 PMCID: PMC9877130 DOI: 10.1002/1873-3468.14518] [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: 08/17/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023]
Abstract
Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa (QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180 mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally among four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.
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Affiliation(s)
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, Davis, CA 95616
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14
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Kurelac I, Cavina B, Sollazzo M, Miglietta S, Fornasa A, De Luise M, Iorio M, Lama E, Traversa D, Nasiri HR, Ghelli A, Musiani F, Porcelli AM, Iommarini L, Gasparre G. NDUFS3 knockout cancer cells and molecular docking reveal specificity and mode of action of anti-cancer respiratory complex I inhibitors. Open Biol 2022; 12:220198. [PMID: 36349549 PMCID: PMC9653258 DOI: 10.1098/rsob.220198] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Inhibition of respiratory complex I (CI) is becoming a promising anti-cancer strategy, encouraging the design and the use of inhibitors, whose mechanism of action, efficacy and specificity remain elusive. As CI is a central player of cellular bioenergetics, a finely tuned dosing of targeting drugs is required to avoid side effects. We compared the specificity and mode of action of CI inhibitors metformin, BAY 87-2243 and EVP 4593 using cancer cell models devoid of CI. Here we show that both BAY 87-2243 and EVP 4593 were selective, while the antiproliferative effects of metformin were considerably independent from CI inhibition. Molecular docking predictions indicated that the high efficiency of BAY 87-2243 and EVP 4593 may derive from the tight network of bonds in the quinone binding pocket, although in different sites. Most of the amino acids involved in such interactions are conserved across species and only rarely found mutated in human. Our data make a case for caution when referring to metformin as a CI-targeting compound, and highlight the need for dosage optimization and careful evaluation of molecular interactions between inhibitors and the holoenzyme.
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Affiliation(s)
- Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Beatrice Cavina
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Manuela Sollazzo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Stefano Miglietta
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Agnese Fornasa
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Monica De Luise
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Maria Iorio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Eleonora Lama
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Daniele Traversa
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Hamid Razi Nasiri
- Department of Cellular Microbiology, University Hohenheim, Stuttgart, Germany
| | - Anna Ghelli
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy,Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Anna Maria Porcelli
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy,Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy,Interdepartmental Centre for Industrial Research ‘Scienze della Vita e Tecnologie per la Salute’, University of Bologna, Bologna, Italy
| | - Luisa Iommarini
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy,Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
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15
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Jarman OD, Hirst J. Membrane-domain mutations in respiratory complex I impede catalysis but do not uncouple proton pumping from ubiquinone reduction. PNAS NEXUS 2022; 1:pgac276. [PMID: 36712358 PMCID: PMC9802314 DOI: 10.1093/pnasnexus/pgac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/01/2022] [Indexed: 12/05/2022]
Abstract
Respiratory complex I [NADH:ubiquinone (UQ) oxidoreductase] captures the free energy released from NADH oxidation and UQ reduction to pump four protons across an energy-transducing membrane and power ATP synthesis. Mechanisms for long-range energy coupling in complex I have been proposed from structural data but not yet evaluated by robust biophysical and biochemical analyses. Here, we use the powerful bacterial model system Paracoccus denitrificans to investigate 14 mutations of key residues in the membrane-domain Nqo13/ND4 subunit, defining the rates and reversibility of catalysis and the number of protons pumped per NADH oxidized. We reveal new insights into the roles of highly conserved charged residues in lateral energy transduction, confirm the purely structural role of the Nqo12/ND5 transverse helix, and evaluate a proposed hydrated channel for proton uptake. Importantly, even when catalysis is compromised the enzyme remains strictly coupled (four protons are pumped per NADH oxidized), providing no evidence for escape cycles that circumvent blocked proton-pumping steps.
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Affiliation(s)
- Owen D Jarman
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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16
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Braasch-Turi MM, Koehn JT, Crans DC. Chemistry of Lipoquinones: Properties, Synthesis, and Membrane Location of Ubiquinones, Plastoquinones, and Menaquinones. Int J Mol Sci 2022; 23:12856. [PMID: 36361645 PMCID: PMC9656164 DOI: 10.3390/ijms232112856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
Lipoquinones are the topic of this review and are a class of hydrophobic lipid molecules with key biological functions that are linked to their structure, properties, and location within a biological membrane. Ubiquinones, plastoquinones, and menaquinones vary regarding their quinone headgroup, isoprenoid sidechain, properties, and biological functions, including the shuttling of electrons between membrane-bound protein complexes within the electron transport chain. Lipoquinones are highly hydrophobic molecules that are soluble in organic solvents and insoluble in aqueous solution, causing obstacles in water-based assays that measure their chemical properties, enzyme activities and effects on cell growth. Little is known about the location and ultimately movement of lipoquinones in the membrane, and these properties are topics described in this review. Computational studies are particularly abundant in the recent years in this area, and there is far less experimental evidence to verify the often conflicting interpretations and conclusions that result from computational studies of very different membrane model systems. Some recent experimental studies have described using truncated lipoquinone derivatives, such as ubiquinone-2 (UQ-2) and menaquinone-2 (MK-2), to investigate their conformation, their location in the membrane, and their biological function. Truncated lipoquinone derivatives are soluble in water-based assays, and hence can serve as excellent analogs for study even though they are more mobile in the membrane than the longer chain counterparts. In this review, we will discuss the properties, location in the membrane, and syntheses of three main classes of lipoquinones including truncated derivatives. Our goal is to highlight the importance of bridging the gap between experimental and computational methods and to incorporate properties-focused considerations when proposing future studies relating to the function of lipoquinones in membranes.
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Affiliation(s)
| | - Jordan T. Koehn
- Chemistry Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Debbie C. Crans
- Chemistry Department, Colorado State University, Fort Collins, CO 80523, USA
- Cell & Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
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17
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Xu JJ, Hu M, Yang L, Chen XY. How plants synthesize coenzyme Q. PLANT COMMUNICATIONS 2022; 3:100341. [PMID: 35614856 PMCID: PMC9483114 DOI: 10.1016/j.xplc.2022.100341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Coenzyme Q (CoQ) is a conserved redox-active lipid that has a wide distribution across the domains of life. CoQ plays a key role in the oxidative electron transfer chain and serves as a crucial antioxidant in cellular membranes. Our understanding of CoQ biosynthesis in eukaryotes has come mostly from studies of yeast. Recently, significant advances have been made in understanding CoQ biosynthesis in plants. Unique mitochondrial flavin-dependent monooxygenase and benzenoid ring precursor biosynthetic pathways have been discovered, providing new insights into the diversity of CoQ biosynthetic pathways and the evolution of phototrophic eukaryotes. We summarize research progress on CoQ biosynthesis and regulation in plants and recent efforts to increase the CoQ content in plant foods.
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Affiliation(s)
- Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Chenshan Plant Science Research Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
| | - Mei Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Chenshan Plant Science Research Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
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18
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Binding of Natural Inhibitors to Respiratory Complex I. Pharmaceuticals (Basel) 2022; 15:ph15091088. [PMID: 36145309 PMCID: PMC9503403 DOI: 10.3390/ph15091088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
NADH:ubiquinone oxidoreductase (respiratory complex I) is a redox-driven proton pump with a central role in mitochondrial oxidative phosphorylation. The ubiquinone reduction site of complex I is located in the matrix arm of this large protein complex and connected to the membrane via a tunnel. A variety of chemically diverse compounds are known to inhibit ubiquinone reduction by complex I. Rotenone, piericidin A, and annonaceous acetogenins are representatives of complex I inhibitors from biological sources. The structure of complex I is determined at high resolution, and inhibitor binding sites are described in detail. In this review, we summarize the state of knowledge of how natural inhibitors bind in the Q reduction site and the Q access pathway and how their inhibitory mechanisms compare with that of a synthetic anti-cancer agent.
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19
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Ishikawa M, Masuya T, Kuroda S, Uno S, Butler NL, Foreman S, Murai M, Barquera B, Miyoshi H. The side chain of ubiquinone plays a critical role in Na + translocation by the NADH-ubiquinone oxidoreductase (Na +-NQR) from Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148547. [PMID: 35337841 DOI: 10.1016/j.bbabio.2022.148547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/18/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022]
Abstract
The Na+-pumping NADH-ubiquinone (UQ) oxidoreductase (Na+-NQR) is an essential bacterial respiratory enzyme that generates a Na+ gradient across the cell membrane. However, the mechanism that couples the redox reactions to Na+ translocation remains unknown. To address this, we examined the relation between reduction of UQ and Na+ translocation using a series of synthetic UQs with Vibrio cholerae Na+-NQR reconstituted into liposomes. UQ0 that has no side chain and UQCH3 and UQC2H5, which have methyl and ethyl side chains, respectively, were catalytically reduced by Na+-NQR, but their reduction generated no membrane potential, indicating that the overall electron transfer and Na+ translocation are not coupled. While these UQs were partly reduced by electron leak from the cofactor(s) located upstream of riboflavin, this complete loss of Na+ translocation cannot be explained by the electron leak. Lengthening the UQ side chain to n-propyl (C3H7) or longer significantly restored Na+ translocation. It has been considered that Na+ translocation is completed when riboflavin, a terminal redox cofactor residing within the membrane, is reduced. In this view, the role of UQ is simply to accept electrons from the reduced riboflavin to regenerate the stable neutral riboflavin radical and reset the catalytic cycle. However, the present study revealed that the final UQ reduction via reduced riboflavin makes an important contribution to Na+ translocation through a critical role of its side chain. Based on the results, we discuss the critical role of the UQ side chain in Na+ translocation.
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Affiliation(s)
- Moe Ishikawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Seina Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shinpei Uno
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Nicole L Butler
- Department of Biological Science, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Sara Foreman
- Department of Biological Science, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Blanca Barquera
- Department of Biological Science, Rensselaer Polytechnic Institute, Troy, NY 12180, United States; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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20
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Uno S, Masuya T, Zdorevskyi O, Ikunishi R, Shinzawa-Itoh K, Lasham J, Sharma V, Murai M, Miyoshi H. Diverse reaction behaviors of artificial ubiquinones in mitochondrial respiratory complex I. J Biol Chem 2022; 298:102075. [PMID: 35643318 PMCID: PMC9243180 DOI: 10.1016/j.jbc.2022.102075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
The ubiquinone (UQ) reduction step catalyzed by NADH-UQ oxidoreductase (mitochondrial respiratory complex I) is key to triggering proton translocation across the inner mitochondrial membrane. Structural studies have identified a long, narrow, UQ-accessing tunnel within the enzyme. We previously demonstrated that synthetic oversized UQs, which are unlikely to transit this narrow tunnel, are catalytically reduced by native complex I embedded in submitochondrial particles but not by the isolated enzyme. To explain this contradiction, we hypothesized that access of oversized UQs to the reaction site is obstructed in the isolated enzyme because their access route is altered following detergent solubilization from the inner mitochondrial membrane. In the present study, we investigated this using two pairs of photoreactive UQs (pUQm-1/pUQp-1 and pUQm-2/pUQp-2), with each pair having the same chemical properties except for a ∼1.0 Å difference in side-chain widths. Despite this subtle difference, reduction of the wider pUQs by the isolated complex was significantly slower than of the narrower pUQs, but both were similarly reduced by the native enzyme. In addition, photoaffinity-labeling experiments using the four [125I]pUQs demonstrated that their side chains predominantly label the ND1 subunit with both enzymes but at different regions around the tunnel. Finally, we show that the suppressive effects of different types of inhibitors on the labeling significantly changed depending on [125I]pUQs used, indicating that [125I]pUQs and these inhibitors do not necessarily share a common binding cavity. Altogether, we conclude that the reaction behaviors of pUQs cannot be simply explained by the canonical UQ tunnel model.
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Affiliation(s)
- Shinpei Uno
- 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
| | | | - Ryo Ikunishi
- 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
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - 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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21
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Wang P, Leontyev I, Stuchebrukhov AA. Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I. J Phys Chem B 2022; 126:4080-4088. [PMID: 35612955 DOI: 10.1021/acs.jpcb.2c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We apply linear response theory to calculate mechanical allosteric couplings in respiratory complex I between the iron sulfur cluster N2, located in the catalytic cavity, and the membrane part of the enzyme, separated from it by more than 50 Å. According to our hypothesis, the redox reaction of ubiquinone in the catalytic cavity of the enzyme generates an unbalanced charge that via repulsion of the charged redox center N2 produces local mechanical stress that transmits into the membrane part of the enzyme where it induces proton pumping. Using coarse-grained simulations of the enzyme, we calculated mechanistic allosteric couplings that reveal the pathways of the mechanical transmission of the stress along the enzyme. The results shed light on the recent experimental studies where a stabilization of the enzyme with an introduced disulfide bridge resulted in the abolishing of proton pumping. Simulation of the disulfide bond action indicates a dramatic change of the mechanistic coupling pathways in line with experimental findings.
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Affiliation(s)
- Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Igor Leontyev
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
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22
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Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy. Nat Commun 2022; 13:2758. [PMID: 35589726 PMCID: PMC9120487 DOI: 10.1038/s41467-022-30506-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q10) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, the mechanisms of Q10 reduction and energy transduction remain controversial. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q10. Using cryo-EM, we reveal a Q10 molecule occupying the full length of the Q-binding site in the 'active' (ready-to-go) resting state together with a matching substrate-free structure, and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q10 binding pose. By comparing ligand-bound and ligand-free forms of the 'deactive' resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.
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23
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Yao Y, Chen X, Chen W, Gao K, Zhang H, Zhang L, Han Y, Xue T, Wang Q, Wang T, Xu Y, Wang J, Qiu X, Que C, Zheng M, Zhu T. Transcriptional pathways of elevated fasting blood glucose associated with short-term exposure to ultrafine particles: A panel study in Beijing, China. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128486. [PMID: 35739669 DOI: 10.1016/j.jhazmat.2022.128486] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/25/2022] [Accepted: 02/11/2022] [Indexed: 06/15/2023]
Abstract
There is growing concern about the strong health effects of ultrafine particles (UFPs). However, less is known about the biological mechanisms. The objective of this study is to examine the association between short-term exposure to UFPs and fasting blood glucose (FBG) levels, and explore the potential physiological mechanisms at transcriptional levels. In a panel study of 135 participants, we measured FBG and the whole blood transcriptome repeatedly. The concentrations of ambient air pollutants were monitored continuously at a station. Linear mixed-effects models coupled with a mediating effect model were used to discriminate transcripts associated with air pollutant exposure and ln-transformed FBG levels. We found that FBG was significantly associated with interquartile range increase in the average UFPs concentrations 1-13 d prior to the clinical visits (ranging from 5.1% [95% CI 2.0-8.1%] in the 1-d time-window to 12.1% [95% CI 6.5-17.8%] in the 13-d time-window). Top 1000 transcripts associated with FBG increase following UFPs exposure were enriched into some biological pathways, such as pro-opiomelanocortin processing, negative regulation of hypoxia-inducible factor 1 A function, ubiquinone metabolism, and antigen presentation by major histocompatibility complex class I, classical pathway. These results suggest that elevated FBG associated with UFPs exposure may be related to regulation of metabolism, immune response, DNA damage, and apoptosis and survival.
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Affiliation(s)
- Yuan Yao
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Xi Chen
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China; Hebei Technology Innovation Center of Human Settlement in Green Building, Shenzhen Institute of Building Research Co., Ltd., Xiong'an, China
| | - Wu Chen
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Ke Gao
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Hanxiyue Zhang
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Lina Zhang
- Shi Cha Hai Community Health Service Center, Beijing, China
| | - Yiqun Han
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China; Environmental Research Group, MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Tao Xue
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China; School of Public Health, Peking University, Beijing, China
| | - Qi Wang
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Teng Wang
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Yifan Xu
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Junxia Wang
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Xinghua Qiu
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Chengli Que
- Peking University First Hospital, Peking University, Beijing, China
| | - Mei Zheng
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Tong Zhu
- SKL-ESPC and BIC-ESAT, College of Environmental Sciences and Engineering, Peking University, Beijing, China.
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24
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Burger N, James AM, Mulvey JF, Hoogewijs K, Ding S, Fearnley IM, Loureiro-López M, Norman AAI, Arndt S, Mottahedin A, Sauchanka O, Hartley RC, Krieg T, Murphy MP. ND3 Cys39 in complex I is exposed during mitochondrial respiration. Cell Chem Biol 2022; 29:636-649.e14. [PMID: 34739852 PMCID: PMC9076552 DOI: 10.1016/j.chembiol.2021.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/21/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Mammalian complex I can adopt catalytically active (A-) or deactive (D-) states. A defining feature of the reversible transition between these two defined states is thought to be exposure of the ND3 subunit Cys39 residue in the D-state and its occlusion in the A-state. As the catalytic A/D transition is important in health and disease, we set out to quantify it by measuring Cys39 exposure using isotopic labeling and mass spectrometry, in parallel with complex I NADH/CoQ oxidoreductase activity. To our surprise, we found significant Cys39 exposure during NADH/CoQ oxidoreductase activity. Furthermore, this activity was unaffected if Cys39 alkylation occurred during complex I-linked respiration. In contrast, alkylation of catalytically inactive complex I irreversibly blocked the reactivation of NADH/CoQ oxidoreductase activity by NADH. Thus, Cys39 of ND3 is exposed in complex I during mitochondrial respiration, with significant implications for our understanding of the A/D transition and the mechanism of complex I.
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Affiliation(s)
- Nils Burger
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Andrew M James
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - John F Mulvey
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Kurt Hoogewijs
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; Medical Research Council-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Shujing Ding
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Marta Loureiro-López
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | | | - Sabine Arndt
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Amin Mottahedin
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Olga Sauchanka
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | - Thomas Krieg
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Michael P Murphy
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
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25
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Wright JJ, Biner O, Chung I, Burger N, Bridges HR, Hirst J. Reverse Electron Transfer by Respiratory Complex I Catalyzed in a Modular Proteoliposome System. J Am Chem Soc 2022; 144:6791-6801. [PMID: 35380814 PMCID: PMC9026280 DOI: 10.1021/jacs.2c00274] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Indexed: 02/02/2023]
Abstract
Respiratory complex I is an essential metabolic enzyme that uses the energy from NADH oxidation and ubiquinone reduction to translocate protons across an energy transducing membrane and generate the proton motive force for ATP synthesis. Under specific conditions, complex I can also catalyze the reverse reaction, Δp-linked oxidation of ubiquinol to reduce NAD+ (or O2), known as reverse electron transfer (RET). Oxidative damage by reactive oxygen species generated during RET underpins ischemia reperfusion injury, but as RET relies on several converging metabolic pathways, little is known about its mechanism or regulation. Here, we demonstrate Δp-linked RET through complex I in a synthetic proteoliposome system for the first time, enabling complete kinetic characterization of RET catalysis. We further establish the capability of our system by showing how RET in the mammalian enzyme is regulated by the active-deactive transition and by evaluating RET by complex I from several species in which direct assessment has not been otherwise possible. We thus provide new insights into the reversibility of complex I catalysis, an important but little understood mechanistic and physiological feature.
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Affiliation(s)
- John J. Wright
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | | | - Injae Chung
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | | | - Hannah R. Bridges
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | - Judy Hirst
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
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26
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Djurabekova A, Galemou Yoga E, Nyman A, Pirttikoski A, Zickermann V, Haapanen O, Sharma V. Docking and molecular simulations reveal a quinone binding site on the surface of respiratory complex I. FEBS Lett 2022; 596:1133-1146. [PMID: 35363885 DOI: 10.1002/1873-3468.14346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 11/07/2022]
Abstract
The first component of the mitochondrial electron transport chain is respiratory complex I. Several high-resolution structures of complex I from different species have been resolved. However, despite these significant achievements, the mechanism of redox-coupled proton pumping remains elusive. Here, we combined atomistic docking, molecular dynamics simulations and site-directed mutagenesis on respiratory complex I from Yarrowia lipolytica to identify a quinone (Q) binding site on its surface near the horizontal amphipathic helices of ND1 and NDUFS7 subunits. The surface-bound Q makes stable interactions with conserved charged and polar residues, including the highly conserved Arg72 from the NDUFS7 subunit. The binding and dynamics of a Q molecule at the surface-binding site raises interesting possibilities about the mechanism of complex I, which are discussed.
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Affiliation(s)
| | - Etienne Galemou Yoga
- 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
| | - Aino Nyman
- Department of Physics, University of 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
| | - Outi Haapanen
- Department of Physics, University of Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Finland.,HiLIFE Institute of Biotechnology, University of Helsinki, Finland
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27
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Grba DN, Blaza JN, Bridges HR, Agip ANA, Yin Z, Murai M, Miyoshi H, Hirst J. Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I. J Biol Chem 2022; 298:101602. [PMID: 35063503 PMCID: PMC8861642 DOI: 10.1016/j.jbc.2022.101602] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a crucial enzyme in energy metabolism, captures the redox potential energy from NADH oxidation/ubiquinone reduction to create the proton motive force used to drive ATP synthesis in oxidative phosphorylation. High-resolution single-particle electron cryo-EM analyses have provided detailed structural knowledge of the catalytic machinery of complex I, but not of the molecular principles of its energy transduction mechanism. Although ubiquinone is considered to bind in a long channel at the interface of the membrane-embedded and hydrophilic domains, with channel residues likely involved in coupling substrate reduction to proton translocation, no structures with the channel fully occupied have yet been described. Here, we report the structure (determined by cryo-EM) of mouse complex I with a tight-binding natural product acetogenin inhibitor, which resembles the native substrate, bound along the full length of the expected ubiquinone-binding channel. Our structure reveals the mode of acetogenin binding and the molecular basis for structure-activity relationships within the acetogenin family. It also shows that acetogenins are such potent inhibitors because they are highly hydrophobic molecules that contain two specific hydrophilic moieties spaced to lock into two hydrophilic regions of the otherwise hydrophobic channel. The central hydrophilic section of the channel does not favor binding of the isoprenoid chain when the native substrate is fully bound but stabilizes the ubiquinone/ubiquinol headgroup as it transits to/from the active site. Therefore, the amphipathic nature of the channel supports both tight binding of the amphipathic inhibitor and rapid exchange of the ubiquinone/ubiquinol substrate and product.
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Affiliation(s)
- Daniel N Grba
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - James N Blaza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Hannah R Bridges
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Ahmed-Noor A Agip
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Zhan Yin
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - 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
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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28
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Gu J, Liu T, Guo R, Zhang L, Yang M. The coupling mechanism of mammalian mitochondrial complex I. Nat Struct Mol Biol 2022; 29:172-182. [PMID: 35145322 DOI: 10.1038/s41594-022-00722-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/06/2022] [Indexed: 01/03/2023]
Abstract
Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.
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Affiliation(s)
- Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China. .,SUSTech Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen, China.
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29
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Kaila VRI. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Acc Chem Res 2021; 54:4462-4473. [PMID: 34894649 PMCID: PMC8697550 DOI: 10.1021/acs.accounts.1c00524] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
Biological energy conversion is catalyzed by membrane-bound proteins
that transduce chemical or light energy into energy forms that power
endergonic processes in the cell. At a molecular level, these catalytic
processes involve elementary electron-, proton-, charge-, and energy-transfer
reactions that take place in the intricate molecular machineries of
cell respiration and photosynthesis. Recent developments in structural
biology, particularly cryo-electron microscopy (cryoEM), have resolved
the molecular architecture of several energy transducing proteins,
but detailed mechanistic principles of their charge transfer reactions
still remain poorly understood and a major challenge for modern biochemical
research. To this end, multiscale molecular simulations provide a
powerful approach to probe mechanistic principles on a broad range
of time scales (femtoseconds to milliseconds) and spatial resolutions
(101–106 atoms), although technical challenges
also require balancing between the computational accuracy, cost, and
approximations introduced within the model. Here we discuss how the
combination of atomistic (aMD) and hybrid quantum/classical molecular
dynamics (QM/MM MD) simulations with free energy (FE) sampling methods
can be used to probe mechanistic principles of enzymes responsible
for biological energy conversion. We present mechanistic explorations
of long-range proton-coupled electron transfer (PCET) dynamics in
the highly intricate respiratory chain enzyme Complex I, which functions
as a redox-driven proton pump in bacterial and mitochondrial respiratory
chains by catalyzing a 300 Å fully reversible PCET process. This
process is initiated by a hydride (H–) transfer
between NADH and FMN, followed by long-range (>100 Å) electron
transfer along a wire of 8 FeS centers leading to a quinone biding
site. The reduction of the quinone to quinol initiates dissociation
of the latter to a second membrane-bound binding site, and triggers
proton pumping across the membrane domain of complex I, in subunits
up to 200 Å away from the active site. Our simulations across
different size and time scales suggest that transient charge transfer
reactions lead to changes in the internal hydration state of key regions,
local electric fields, and the conformation of conserved ion pairs,
which in turn modulate the dynamics of functional steps along the
reaction cycle. Similar functional principles, which operate on much
shorter length scales, are also found in some unrelated proteins,
suggesting that enzymes may employ conserved principles in the catalysis
of biological energy transduction processes.
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Affiliation(s)
- Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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30
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Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site. Photochem Photobiol Sci 2021; 21:1-12. [PMID: 34813075 PMCID: PMC8799541 DOI: 10.1007/s43630-021-00113-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/04/2021] [Indexed: 02/02/2023]
Abstract
At the joint between the membrane and hydrophilic arms of the enzyme, the structure of the respiratory complex I reveals a tunnel-like Q-chamber for ubiquinone binding and reduction. The narrow entrance of the quinone chamber located in ND1 subunit forms a bottleneck (eye of a needle) which in all resolved structures was shown to be too small for a bulky quinone to pass through, and it was suggested that a conformational change is required to open the channel. The closed bottleneck appears to be a well-established feature of all structures reported so-far, both for the so-called open and closed states of the enzyme, with no indication of a stable open state of the bottleneck. We propose a squeeze-in mechanism of the bottleneck passage, where dynamic thermal conformational fluctuations allow quinone to get in and out. Here, using molecular dynamics simulations of the bacterial enzyme, we have identified collective conformational changes that open the quinone chamber bottleneck. The model predicts a significant reduction—due to a need for a rare opening of the bottleneck—of the effective bi-molecular rate constant, in line with the available kinetic data. We discuss possible reasons for such a tight control of the quinone passage into the binding chamber and mechanistic consequences for the quinone two-electron reduction.
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31
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Xu M, Kopajtich R, Elstner M, Li H, Liu Z, Wang J, Prokisch H, Fang F. Identification of a novel m.3955G > A variant in MT-ND1 associated with Leigh syndrome. Mitochondrion 2021; 62:13-23. [PMID: 34656796 DOI: 10.1016/j.mito.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/26/2021] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Leigh syndrome (LS) is one of the most common mitochondrial diseases in children, for which at least 90 causative genes have been identified. However, many LS patients have no genetic diagnosis, indicating that more disease-related genes remain to be identified. In this study, we identified a novel variant, m.3955G > A, in mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) in two unrelated LS patients, manifesting as infancy-onset frequent seizures, neurodegeneration, elevated lactate levels, and bilateral symmetrical lesions in the brainstem, basal ganglia, and thalamus. Transfer of the mutant mtDNA with m.3955G > A into cybrids disturbed the MT-ND1 expression and CI assembly, followed by remarkable mitochondrial dysfunction, reactive oxygen species production, and mitochondrial membrane potential reduction. Our findings demonstrated the pathogenicity of the novel m.3955G > A variant, and extend the spectrum of pathogenic mtDNA variants.
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Affiliation(s)
- Manting Xu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Robert Kopajtich
- Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Munich 85764, Germany
| | - Matthias Elstner
- Department of Neurology, Technical University of Munich, School of Medicine, Munich 81675, Germany
| | - Hua Li
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Zhimei Liu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Junling Wang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Holger Prokisch
- Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Munich 85764, Germany
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China.
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32
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Čėnas N, Nemeikaitė-Čėnienė A, Kosychova L. Single- and Two-Electron Reduction of Nitroaromatic Compounds by Flavoenzymes: Mechanisms and Implications for Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168534. [PMID: 34445240 PMCID: PMC8395237 DOI: 10.3390/ijms22168534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Nitroaromatic compounds (ArNO2) maintain their importance in relation to industrial processes, environmental pollution, and pharmaceutical application. The manifestation of toxicity/therapeutic action of nitroaromatics may involve their single- or two-electron reduction performed by various flavoenzymes and/or their physiological redox partners, metalloproteins. The pivotal and still incompletely resolved questions in this area are the identification and characterization of the specific enzymes that are involved in the bioreduction of ArNO2 and the establishment of their contribution to cytotoxic/therapeutic action of nitroaromatics. This review addresses the following topics: (i) the intrinsic redox properties of ArNO2, in particular, the energetics of their single- and two-electron reduction in aqueous medium; (ii) the mechanisms and structure-activity relationships of reduction in ArNO2 by flavoenzymes of different groups, dehydrogenases-electrontransferases (NADPH:cytochrome P-450 reductase, ferredoxin:NADP(H) oxidoreductase and their analogs), mammalian NAD(P)H:quinone oxidoreductase, bacterial nitroreductases, and disulfide reductases of different origin (glutathione, trypanothione, and thioredoxin reductases, lipoamide dehydrogenase), and (iii) the relationships between the enzymatic reactivity of compounds and their activity in mammalian cells, bacteria, and parasites.
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Affiliation(s)
- Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-5-223-4392
| | - Aušra Nemeikaitė-Čėnienė
- State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08406 Vilnius, Lithuania;
| | - Lidija Kosychova
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
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33
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Copsey AC, Barsottini MRO, May B, Xu F, Albury MS, Young L, Moore AL. Kinetic characterisation and inhibitor sensitivity of Candida albicans and Candida auris recombinant AOX expressed in a self-assembled proteoliposome system. Sci Rep 2021; 11:14748. [PMID: 34285303 PMCID: PMC8292455 DOI: 10.1038/s41598-021-94320-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Candidemia caused by Candida spp. is a serious threat in hospital settings being a major cause of acquired infection and death and a possible contributor to Covid-19 mortality. Candidemia incidence has been rising worldwide following increases in fungicide-resistant pathogens highlighting the need for more effective antifungal agents with novel modes of action. The membrane-bound enzyme alternative oxidase (AOX) promotes fungicide resistance and is absent in humans making it a desirable therapeutic target. However, the lipophilic nature of the AOX substrate (ubiquinol-10) has hindered its kinetic characterisation in physiologically-relevant conditions. Here, we present the purification and expression of recombinant AOXs from C. albicans and C. auris in a self-assembled proteoliposome (PL) system. Kinetic parameters (Km and Vmax) with respect to ubiquinol-10 have been determined. The PL system has also been employed in dose-response assays with novel AOX inhibitors. Such information is critical for the future development of novel treatments for Candidemia.
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Affiliation(s)
- Alice C Copsey
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Mario R O Barsottini
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Benjamin May
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
- Theradex (Europe) Ltd, 2nd Floor, The Pinnacle, Station Way, Crawley, RH10 1JH, UK
| | - Fei Xu
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
- Applied Biotechnology Center, Wuhan University of Bioengineering, Wuhan, China
| | - Mary S Albury
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Luke Young
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Anthony L Moore
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK.
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34
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Zhang YY, Elam E, Ni ZJ, Zhang F, Thakur K, Wang S, Zhang JG, Wei ZJ. LC-MS/MS targeting analysis of terpenoid metabolism in Carya cathayensis at different developmental stages. Food Chem 2021; 366:130583. [PMID: 34303203 DOI: 10.1016/j.foodchem.2021.130583] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/23/2021] [Accepted: 07/09/2021] [Indexed: 11/18/2022]
Abstract
Terpenoid metabolism at different developmental stages of Carya cathayensis was elucidated based on LC-MS/MS analysis and multi-omics. Terpenoid metabolites 2-hydroxy-1,4-naphoquinone and 3-hydroxybenzoic acid reached the maximum at 105 days after pollination (DAP) (P2 stage). To reveal the complex mechanism of C. cathayensis embryogenesis in relation to terpenoid metabolites (90-165 DAP), a metabolomic and transcriptional co-expression analysis was conducted. Based on RNA-Seq analysis, 679 genes of 1144 terpenoid biosynthesis were differentially expressed. Six terpenoid metabolites and 86 differentially expressed genes related to terpenoquinone metabolism were identified. Comprehensive analysis of metabolome and transcriptional data revealed that terpenoquinone accumulated in the early phase was active in the later phase. Overall, we profiled the transcriptome and metabolome changes in C. cathayensis during the developmental phase to investigate the metabolic pathways and candidate genes underlying the changes at different growth stages.
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Affiliation(s)
- Yuan-Yuan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China; Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
| | - Elnur Elam
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
| | - Zhi-Jing Ni
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
| | - Fan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China; Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China; Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
| | - Shaoyun Wang
- College of Biological Science and Technology, Fuzhou University, Fuzhou 350108, People's Republic of China.
| | - Jian-Guo Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China; Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China; Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
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35
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Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly. Life (Basel) 2021; 11:life11050455. [PMID: 34069703 PMCID: PMC8161149 DOI: 10.3390/life11050455] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022] Open
Abstract
NADH:ubiquinone-oxidoreductase (complex I) is the largest membrane protein complex of the respiratory chain. Complex I couples electron transfer to vectorial proton translocation across the inner mitochondrial membrane. The L shaped structure of complex I is divided into a membrane arm and a matrix arm. Fourteen central subunits are conserved throughout species, while some 30 accessory subunits are typically found in eukaryotes. Complex I dysfunction is associated with mutations in the nuclear and mitochondrial genome, resulting in a broad spectrum of neuromuscular and neurodegenerative diseases. Accessory subunit NDUFS4 in the matrix arm is a hot spot for mutations causing Leigh or Leigh-like syndrome. In this review, we focus on accessory subunits of the matrix arm and discuss recent reports on the function of accessory subunit NDUFS4 and its interplay with NDUFS6, NDUFA12, and assembly factor NDUFAF2 in complex I assembly.
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36
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Galemou Yoga E, Schiller J, Zickermann V. Ubiquinone Binding and Reduction by Complex I-Open Questions and Mechanistic Implications. Front Chem 2021; 9:672851. [PMID: 33996767 PMCID: PMC8119997 DOI: 10.3389/fchem.2021.672851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
NADH: ubiquinone oxidoreductase (complex I) is the first enzyme complex of the respiratory chain. Complex I is a redox-driven proton pump that contributes to the proton motive force that drives ATP synthase. The structure of complex I has been analyzed by x-ray crystallography and electron cryo-microscopy and is now well-described. The ubiquinone (Q) reduction site of complex I is buried in the peripheral arm and a tunnel-like structure is thought to provide access for the hydrophobic substrate from the membrane. Several intermediate binding positions for Q in the tunnel were identified in molecular simulations. Structural data showed the binding of native Q molecules and short chain analogs and inhibitors in the access pathway and in the Q reduction site, respectively. We here review the current knowledge on the interaction of complex I with Q and discuss recent hypothetical models for the coupling mechanism.
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Affiliation(s)
- Etienne Galemou Yoga
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt, Germany
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37
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Jarman OD, Biner O, Wright JJ, Hirst J. Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I. Sci Rep 2021; 11:10143. [PMID: 33980947 PMCID: PMC8115037 DOI: 10.1038/s41598-021-89575-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/27/2021] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a crucial metabolic enzyme that couples the free energy released from NADH oxidation and ubiquinone reduction to the translocation of four protons across the inner mitochondrial membrane, creating the proton motive force for ATP synthesis. The mechanism by which the energy is captured, and the mechanism and pathways of proton pumping, remain elusive despite recent advances in structural knowledge. Progress has been limited by a lack of model systems able to combine functional and structural analyses with targeted mutagenic interrogation throughout the entire complex. Here, we develop and present the α-proteobacterium Paracoccus denitrificans as a suitable bacterial model system for mitochondrial complex I. First, we develop a robust purification protocol to isolate highly active complex I by introducing a His6-tag on the Nqo5 subunit. Then, we optimize the reconstitution of the enzyme into liposomes, demonstrating its proton pumping activity. Finally, we develop a strain of P. denitrificans that is amenable to complex I mutagenesis and create a catalytically inactive variant of the enzyme. Our model provides new opportunities to disentangle the mechanism of complex I by combining mutagenesis in every subunit with established interrogative biophysical measurements on both the soluble and membrane bound enzymes.
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Affiliation(s)
- Owen D. Jarman
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Olivier Biner
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - John J. Wright
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Judy Hirst
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
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38
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Chung I, Serreli R, Cross JB, Di Francesco ME, Marszalek JR, Hirst J. Cork-in-bottle mechanism of inhibitor binding to mammalian complex I. SCIENCE ADVANCES 2021; 7:7/20/eabg4000. [PMID: 33990335 PMCID: PMC8121435 DOI: 10.1126/sciadv.abg4000] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/26/2021] [Indexed: 05/08/2023]
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a major contributor of free energy for oxidative phosphorylation, is increasingly recognized as a promising drug target for ischemia-reperfusion injury, metabolic disorders, and various cancers. Several pharmacologically relevant but structurally unrelated small molecules have been identified as specific complex I inhibitors, but their modes of action remain unclear. Here, we present a 3.0-Å resolution cryo-electron microscopy structure of mammalian complex I inhibited by a derivative of IACS-010759, which is currently in clinical development against cancers reliant on oxidative phosphorylation, revealing its unique cork-in-bottle mechanism of inhibition. We combine structural and kinetic analyses to deconvolute cross-species differences in inhibition and identify the structural motif of a "chain" of aromatic rings as a characteristic that promotes inhibition. Our findings provide insights into the importance of π-stacking residues for inhibitor binding in the long substrate-binding channel in complex I and a guide for future biorational drug design.
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Affiliation(s)
- Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Riccardo Serreli
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Jason B Cross
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Joseph R Marszalek
- TRACTION-Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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39
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Masuya T, Uno S, Murai M, Miyoshi H. Pinpoint Dual Chemical Cross-Linking Explores the Structural Dynamics of the Ubiquinone Reaction Site in Mitochondrial Complex I. Biochemistry 2021; 60:813-824. [PMID: 33650850 DOI: 10.1021/acs.biochem.0c00991] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ubiquinone reduction step in NADH-ubiquinone oxidoreductase (complex I) is the key to triggering proton translocation in its membrane part. Although the existence of a long and narrow quinone-access channel has been identified, it remains debatable whether the channel model can account for binding of various ligands (ubiquinones and inhibitors) to the enzyme. We previously proposed that the matrix-side interfacial region of the 49 kDa, ND1, PSST, and 39 kDa subunits, which is covered by a loop connecting transmembrane helices (TMHs) 1 and 2 of ND3, may be the area for entry of some bulky ligands into the quinone reaction cavity. However, this proposition lacks direct evidence that the cavity is accessible from the putative matrix-side region, which allows ligands to pass. To address this, we examined whether Cys39 of ND3 and Asp160 of 49 kDa can be specifically cross-linked by bifunctional cross-linkers (tetrazine-maleimide hybrid, named TMBC). On the basis of the structural models of complex I, such dual cross-linking is unexpected because ND3 Cys39 and 49 kDa Asp160 are located on the TMH1-2 loop and deep inside the channel, respectively, and hence, they are physically separated by peptide chains forming the channel wall. However, three TMBCs with different spacer lengths did cross-link the two residues, resulting in the formation of new cross-linked ND3/49 kDa subunits. Chemical modification of either ND3 Cys39 or 49 kDa Asp160 blocked the dual cross-linking, ensuring the specificity of the cross-linking. Altogether, this study provides direct evidence that the quinone reaction cavity is indeed accessible from the proposed matrix-side region covered by the ND3 TMH1-2 loop.
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Affiliation(s)
- Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shinpei Uno
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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40
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Di Luca A, Kaila VRI. Molecular strain in the active/deactive-transition modulates domain coupling in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148382. [PMID: 33513365 DOI: 10.1016/j.bbabio.2021.148382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022]
Abstract
Complex I functions as a primary redox-driven proton pump in aerobic respiratory chains, establishing a proton motive force that powers ATP synthesis and active transport. Recent cryo-electron microscopy (cryo-EM) experiments have resolved the mammalian complex I in the biomedically relevant active (A) and deactive (D) states (Zhu et al., 2016; Fiedorczuk et al., 2016; Agip et al., 2018 [1-3]) that could regulate enzyme turnover, but it still remains unclear how the conformational state and activity are linked. We show here how global motion along the A/D transition accumulates molecular strain at specific coupling regions important for both redox chemistry and proton pumping. Our data suggest that the A/D motion modulates force propagation pathways between the substrate-binding site and the proton pumping machinery that could alter electrostatic and conformational coupling across large distances. Our findings provide a molecular basis to understand how global protein dynamics can modulate the biological activity of large molecular complexes.
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Affiliation(s)
- Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
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41
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Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across the mitochondrial inner membrane and power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of the mammalian complex, but leave the molecular principles of its long-range energy coupling mechanism open to debate. Here, we describe the 3.0-Å resolution cryo-EM structure of complex I from mouse heart mitochondria with a substrate-like inhibitor, piericidin A, bound in the ubiquinone-binding active site. We combine our structural analyses with both functional and computational studies to demonstrate competitive inhibitor binding poses and provide evidence that two inhibitor molecules bind end-to-end in the long substrate binding channel. Our findings reveal information about the mechanisms of inhibition and substrate reduction that are central for understanding the principles of energy transduction in mammalian complex I. The respiratory complex I (NADH:ubiquinone oxidoreductase) is a large redox-driven proton pump that initiates respiration in mitochondria. Here, the authors present the 3.0 Å cryo-EM structure of complex I from mouse heart mitochondria with the ubiquinone-analogue inhibitor piericidin A bound in the active site and with kinetic measurements and MD simulations they further show that this inhibitor acts competitively against the native ubiquinone-10 substrate.
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42
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Wang P, Dhananjayan N, Hagras MA, Stuchebrukhov AA. Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148326. [PMID: 33045211 DOI: 10.1016/j.bbabio.2020.148326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022]
Abstract
The structure of the entire respiratory complex I is now known at reasonably high resolution for many species - bacteria, yeast, and several mammals, including human. The structure reveals an almost 30 angstrom tunnel-like chamber for ubiquinone binding in the core part of the enzyme, at the joint between the membrane and hydrophilic arms of the enzyme. Here we characterize the geometric bottleneck forming the entrance of the quinone reaction chamber. Computer simulations of quinone/quinol passage through the bottleneck suggest that in all structures available, from bacterial to human, this bottleneck is too narrow for the quinone or quinol to pass and that a conformational change is required to open the channel. Moreover, the bottleneck is too narrow even for isoprenoid tail free passage. The closed structure can be an artifact of the crystallization packing forces, low temperature, or other unnatural conditions occurring in the structural data acquisition procedure that affect this flexible part of the enzyme. Two of the helices forming the bottleneck are in direct contact with the subunit (ND3) that was recently demonstrated to be involved in conformational changes during the redox proton pumping cycle, which indicates flexibility of that part of the enzyme. We conclude that the published structures are all locked in the unfunctional states and do not represent correctly the functional enzyme; we discuss possible ways to open the structure in the context of possible mechanisms of the enzyme.
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Affiliation(s)
- Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America
| | - Nithin Dhananjayan
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America
| | - Muhammad A Hagras
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America.
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43
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Grba DN, Hirst J. Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation. Nat Struct Mol Biol 2020; 27:892-900. [PMID: 32747785 PMCID: PMC7612091 DOI: 10.1038/s41594-020-0473-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/26/2020] [Indexed: 01/09/2023]
Abstract
Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine.
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Affiliation(s)
- Daniel N Grba
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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44
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Mühlbauer ME, Saura P, Nuber F, Di Luca A, Friedrich T, Kaila VRI. Water-Gated Proton Transfer Dynamics in Respiratory Complex I. J Am Chem Soc 2020; 142:13718-13728. [PMID: 32643371 PMCID: PMC7659035 DOI: 10.1021/jacs.0c02789] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The respiratory complex I transduces
redox energy into an electrochemical
proton gradient in aerobic respiratory chains, powering energy-requiring
processes in the cell. However, despite recently resolved molecular
structures, the mechanism of this gigantic enzyme remains poorly understood.
By combining large-scale quantum and classical simulations with site-directed
mutagenesis and biophysical experiments, we show here how the conformational
state of buried ion-pairs and water molecules control the protonation
dynamics in the membrane domain of complex I and establish evolutionary
conserved long-range coupling elements. We suggest that an electrostatic
wave propagates in forward and reverse directions across the 200 Å
long membrane domain during enzyme turnover, without significant dissipation
of energy. Our findings demonstrate molecular principles that enable
efficient long-range proton–electron coupling (PCET) and how
perturbation of this PCET machinery may lead to development of mitochondrial
disease.
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Affiliation(s)
- Max E Mühlbauer
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Franziska Nuber
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
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45
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Lin Y, Xu X, Zhao D, Liu F, Luo Y, Du J, Wang D, Ji K, Zhao Y, Yan C. A novel m.11406 T > A mutation in mitochondrial ND4 gene causes MELAS syndrome. Mitochondrion 2020; 54:57-64. [PMID: 32659360 DOI: 10.1016/j.mito.2020.06.011] [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: 01/09/2020] [Revised: 05/16/2020] [Accepted: 06/25/2020] [Indexed: 10/23/2022]
Abstract
Pathogenic point mutations of mitochondrial DNA (mtDNA) are associated with a large number of heterogeneous diseases involving multiple systems with which patients may present with a wide range of clinical phenotypes. In this study, we describe a novel heteroplasmic missense mutation, m.11406 T > A, of the ND4 gene encoding the subunit 4 of mitochondrial complex I in a 32-year-old woman with recurrent epileptic seizure, headache and bilateral hearing loss. Skeletal muscle histochemistry demonstrated that approximately 20% of fibers were cytochrome C oxidase (COX) deficient with increased activity of succinate dehydrogenase (SDH). Further investigations in muscle specimens showed significantly reduced level of ND4 protein. It is interesting that the subunits of complex I (ND1 and NDFUB8) and complex IV(CO1) were also remarkably decreased. These findings indicate that ND1, NDFUB8 and CO1 are more susceptible than other subunits to mutations in the mitochondrial ND4 gene.
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Affiliation(s)
- Yan Lin
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xuebi Xu
- Department of Neurology, First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou 325000, China
| | - Dandan Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Fuchen Liu
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Yuebei Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jixiang Du
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Dongdong Wang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kunqian Ji
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Shandong University, Qingdao, Shandong 266035, China; Brain Science Research Institute, Shandong University, Jinan, Shandong 250012, China.
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46
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Biner O, Fedor JG, Yin Z, Hirst J. Bottom-Up Construction of a Minimal System for Cellular Respiration and Energy Regeneration. ACS Synth Biol 2020; 9:1450-1459. [PMID: 32383867 PMCID: PMC7611821 DOI: 10.1021/acssynbio.0c00110] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adenosine triphosphate (ATP), the cellular energy currency, is essential for life. The ability to provide a constant supply of ATP is therefore crucial for the construction of artificial cells in synthetic biology. Here, we describe the bottom-up assembly and characterization of a minimal respiratory system that uses NADH as a fuel to produce ATP from ADP and inorganic phosphate, and is thus capable of sustaining both upstream metabolic processes that rely on NAD+, and downstream energy-demanding processes that are powered by ATP hydrolysis. A detergent-mediated approach was used to co-reconstitute respiratory mitochondrial complex I and an F-type ATP synthase into nanosized liposomes. Addition of the alternative oxidase to the resulting proteoliposomes produced a minimal artificial "organelle" that reproduces the energy-converting catalytic reactions of the mitochondrial respiratory chain: NADH oxidation, ubiquinone cycling, oxygen reduction, proton pumping, and ATP synthesis. As a proof-of-principle, we demonstrate that our nanovesicles are capable of using an NAD+-linked substrate to drive cell-free protein expression. Our nanovesicles are both efficient and durable and may be applied to sustain artificial cells in future work.
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Affiliation(s)
- Olivier Biner
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Justin G Fedor
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Zhan Yin
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
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47
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Barsottini MRO, Copsey A, Young L, Baroni RM, Cordeiro AT, Pereira GAG, Moore AL. Biochemical characterization and inhibition of the alternative oxidase enzyme from the fungal phytopathogen Moniliophthora perniciosa. Commun Biol 2020; 3:263. [PMID: 32451394 PMCID: PMC7248098 DOI: 10.1038/s42003-020-0981-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/30/2020] [Indexed: 01/27/2023] Open
Abstract
Moniliophthora perniciosa is a fungal pathogen and causal agent of the witches' broom disease of cocoa, a threat to the chocolate industry and to the economic and social security in cocoa-planting countries. The membrane-bound enzyme alternative oxidase (MpAOX) is crucial for pathogen survival; however a lack of information on the biochemical properties of MpAOX hinders the development of novel fungicides. In this study, we purified and characterised recombinant MpAOX in dose-response assays with activators and inhibitors, followed by a kinetic characterization both in an aqueous environment and in physiologically-relevant proteoliposomes. We present structure-activity relationships of AOX inhibitors such as colletochlorin B and analogues which, aided by an MpAOX structural model, indicates key residues for protein-inhibitor interaction. We also discuss the importance of the correct hydrophobic environment for MpAOX enzymatic activity. We envisage that such results will guide the future development of AOX-targeting antifungal agents against M. perniciosa, an important outcome for the chocolate industry.
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Affiliation(s)
- Mario R O Barsottini
- Genomics and bioEnergy Laboratory, Institute of Biology, University of Campinas, Campinas, Brazil.,Biochemistry & Biomedicine, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Alice Copsey
- Biochemistry & Biomedicine, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Luke Young
- Biochemistry & Biomedicine, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Renata M Baroni
- Genomics and bioEnergy Laboratory, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Artur T Cordeiro
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Gonçalo A G Pereira
- Genomics and bioEnergy Laboratory, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - Anthony L Moore
- Biochemistry & Biomedicine, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.
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48
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Tsuji A, Akao T, Masuya T, Murai M, Miyoshi H. IACS-010759, a potent inhibitor of glycolysis-deficient hypoxic tumor cells, inhibits mitochondrial respiratory complex I through a unique mechanism. J Biol Chem 2020; 295:7481-7491. [PMID: 32295842 PMCID: PMC7247293 DOI: 10.1074/jbc.ra120.013366] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/13/2020] [Indexed: 12/14/2022] Open
Abstract
The small molecule IACS-010759 has been reported to potently inhibit the proliferation of glycolysis-deficient hypoxic tumor cells by interfering with the functions of mitochondrial NADH-ubiquinone oxidoreductase (complex I) without exhibiting cytotoxicity at tolerated doses in normal cells. Considering the significant cytotoxicity of conventional quinone-site inhibitors of complex I, such as piericidin and acetogenin families, we hypothesized that the mechanism of action of IACS-010759 on complex I differs from that of other known quinone-site inhibitors. To test this possibility, here we investigated IACS-010759's mechanism in bovine heart submitochondrial particles. We found that IACS-010759, like known quinone-site inhibitors, suppresses chemical modification by the tosyl reagent AL1 of Asp160 in the 49-kDa subunit, located deep in the interior of a previously proposed quinone-access channel. However, contrary to the other inhibitors, IACS-010759 direction-dependently inhibited forward and reverse electron transfer and did not suppress binding of the quinazoline-type inhibitor [125I]AzQ to the N terminus of the 49-kDa subunit. Photoaffinity labeling experiments revealed that the photoreactive derivative [125I]IACS-010759-PD1 binds to the middle of the membrane subunit ND1 and that inhibitors that bind to the 49-kDa or PSST subunit cannot suppress the binding. We conclude that IACS-010759's binding location in complex I differs from that of any other known inhibitor of the enzyme. Our findings, along with those from previous study, reveal that the mechanisms of action of complex I inhibitors with widely different chemical properties are more diverse than can be accounted for by the quinone-access channel model proposed by structural biology studies.
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Affiliation(s)
- Atsuhito Tsuji
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takumi Akao
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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49
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Izreig S, Gariepy A, Kaymak I, Bridges HR, Donayo AO, Bridon G, DeCamp LM, Kitchen-Goosen SM, Avizonis D, Sheldon RD, Laister RC, Minden MD, Johnson NA, Duchaine TF, Rudoltz MS, Yoo S, Pollak MN, Williams KS, Jones RG. Repression of LKB1 by miR-17∼92 Sensitizes MYC-Dependent Lymphoma to Biguanide Treatment. Cell Rep Med 2020; 1:100014. [PMID: 32478334 PMCID: PMC7249503 DOI: 10.1016/j.xcrm.2020.100014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 04/21/2020] [Indexed: 12/17/2022]
Abstract
Cancer cells display metabolic plasticity to survive stresses in the tumor microenvironment. Cellular adaptation to energetic stress is coordinated in part by signaling through the liver kinase B1 (LKB1)-AMP-activated protein kinase (AMPK) pathway. Here, we demonstrate that miRNA-mediated silencing of LKB1 confers sensitivity of lymphoma cells to mitochondrial inhibition by biguanides. Using both classic (phenformin) and newly developed (IM156) biguanides, we demonstrate that elevated miR-17∼92 expression in Myc+ lymphoma cells promotes increased apoptosis to biguanide treatment in vitro and in vivo. This effect is driven by the miR-17-dependent silencing of LKB1, which reduces AMPK activation in response to complex I inhibition. Mechanistically, biguanide treatment induces metabolic stress in Myc+ lymphoma cells by inhibiting TCA cycle metabolism and mitochondrial respiration, exposing metabolic vulnerability. Finally, we demonstrate a direct correlation between miR-17∼92 expression and biguanide sensitivity in human cancer cells. Our results identify miR-17∼92 expression as a potential biomarker for biguanide sensitivity in malignancies.
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Affiliation(s)
- Said Izreig
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Alexandra Gariepy
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Irem Kaymak
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Hannah R. Bridges
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ariel O. Donayo
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Gaëlle Bridon
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Metabolomics Core Facility, McGill University, Montreal, QC H3A 1A3, Canada
| | - Lisa M. DeCamp
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Susan M. Kitchen-Goosen
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Daina Avizonis
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Metabolomics Core Facility, McGill University, Montreal, QC H3A 1A3, Canada
| | - Ryan D. Sheldon
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rob C. Laister
- Princess Margaret Cancer Centre, Department of Medical Oncology and Hematology, Toronto, ON M5G 2M9, Canada
| | - Mark D. Minden
- Princess Margaret Cancer Centre, Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Nathalie A. Johnson
- Lady Davis Institute of the Jewish General Hospital and Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Thomas F. Duchaine
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | | | - Sanghee Yoo
- ImmunoMet Therapeutics, Houston, TX 77021, USA
| | - Michael N. Pollak
- Lady Davis Institute of the Jewish General Hospital and Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Kelsey S. Williams
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Russell G. Jones
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
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50
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Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov L, Chipot C, Singharoy A. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. J Am Chem Soc 2020; 142:9220-9230. [PMID: 32347721 DOI: 10.1021/jacs.9b13450] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron-sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron-sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form-a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.
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Affiliation(s)
- Chitrak Gupta
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States.,Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, City University of New York, New York, New York 10017, United States
| | - Chun Kit Chan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Mrinal Shekhar
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - M R Gunner
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, City University of New York, New York, New York 10017, United States
| | - Leonid Sazanov
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,University of Lorraine, Nancy 54000, France
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States.,Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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