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Martin FJO, Santiveri M, Hu H, Taylor NMI. Ion-driven rotary membrane motors: From structure to function. Curr Opin Struct Biol 2024; 88:102884. [PMID: 39053417 DOI: 10.1016/j.sbi.2024.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/16/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Ion-driven membrane motors, essential across all domains of life, convert a gradient of ions across a membrane into rotational energy, facilitating diverse biological processes including ATP synthesis, substrate transport, and bacterial locomotion. Herein, we highlight recent structural advances in the understanding of two classes of ion-driven membrane motors: rotary ATPases and 5:2 motors. The recent structure of the human F-type ATP synthase is emphasised along with the gained structural insight into clinically relevant mutations. Furthermore, we highlight the diverse roles of 5:2 motors and recent mechanistic understanding gained through the resolution of ions in the structure of a sodium-driven motor, combining insights into potential unifying mechanisms of ion selectivity and rotational torque generation in the context of their function as part of complex biological systems.
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Affiliation(s)
- Freddie J O Martin
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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2
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Guo L. F-ATP synthase inhibitory factor 1 and mitochondria-organelle interactions: New insight and implications. Pharmacol Res 2024; 208:107393. [PMID: 39233058 DOI: 10.1016/j.phrs.2024.107393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/08/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Mitochondria are metabolic hub, and act as primary sites for reactive oxygen species (ROS) and metabolites generation. Mitochondrial Ca2+ uptake contributes to Ca2+ storage. Mitochondria-organelle interactions are important for cellular metabolic adaptation, biosynthesis, redox balance, cell fate. Organelle communications are mediated by Ca2+/ROS signals, vesicle transport and membrane contact sites. The permeability transition pore (PTP) is an unselective channel that provides a release pathway for Ca2+/ROS, mtDNA and metabolites. F-ATP synthase inhibitory factor 1 (IF1) participates in regulation of PTP opening and is required for the translocation of transcriptional factors c-Myc/PGC1α to mitochondria to stimulate metabolic switch. IF1, a mitochondrial specific protein, has been suggested to regulate other organelles including nucleus, endoplasmic reticulum and lysosomes. IF1 may be able to mediate mitochondria-organelle interactions and cellular physiology through regulation of PTP activity.
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Affiliation(s)
- Lishu Guo
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China; Department of Anesthesiology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
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3
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Gerle C, Jiko C, Nakano A, Yokoyama K, Gopalasingam CC, Shigematsu H, Abe K. Human F-ATP synthase as a drug target. Pharmacol Res 2024; 209:107423. [PMID: 39303772 DOI: 10.1016/j.phrs.2024.107423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Practical and conceptual barriers have kept human F-ATP synthase out of reach as a target for the treatment of human diseases. Although this situation has persisted for decades, it may change in the near future. In this review the principal functionalities of human F-ATP synthase--proton motive force / ATP interconversion, membrane bending and mitochondrial permeability transition--are surveyed in the context of their respective potential for pharmaceutical intervention. Further, the technical requirements necessary to allow drug designs that are effective at the multiple levels of functionality and modality of human F-ATP synthase are discussed. The structure-based development of gastric proton pump inhibitors is used to exemplify what might be feasible for human F-ATP synthase. And finally, four structural regions of the human F-ATP synthase are examined as potential sites for the development of structure based drug development.
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Affiliation(s)
- Christoph Gerle
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, 1-1-1, Sayo, Hyogo, Japan.
| | - Chimari Jiko
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Atsuki Nakano
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Chai C Gopalasingam
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, 1-1-1, Sayo, Hyogo, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo, Japan
| | - Kazuhiro Abe
- Molecular Biochemistry Lab, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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4
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Kubo S, Okada Y, Takada S. Theoretical insights into rotary mechanism of MotAB in the bacterial flagellar motor. Biophys J 2024:S0006-3495(24)00602-7. [PMID: 39262115 DOI: 10.1016/j.bpj.2024.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/06/2024] [Accepted: 09/09/2024] [Indexed: 09/13/2024] Open
Abstract
Many bacteria enable locomotion by rotating their flagellum. It has been suggested that this rotation is realized by the rotary motion of the stator unit, MotAB, which is driven by proton transfer across the membrane. Recent cryo-electron microscopy studies have revealed a 5:2 MotAB configuration, in which a MotB dimer is encircled by a ring-shaped MotA pentamer. Although the structure implicates the rotary motion of the MotA wheel around the MotB axle, the molecular mechanisms of rotary motion and how they are coupled with proton transfer across the membrane remain elusive. In this study, we built a structure-based computational model for Campylobacter jejuni MotAB, conducted comprehensive protonation-state-dependent molecular dynamics simulations, and revealed a plausible proton-transfer-coupled rotation pathway. The model assumes rotation-dependent proton transfer, in which proton uptake from the periplasmic side to the conserved aspartic acid in MotB is followed by proton hopping to the MotA proton-carrying site, followed by proton export to the CP. We suggest that, by maintaining two of the proton-carrying sites of MotA in the deprotonated state, the MotA pentamer robustly rotates by ∼36° per proton transfer across the membrane. Our results provide a structure-based mechanistic model of the rotary motion of MotAB in bacterial flagellar motors and provide insights into various ion-driven rotary molecular motors.
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Affiliation(s)
- Shintaroh Kubo
- Department of Cell Biology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan; Department of Physics, Graduate School of Science, the University of Tokyo, Tokyo, Japan; Universal Biology Institute and International Research Center for Neurointelligence, the University of Tokyo, Tokyo, Japan; Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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5
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Dietrich L, Agip ANA, Kunz C, Schwarz A, Kühlbrandt W. In situ structure and rotary states of mitochondrial ATP synthase in whole Polytomella cells. Science 2024; 385:1086-1090. [PMID: 39236170 DOI: 10.1126/science.adp4640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/31/2024] [Indexed: 09/07/2024]
Abstract
Cells depend on a continuous supply of adenosine triphosphate (ATP), the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical gradient is established across the inner mitochondrial membrane. The ATP synthase harnesses the energy of the gradient to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. We determined the structure of ATP synthase within mitochondria of the unicellular flagellate Polytomella by electron cryo-tomography and subtomogram averaging at up to 4.2-angstrom resolution, revealing six rotary positions of the central stalk, subclassified into 21 substates of the F1 head. The Polytomella ATP synthase forms helical arrays with multiple adjacent rows defining the cristae ridges. The structure of ATP synthase under native operating conditions in the presence of a membrane potential represents a pivotal step toward the analysis of membrane protein complexes in situ.
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Affiliation(s)
- Lea Dietrich
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt, Germany
| | - Ahmed-Noor A Agip
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt, Germany
| | - Christina Kunz
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt, Germany
| | - Andre Schwarz
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, 60438 Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt, Germany
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6
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Balderas E, Lee SHJ, Rai NK, Mollinedo DM, Duron HE, Chaudhuri D. Mitochondrial Calcium Regulation of Cardiac Metabolism in Health and Disease. Physiology (Bethesda) 2024; 39:0. [PMID: 38713090 PMCID: PMC11460536 DOI: 10.1152/physiol.00014.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024] Open
Abstract
Oxidative phosphorylation is regulated by mitochondrial calcium (Ca2+) in health and disease. In physiological states, Ca2+ enters via the mitochondrial Ca2+ uniporter and rapidly enhances NADH and ATP production. However, maintaining Ca2+ homeostasis is critical: insufficient Ca2+ impairs stress adaptation, and Ca2+ overload can trigger cell death. In this review, we delve into recent insights further defining the relationship between mitochondrial Ca2+ dynamics and oxidative phosphorylation. Our focus is on how such regulation affects cardiac function in health and disease, including heart failure, ischemia-reperfusion, arrhythmias, catecholaminergic polymorphic ventricular tachycardia, mitochondrial cardiomyopathies, Barth syndrome, and Friedreich's ataxia. Several themes emerge from recent data. First, mitochondrial Ca2+ regulation is critical for fuel substrate selection, metabolite import, and matching of ATP supply to demand. Second, mitochondrial Ca2+ regulates both the production and response to reactive oxygen species (ROS), and the balance between its pro- and antioxidant effects is key to how it contributes to physiological and pathological states. Third, Ca2+ exerts localized effects on the electron transport chain (ETC), not through traditional allosteric mechanisms but rather indirectly. These effects hinge on specific transporters, such as the uniporter or the Na+/Ca2+ exchanger, and may not be noticeable acutely, contributing differently to phenotypes depending on whether Ca2+ transporters are acutely or chronically modified. Perturbations in these novel relationships during disease states may either serve as compensatory mechanisms or exacerbate impairments in oxidative phosphorylation. Consequently, targeting mitochondrial Ca2+ holds promise as a therapeutic strategy for a variety of cardiac diseases characterized by contractile failure or arrhythmias.
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Affiliation(s)
- Enrique Balderas
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Sandra H J Lee
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Neeraj K Rai
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - David M Mollinedo
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Hannah E Duron
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Dipayan Chaudhuri
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, Biochemistry, Biomedical Engineering, University of Utah, Salt Lake City, Utah, United States
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7
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Kshirsagar S, Islam MA, Reddy AP, Reddy PH. Resolving the current controversy of use and reuse of housekeeping proteins in ageing research: Focus on saving people's tax dollars. Ageing Res Rev 2024; 100:102437. [PMID: 39067773 PMCID: PMC11384260 DOI: 10.1016/j.arr.2024.102437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]
Abstract
The use of housekeeping genes and proteins to normalize mRNA and protein levels in biomedical research has faced growing scrutiny. Researchers encounter challenges in determining the optimal frequency for running housekeeping proteins such as β-actin, Tubulin, and GAPDH for nuclear-encoded proteins, and Porin, HSP60, and TOM20 for mitochondrial proteins alongside experimental proteins. The regulation of these proteins varies with age, gender, disease progression, epitope nature, gel running conditions, and their reported sizes can differ among antibody suppliers. Additionally, anonymous readers have raised concerns about peer-reviewed and published articles, creating confusion and concern within the research and academic institutions. To clarify these matters, this minireview discusses the role of reference housekeeping proteins in Western blot analysis and outlines key considerations for their use as normalization controls. Instead of Western blotting of housekeeping proteins, staining of total proteins, using Amido Black and Coomassie Blue can be visualized the total protein content on a membrane. The reducing repeated Western blotting analysis of housekeeping proteins, will save resources, time and efforts and in turn increase the number of competitive grants from NIH and funding agencies. We also discussed the use of dot blots over traditional Western blots, when protein levels are low in rare tissues/specimens and cell lines. We sincerely hope that the facts, figures, and discussions presented in this article will clarify the current controversy regarding housekeeping protein(s) use, reuse, and functional aspects of housekeeping proteins. The contents presented in our article will be useful to students, scholars and researchers of all levels in cell biology, protein chemistry and mitochondrial research.
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Affiliation(s)
- Sudhir Kshirsagar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Md Ariful Islam
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Arubala P Reddy
- Nutritional Sciences Department, College Human Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College Human Sciences, Texas Tech University, Lubbock, TX 79409, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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8
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Liu H, Liu Z, Qin A, Zhou Y, Sun S, Liu Y, Hu M, Yang J, Sun X. Mitochondrial ATP Synthase beta-Subunit Affects Plastid Retrograde Signaling in Arabidopsis. Int J Mol Sci 2024; 25:7829. [PMID: 39063070 PMCID: PMC11277312 DOI: 10.3390/ijms25147829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Plastid retrograde signaling plays a key role in coordinating the expression of plastid genes and photosynthesis-associated nuclear genes (PhANGs). Although plastid retrograde signaling can be substantially compromised by mitochondrial dysfunction, it is not yet clear whether specific mitochondrial factors are required to regulate plastid retrograde signaling. Here, we show that mitochondrial ATP synthase beta-subunit mutants with decreased ATP synthase activity are impaired in plastid retrograde signaling in Arabidopsis thaliana. Transcriptome analysis revealed that the expression levels of PhANGs were significantly higher in the mutants affected in the AT5G08670 gene encoding the mitochondrial ATP synthase beta-subunit, compared to wild-type (WT) seedlings when treated with lincomycin (LIN) or norflurazon (NF). Further studies indicated that the expression of nuclear genes involved in chloroplast and mitochondrial retrograde signaling was affected in the AT5G08670 mutant seedlings treated with LIN. These changes might be linked to the modulation of some transcription factors (TFs), such as LHY (Late Elongated Hypocotyl), PIF (Phytochrome-Interacting Factors), MYB, WRKY, and AP2/ERF (Ethylene Responsive Factors). These findings suggest that the activity of mitochondrial ATP synthase significantly influences plastid retrograde signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (H.L.); (Z.L.); (A.Q.); (Y.Z.); (S.S.); (Y.L.); (M.H.); (J.Y.)
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9
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Ren M, Zhou C, Li X, Zhang Y, Li M, Song H, Liu F, Chen T, Xu X, Yang S. Mn-Based Artificial Mitochondrial Complex "VI" Acts as an Electron and Free Radical Conversion Factory to Suppress Macrophage Inflammatory Response. Adv Healthc Mater 2024; 13:e2304125. [PMID: 38301194 DOI: 10.1002/adhm.202304125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Indexed: 02/03/2024]
Abstract
Disturbance in the mitochondrial electron transport chain (ETC) is a key factor in the emerging discovery of immune cell activation in inflammatory diseases, yet specific regulation of ETC homeostasis is extremely challenging. In this paper, a mitochondrial complex biomimetic nanozyme (MCBN), which plays the role of an artificial "VI" complex and acts as an electron and free radical conversion factory to regulate ETC homeostasis is creatively developed. MCBN is composed of bovine serum albumin (BSA), polyethylene glycol (PEG), and triphenylphosphine (TPP) hierarchically encapsulating MnO2 polycrystalline particles. It has nanoscale size and biological properties like natural complexes. In vivo and in vitro experiments confirm that MCBN can target the mitochondrial complexes of inflammatory macrophages, absorb excess electrons in ETC, and convert the electrons to decompose H2O2. By reducing the ROS and ATP bursts and converting existing free radicals, inhibiting NLRP3 inflammatory vesicle activation and NF-κB signaling pathway, MCBN effectively suppresses macrophage M1 activation and inflammatory factor secretion. It also demonstrates good inflammation control and significantly alleviates alveolar bone loss in a mouse model of ligation-induced periodontitis. This is the first nanozyme that mimics the mitochondrial complex and regulates ETC, demonstrating the potential application of MCBN in immune diseases.
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Affiliation(s)
- Mingxing Ren
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Chongjing Zhou
- Department of Stomatology, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Xinyi Li
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Yining Zhang
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Meng Li
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Haoyue Song
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Fengyi Liu
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Tao Chen
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Xinxin Xu
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
| | - Sheng Yang
- College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, China
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10
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Edrich ESM, Duvenage L, Gourlay CW. Alternative Oxidase - Aid or obstacle to combat the rise of fungal pathogens? BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149031. [PMID: 38195037 DOI: 10.1016/j.bbabio.2024.149031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/16/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024]
Abstract
Fungal pathogens present a growing threat to both humans and global health security alike. Increasing evidence of antifungal resistance in fungal populations that infect both humans and plant species has increased reliance on combination therapies and shown the need for new antifungal therapeutic targets to be investigated. Here, we review the roles of mitochondria and fungal respiration in pathogenesis and discuss the role of the Alternative Oxidase enzyme (Aox) in both human fungal pathogens and phytopathogens. Increasing evidence exists for Aox within mechanisms that underpin fungal virulence. Aox also plays important roles in adaptability that may prove useful within dual targeted fungal-specific therapeutic approaches. As improved fungal specific mitochondrial and Aox inhibitors are under development we may see this as an emerging target for future approaches to tackling the growing challenge of fungal infection.
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Affiliation(s)
| | - Lucian Duvenage
- CMM AFRICA Medical Mycology Research Unit, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Campbell W Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Kent CT2 9HY, UK.
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11
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Kubo S, Okada Y. The ATPase asymmetry: Novel computational insight into coupling diverse F O motors with tripartite F 1. Biophys J 2024:S0006-3495(24)00178-4. [PMID: 38459696 DOI: 10.1016/j.bpj.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/10/2024] Open
Abstract
ATP synthase, a crucial enzyme for cellular bioenergetics, operates via the coordinated coupling of an FO motor, which presents variable symmetry, and a tripartite F1 motor. Despite extensive research, the understanding of their coupling dynamics, especially with non-10-fold symmetrical FO motors, remains incomplete. This study investigates the coupling patterns between eightfold and ninefold FO motors and the constant threefold F1 motor using coarse-grained molecular dynamics simulations. We unveil that in the case of a ninefold FO motor, a 3-3-3 motion is most likely to occur, whereas a 3-3-2 motion predominates with an eightfold FO motor. Furthermore, our findings propose a revised model for the coupling method, elucidating that the pathways' energy usage is primarily influenced by F1 rotation and conformational changes hindered by the b-subunits. Our results present a crucial step toward comprehending the energy landscape and mechanisms governing ATP synthase operation.
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Affiliation(s)
- Shintaroh Kubo
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan; Universal Biology Institute and International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan; Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka, Japan
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12
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Del Dotto V, Musiani F, Baracca A, Solaini G. Variants in Human ATP Synthase Mitochondrial Genes: Biochemical Dysfunctions, Associated Diseases, and Therapies. Int J Mol Sci 2024; 25:2239. [PMID: 38396915 PMCID: PMC10889682 DOI: 10.3390/ijms25042239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial ATP synthase (Complex V) catalyzes the last step of oxidative phosphorylation and provides most of the energy (ATP) required by human cells. The mitochondrial genes MT-ATP6 and MT-ATP8 encode two subunits of the multi-subunit Complex V. Since the discovery of the first MT-ATP6 variant in the year 1990 as the cause of Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome, a large and continuously increasing number of inborn variants in the MT-ATP6 and MT-ATP8 genes have been identified as pathogenic. Variants in these genes correlate with various clinical phenotypes, which include several neurodegenerative and multisystemic disorders. In the present review, we report the pathogenic variants in mitochondrial ATP synthase genes and highlight the molecular mechanisms underlying ATP synthase deficiency that promote biochemical dysfunctions. We discuss the possible structural changes induced by the most common variants found in patients by considering the recent cryo-electron microscopy structure of human ATP synthase. Finally, we provide the state-of-the-art of all therapeutic proposals reported in the literature, including drug interventions targeting mitochondrial dysfunctions, allotopic gene expression- and nuclease-based strategies, and discuss their potential translation into clinical trials.
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Affiliation(s)
- Valentina Del Dotto
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40127 Bologna, Italy;
| | - Alessandra Baracca
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
| | - Giancarlo Solaini
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
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13
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Amthor JS. ATP yield of plant respiration: potential, actual and unknown. ANNALS OF BOTANY 2023; 132:133-162. [PMID: 37409716 PMCID: PMC10550282 DOI: 10.1093/aob/mcad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND AND AIMS The ATP yield of plant respiration (ATP/hexose unit respired) quantitatively links active heterotrophic processes with substrate consumption. Despite its importance, plant respiratory ATP yield is uncertain. The aim here was to integrate current knowledge of cellular mechanisms with inferences required to fill knowledge gaps to generate a contemporary estimate of respiratory ATP yield and identify important unknowns. METHOD A numerical balance sheet model combining respiratory carbon metabolism and electron transport pathways with uses of the resulting transmembrane electrochemical proton gradient was created and parameterized for healthy, non-photosynthesizing plant cells catabolizing sucrose or starch to produce cytosolic ATP. KEY RESULTS Mechanistically, the number of c subunits in the mitochondrial ATP synthase Fo sector c-ring, which is unquantified in plants, affects ATP yield. A value of 10 was (justifiably) used in the model, in which case respiration of sucrose potentially yields about 27.5 ATP/hexose (0.5 ATP/hexose more from starch). Actual ATP yield often will be smaller than its potential due to bypasses of energy-conserving reactions in the respiratory chain, even in unstressed plants. Notably, all else being optimal, if 25 % of respiratory O2 uptake is via the alternative oxidase - a typically observed fraction - ATP yield falls 15 % below its potential. CONCLUSIONS Plant respiratory ATP yield is smaller than often assumed (certainly less than older textbook values of 36-38 ATP/hexose) leading to underestimation of active-process substrate requirements. This hinders understanding of ecological/evolutionary trade-offs between competing active processes and assessments of crop growth gains possible through bioengineering of processes that consume ATP. Determining the plant mitochondrial ATP synthase c-ring size, the degree of any minimally required (useful) bypasses of energy-conserving reactions in the respiratory chain, and the magnitude of any 'leaks' in the inner mitochondrial membrane are key research needs.
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Affiliation(s)
- J S Amthor
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
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14
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Lee SH, Duron HE, Chaudhuri D. Beyond the TCA cycle: new insights into mitochondrial calcium regulation of oxidative phosphorylation. Biochem Soc Trans 2023; 51:1661-1673. [PMID: 37641565 PMCID: PMC10508640 DOI: 10.1042/bst20230012] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
While mitochondria oxidative phosphorylation is broadly regulated, the impact of mitochondrial Ca2+ on substrate flux under both physiological and pathological conditions is increasingly being recognized. Under physiologic conditions, mitochondrial Ca2+ enters through the mitochondrial Ca2+ uniporter and boosts ATP production. However, maintaining Ca2+ homeostasis is crucial as too little Ca2+ inhibits adaptation to stress and Ca2+ overload can trigger cell death. In this review, we discuss new insights obtained over the past several years expanding the relationship between mitochondrial Ca2+ and oxidative phosphorylation, with most data obtained from heart, liver, or skeletal muscle. Two new themes are emerging. First, beyond boosting ATP synthesis, Ca2+ appears to be a critical determinant of fuel substrate choice between glucose and fatty acids. Second, Ca2+ exerts local effects on the electron transport chain indirectly, not via traditional allosteric mechanisms. These depend critically on the transporters involved, such as the uniporter or the Na+-Ca2+ exchanger. Alteration of these new relationships during disease can be either compensatory or harmful and suggest that targeting mitochondrial Ca2+ may be of therapeutic benefit during diseases featuring impairments in oxidative phosphorylation.
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Affiliation(s)
- Sandra H. Lee
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, USA
| | - Hannah E. Duron
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, USA
| | - Dipayan Chaudhuri
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, Biochemistry, Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
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15
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Coluccino G, Muraca VP, Corazza A, Lippe G. Cyclophilin D in Mitochondrial Dysfunction: A Key Player in Neurodegeneration? Biomolecules 2023; 13:1265. [PMID: 37627330 PMCID: PMC10452829 DOI: 10.3390/biom13081265] [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: 07/05/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial dysfunction plays a pivotal role in numerous complex diseases. Understanding the molecular mechanisms by which the "powerhouse of the cell" turns into the "factory of death" is an exciting yet challenging task that can unveil new therapeutic targets. The mitochondrial matrix protein CyPD is a peptidylprolyl cis-trans isomerase involved in the regulation of the permeability transition pore (mPTP). The mPTP is a multi-conductance channel in the inner mitochondrial membrane whose dysregulated opening can ultimately lead to cell death and whose involvement in pathology has been extensively documented over the past few decades. Moreover, several mPTP-independent CyPD interactions have been identified, indicating that CyPD could be involved in the fine regulation of several biochemical pathways. To further enrich the picture, CyPD undergoes several post-translational modifications that regulate both its activity and interaction with its clients. Here, we will dissect what is currently known about CyPD and critically review the most recent literature about its involvement in neurodegenerative disorders, focusing on Alzheimer's Disease and Parkinson's Disease, supporting the notion that CyPD could serve as a promising therapeutic target for the treatment of such conditions. Notably, significant efforts have been made to develop CyPD-specific inhibitors, which hold promise for the treatment of such complex disorders.
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Affiliation(s)
- Gabriele Coluccino
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy; (V.P.M.); (A.C.)
| | | | | | - Giovanna Lippe
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy; (V.P.M.); (A.C.)
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16
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Selvarajan S, Shim H, Byun E, Kim A, Song SH. Protein redox by a piezoelectric acousto-nanodevice. NANOSCALE 2023; 15:12889-12893. [PMID: 37477602 DOI: 10.1039/d3nr01523h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Protein redox is responsible for many crucial biological processes; thus, the ability to modulate the redox proteins through external stimuli presents a unique opportunity to tune the system. In this work, we present an acousto-nanodevice that is capable of oxidizing redox protein under ultrasonic irradiation via surface-engineered barium titanate (BTO) nanoparticles with a gold half-coating. Using cytochrome c as the model protein, we demonstrate nanodevice-mediated protein oxidation. BINased on our experimental observations, we reveal that the electron transfer occurs in one direction due to the alternating electrical polarization of BTO under ultrasound. Such unique unidirectional electron transfer is enabled by modulating the work function of the gold surface with respect to the redox center. The new class of ultrasonically powered nano-sized protein redox agents could be a modulator for biological processes with high selectivity and deeper treatment sites.
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Affiliation(s)
- Sophia Selvarajan
- Department of Electronics Engineering, Sookmyung Women's University, Seoul 04310, Republic of Korea.
- Department of Medical Engineering, University of South Florida, Tampa, FL, 33602, USA.
| | - Hyunji Shim
- Department of Electronics Engineering, Sookmyung Women's University, Seoul 04310, Republic of Korea.
| | - Eunjeong Byun
- Department of Electronics Engineering, Sookmyung Women's University, Seoul 04310, Republic of Korea.
| | - Albert Kim
- Department of Medical Engineering, University of South Florida, Tampa, FL, 33602, USA.
| | - Seung Hyun Song
- Department of Electronics Engineering, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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17
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Jacobs HT. A century of mitochondrial research, 1922-2022. Enzymes 2023; 54:37-70. [PMID: 37945177 DOI: 10.1016/bs.enz.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Although recognized earlier as subcellular entities by microscopists, mitochondria have been the subject of functional studies since 1922, when their biochemical similarities with bacteria were first noted. In this overview I trace the history of research on mitochondria from that time up to the present day, focussing on the major milestones of the overlapping eras of mitochondrial biochemistry, genetics, pathology and cell biology, and its explosion into new areas in the past 25 years. Nowadays, mitochondria are considered to be fully integrated into cell physiology, rather than serving specific functions in isolation.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia.
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18
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Kubo S, Niina T, Takada S. F O-F 1 coupling and symmetry mismatch in ATP synthase resolved in every F O rotation step. Biophys J 2023; 122:2898-2909. [PMID: 36171725 PMCID: PMC10397808 DOI: 10.1016/j.bpj.2022.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/18/2022] [Accepted: 09/26/2022] [Indexed: 11/19/2022] Open
Abstract
FOF1 ATP synthase, a ubiquitous enzyme that synthesizes most ATP in living cells, is composed of two rotary motors: a membrane-embedded proton-driven FO motor and a catalytic F1 motor. These motors share both central and peripheral stalks. Although both FO and F1 have pseudo-symmetric structures, their symmetries do not match. How symmetry mismatch is solved remains elusive because of the missing intermediate structures of the rotational steps. Here, for the case of Bacillus PS3 ATP synthases with three- and 10-fold symmetries in F1 and FO, respectively, we uncovered the mechanical couplings between FO and F1 at every 36° rotation step via molecular dynamics simulations and comparative studies of cryoelectron microscopy (cryo-EM) structures from three species. We found that the mismatch could be solved using several elements: 1) the F1 head partially rotates relative to the FO a subunit via elastic distortion of the b subunits, 2) the rotor is twisted, and 3) comparisons of cryo-EM structures further suggest that the c ring rotary angles can deviate from the symmetric ones. In addition, the F1 motor may have non-canonical structures, relieving stronger frustration. Thus, we provide new insights for solving the symmetry mismatch problem.
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Affiliation(s)
- Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada.
| | - Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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19
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Osipov SD, Ryzhykau YL, Zinovev EV, Minaeva AV, Ivashchenko SD, Verteletskiy DP, Sudarev VV, Kuklina DD, Nikolaev MY, Semenov YS, Zagryadskaya YA, Okhrimenko IS, Gette MS, Dronova EA, Shishkin AY, Dencher NA, Kuklin AI, Ivanovich V, Uversky VN, Vlasov AV. I-Shaped Dimers of a Plant Chloroplast F OF 1-ATP Synthase in Response to Changes in Ionic Strength. Int J Mol Sci 2023; 24:10720. [PMID: 37445905 DOI: 10.3390/ijms241310720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
F-type ATP synthases play a key role in oxidative and photophosphorylation processes generating adenosine triphosphate (ATP) for most biochemical reactions in living organisms. In contrast to the mitochondrial FOF1-ATP synthases, those of chloroplasts are known to be mostly monomers with approx. 15% fraction of oligomers interacting presumably non-specifically in a thylakoid membrane. To shed light on the nature of this difference we studied interactions of the chloroplast ATP synthases using small-angle X-ray scattering (SAXS) method. Here, we report evidence of I-shaped dimerization of solubilized FOF1-ATP synthases from spinach chloroplasts at different ionic strengths. The structural data were obtained by SAXS and demonstrated dimerization in response to ionic strength. The best model describing SAXS data was two ATP-synthases connected through F1/F1' parts, presumably via their δ-subunits, forming "I" shape dimers. Such I-shaped dimers might possibly connect the neighboring lamellae in thylakoid stacks assuming that the FOF1 monomers comprising such dimers are embedded in parallel opposing stacked thylakoid membrane areas. If this type of dimerization exists in nature, it might be one of the pathways of inhibition of chloroplast FOF1-ATP synthase for preventing ATP hydrolysis in the dark, when ionic strength in plant chloroplasts is rising. Together with a redox switch inserted into a γ-subunit of chloroplast FOF1 and lateral oligomerization, an I-shaped dimerization might comprise a subtle regulatory process of ATP synthesis and stabilize the structure of thylakoid stacks in chloroplasts.
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Affiliation(s)
- Stepan D Osipov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Yury L Ryzhykau
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
| | - Egor V Zinovev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andronika V Minaeva
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Sergey D Ivashchenko
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Dmitry P Verteletskiy
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Vsevolod V Sudarev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Daria D Kuklina
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Mikhail Yu Nikolaev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Yury S Semenov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Yuliya A Zagryadskaya
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Ivan S Okhrimenko
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Margarita S Gette
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Elizaveta A Dronova
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Aleksei Yu Shishkin
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Norbert A Dencher
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Alexander I Kuklin
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
| | - Valentin Ivanovich
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Alexey V Vlasov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
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20
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Ni J, Song W, Ali NA, Zhang Y, Xing J, Su K, Sun X, Zhao X. The ATP Synthase γ Subunit ATPC1 Regulates RNA Editing in Chloroplasts. Int J Mol Sci 2023; 24:ijms24119203. [PMID: 37298153 DOI: 10.3390/ijms24119203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
RNA editing is the process of modifying RNA molecules by inserting, deleting, or substituting nucleotides. In flowering plants, RNA editing occurs predominantly in RNAs encoded by the organellar genomes of mitochondria and chloroplasts, and the main type of editing involves the substitution of cytidine with uridine at specific sites. Abnormal RNA editing in plants can affect gene expression, organelle function, plant growth, and reproduction. In this study, we report that ATPC1, the gamma subunit of ATP synthase in Arabidopsis chloroplasts, has an unexpected role in the regulation of editing at multiple sites of plastid RNAs. The loss of function of ATPC1 severely arrests chloroplast development, causing a pale-green phenotype and early seedling lethality. Disruption of ATPC1 increases the editing of matK-640, rps12-i-58, atpH-3'UTR-13210, and ycf2-as-91535 sites while decreasing the editing of rpl23-89, rpoA-200, rpoC1-488, and ndhD-2 sites. We further show that ATPC1 participates in RNA editing by interacting with known multiple-site chloroplast RNA editing factors, including MORFs, ORRM1, and OZ1. The transcriptome in the atpc1 mutant is profoundly affected, with a pattern of defective expression of chloroplast development-related genes. These results reveal that the ATP synthase γ subunit ATPC1 is involved in multiple-site RNA editing in Arabidopsis chloroplasts.
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Affiliation(s)
- Jia Ni
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wenjian Song
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nadia Ahmed Ali
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yayi Zhang
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiani Xing
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kexing Su
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xingxing Sun
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaobo Zhao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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21
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Lai Y, Zhang Y, Zhou S, Xu J, Du Z, Feng Z, Yu L, Zhao Z, Wang W, Tang Y, Yang X, Guddat LW, Liu F, Gao Y, Rao Z, Gong H. Structure of the human ATP synthase. Mol Cell 2023:S1097-2765(23)00324-6. [PMID: 37244256 DOI: 10.1016/j.molcel.2023.04.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/29/2023]
Abstract
Biological energy currency ATP is produced by F1Fo-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of F1Fo-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F1 and Fo motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
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Affiliation(s)
- Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Jinxu Xu
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhanqiang Du
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ziyan Feng
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Long Yu
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ziqing Zhao
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China.
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300350, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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22
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Lamas-Maceiras M, Vizoso-Vázquez Á, Barreiro-Alonso A, Cámara-Quílez M, Cerdán ME. Thanksgiving to Yeast, the HMGB Proteins History from Yeast to Cancer. Microorganisms 2023; 11:microorganisms11040993. [PMID: 37110415 PMCID: PMC10142021 DOI: 10.3390/microorganisms11040993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Yeasts have been a part of human life since ancient times in the fermentation of many natural products used for food. In addition, in the 20th century, they became powerful tools to elucidate the functions of eukaryotic cells as soon as the techniques of molecular biology developed. Our molecular understandings of metabolism, cellular transport, DNA repair, gene expression and regulation, and the cell division cycle have all been obtained through biochemistry and genetic analysis using different yeasts. In this review, we summarize the role that yeasts have had in biological discoveries, the use of yeasts as biological tools, as well as past and on-going research projects on HMGB proteins along the way from yeast to cancer.
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Affiliation(s)
- Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Cámara-Quílez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Esperanza Cerdán
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
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23
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Wang H, Hu L, Li H, Lai YT, Wei X, Xu X, Cao Z, Cao H, Wan Q, Chang YY, Xu A, Zhou Q, Jiang G, He ML, Sun H. Mitochondrial ATP synthase as a direct molecular target of chromium(III) to ameliorate hyperglycaemia stress. Nat Commun 2023; 14:1738. [PMID: 36977671 PMCID: PMC10050403 DOI: 10.1038/s41467-023-37351-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Chromium(III) is extensively used as a supplement for muscle development and the treatment of diabetes mellitus. However, its mode of action, essentiality, and physiological/pharmacological effects have been a subject of scientific debate for over half a century owing to the failure in identifying the molecular targets of Cr(III). Herein, by integrating fluorescence imaging with a proteomic approach, we visualized the Cr(III) proteome being mainly localized in the mitochondria, and subsequently identified and validated eight Cr(III)-binding proteins, which are predominately associated with ATP synthesis. We show that Cr(III) binds to ATP synthase at its beta subunit via the catalytic residues of Thr213/Glu242 and the nucleotide in the active site. Such a binding suppresses ATP synthase activity, leading to the activation of AMPK, improving glucose metabolism, and rescuing mitochondria from hyperglycaemia-induced fragmentation. The mode of action of Cr(III) in cells also holds true in type II diabetic male mice. Through this study, we resolve the long-standing question of how Cr(III) ameliorates hyperglycaemia stress at the molecular level, opening a new horizon for further exploration of the pharmacological effects of Cr(III).
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Affiliation(s)
- Haibo Wang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Ligang Hu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Yau-Tsz Lai
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Xiaohan Xu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Zhenkun Cao
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Huiming Cao
- Institute of Environment and Health, Jianghan University, Wuhan, 430056, P.R. China
| | - Qianya Wan
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong, P.R. China
| | - Yuen-Yan Chang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China
| | - Aimin Xu
- Department of Pharmacology and Pharmacy, and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong, P.R. China
| | - Qunfang Zhou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P.R. China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ming-Liang He
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong, P.R. China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pok Fu Lam, Hong Kong S.A.R., P.R. China.
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24
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Mackieh R, Al-Bakkar N, Kfoury M, Roufayel R, Sabatier JM, Fajloun Z. Inhibitors of ATP Synthase as New Antibacterial Candidates. Antibiotics (Basel) 2023; 12:antibiotics12040650. [PMID: 37107012 PMCID: PMC10135114 DOI: 10.3390/antibiotics12040650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
ATP, the power of all cellular functions, is constantly used and produced by cells. The enzyme called ATP synthase is the energy factory in all cells, which produces ATP by adding inorganic phosphate (Pi) to ADP. It is found in the inner, thylakoid and plasma membranes of mitochondria, chloroplasts and bacteria, respectively. Bacterial ATP synthases have been the subject of multiple studies for decades, since they can be genetically manipulated. With the emergence of antibiotic resistance, many combinations of antibiotics with other compounds that enhance the effect of these antibiotics have been proposed as approaches to limit the spread of antibiotic-resistant bacteria. ATP synthase inhibitors, such as resveratrol, venturicidin A, bedaquiline, tomatidine, piceatannol, oligomycin A and N,N-dicyclohexylcarbodiimide were the starting point of these combinations. However, each of these inhibitors target ATP synthase differently, and their co-administration with antibiotics increases the susceptibility of pathogenic bacteria. After a brief description of the structure and function of ATP synthase, we aim in this review to highlight therapeutic applications of the major bacterial ATP synthase inhibitors, including animal’s venoms, and to emphasize their importance in decreasing the activity of this enzyme and subsequently eradicating resistant bacteria as ATP synthase is their source of energy.
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25
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Albornoz RI, Kennedy KM, Bradford BJ. Symposium review: Fueling appetite: Nutrient metabolism and the control of feed intake. J Dairy Sci 2023; 106:2161-2166. [PMID: 36543641 DOI: 10.3168/jds.2022-22429] [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: 06/19/2022] [Accepted: 09/10/2022] [Indexed: 12/24/2022]
Abstract
Conceptual models developed over the past century describe 2 key constraints to feed intake (FI) of healthy animals: gut capacity and metabolic demand. Evidence that greater energy demands (e.g., greater milk production) drive a corresponding increase in caloric intake led to the dominant concept that animals "eat to energy requirements." Although this model provides reasonable initial estimates of FI, it lacks a proposed physiological basis for the control system, does not consider nutrient constraints beyond energy, and fails to explain differential energy intake responses to different fuels. To address these gaps, research has focused on mechanisms for sensing nutrient availability and providing feedback to hypothalamic centers that integrate signals to control feeding behavior. The elimination of FI response to certain nutrients by vagotomy suggests that peripheral tissues play a role in nutrient sensing. These findings and the central role of the liver in metabolic flux led to the development of the hepatic oxidation theory (HOT). According to the HOT, liver energy charge is the regulated variable that induces dietary intake changes and consequently affects whole-body energy balance. Evidence in support of HOT includes associations between hepatic energy charge and meal patterns, increased FI in response to phosphate trapping, and reduced FI in response to phosphate loading. In accordance with the HOT, infusion studies in dairy cattle have consistently demonstrated that providing fuels that either oxidize or stimulate oxidation in the liver decreases FI and energy intake to a greater extent than fuels that bypass the liver. Importantly, this holds true for glucose, which is readily oxidized by nerve cells, but is rarely taken up by the bovine liver. Although the brain integrates multiple signals including those related to gastric distention and illness, the HOT provides a physiological framework for understanding the dominant role the liver likely plays in sensing short-term energy status. Understanding this model provides insights into how to use or bypass the regulatory system to manage FI of animals.
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Affiliation(s)
| | | | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing 48824
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26
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Liu J, Wu Y, Li Y, Yang L, Wu H, He Q. Rotary biomolecular motor-powered supramolecular colloidal motor. SCIENCE ADVANCES 2023; 9:eabg3015. [PMID: 36812329 PMCID: PMC9946340 DOI: 10.1126/sciadv.abg3015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Cells orchestrate the motion and force of hundreds of protein motors to perform various mechanical tasks over multiple length scales. However, engineering active biomimetic materials from protein motors that consume energy to propel continuous motion of micrometer-sized assembling systems remains challenging. Here, we report rotary biomolecular motor-powered supramolecular (RBMS) colloidal motors that are hierarchically assembled from a purified chromatophore membrane containing FOF1-ATP synthase molecular motors, and an assembled polyelectrolyte microcapsule. The micro-sized RBMS motor with asymmetric distribution of FOF1-ATPases can autonomously move under light illumination and is collectively powered by hundreds of rotary biomolecular motors. The propulsive mechanism is that a transmembrane proton gradient generated by a photochemical reaction drives FOF1-ATPases to rotate for ATP biosynthesis, which creates a local chemical field for self-diffusiophoretic force. Such an active supramolecular architecture endowed with motility and biosynthesis offers a promising platform for intelligent colloidal motors resembling the propulsive units in swimming bacteria.
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Affiliation(s)
- Jun Liu
- School of Medicine and Health, Harbin Institute of Technology, Yi Kuang Jie 2, Harbin 150080, China
| | - Yingjie Wu
- School of Medicine and Health, Harbin Institute of Technology, Yi Kuang Jie 2, Harbin 150080, China
| | - Yue Li
- School of Medicine and Health, Harbin Institute of Technology, Yi Kuang Jie 2, Harbin 150080, China
| | - Ling Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, 1 Jinlian Street, Wenzhou 325000, China
| | - Hao Wu
- Wenzhou Institute, University of Chinese Academy of Sciences, 1 Jinlian Street, Wenzhou 325000, China
| | - Qiang He
- School of Medicine and Health, Harbin Institute of Technology, Yi Kuang Jie 2, Harbin 150080, China
- Wenzhou Institute, University of Chinese Academy of Sciences, 1 Jinlian Street, Wenzhou 325000, China
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27
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Changes within the central stalk of E. coli F 1F o ATP synthase observed after addition of ATP. Commun Biol 2023; 6:26. [PMID: 36631659 PMCID: PMC9834311 DOI: 10.1038/s42003-023-04414-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
F1Fo ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the Fo motor that is transferred to the F1 motor to catalyze ATP production, with flexible F1/Fo coupling required for efficient catalysis. F1Fo ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F1Fo ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the Fο motor. This highlights the importance of the central rotor for flexible coupling of the F1 and Fo motors and provides further insight into the regulatory mechanism mediated by subunit ε.
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28
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Song J, Steidle L, Steymans I, Singh J, Sanner A, Böttinger L, Winter D, Becker T. The mitochondrial Hsp70 controls the assembly of the F 1F O-ATP synthase. Nat Commun 2023; 14:39. [PMID: 36596815 PMCID: PMC9810599 DOI: 10.1038/s41467-022-35720-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
The mitochondrial F1FO-ATP synthase produces the bulk of cellular ATP. The soluble F1 domain contains the catalytic head that is linked via the central stalk and the peripheral stalk to the membrane embedded rotor of the FO domain. The assembly of the F1 domain and its linkage to the peripheral stalk is poorly understood. Here we show a dual function of the mitochondrial Hsp70 (mtHsp70) in the formation of the ATP synthase. First, it cooperates with the assembly factors Atp11 and Atp12 to form the F1 domain of the ATP synthase. Second, the chaperone transfers Atp5 into the assembly line to link the catalytic head with the peripheral stalk. Inactivation of mtHsp70 leads to integration of assembly-defective Atp5 variants into the mature complex, reflecting a quality control function of the chaperone. Thus, mtHsp70 acts as an assembly and quality control factor in the biogenesis of the F1FO-ATP synthase.
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Affiliation(s)
- Jiyao Song
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany.,Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Liesa Steidle
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Isabelle Steymans
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jasjot Singh
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Anne Sanner
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Lena Böttinger
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany.
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29
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Krah A, Vogelaar T, de Jong SI, Claridge JK, Bond PJ, McMillan DGG. ATP binding by an F 1F o ATP synthase ε subunit is pH dependent, suggesting a diversity of ε subunit functional regulation in bacteria. Front Mol Biosci 2023; 10:1059673. [PMID: 36923639 PMCID: PMC10010621 DOI: 10.3389/fmolb.2023.1059673] [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: 10/17/2022] [Accepted: 01/03/2023] [Indexed: 03/03/2023] Open
Abstract
It is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydrolysis. The ε subunit takes a contracted conformation when bound to ATP, thus would not interfere with catalysis. A recent crystallographic study has disputed this; the Caldalkalibacillus thermarum TA2.A1 F1Fo ATP synthase cannot natively hydrolyse ATP, yet studies have demonstrated that the loss of the ε subunit terminal helix results in an ATP synthase capable of ATP hydrolysis, supporting ε subunit function. Analysis of sequence and crystallographic data of the C. thermarum F1Fo ATP synthase revealed two unique histidine residues. Molecular dynamics simulations suggested that the protonation state of these residues may influence ATP binding site stability. Yet these residues lie outside the ATP/Mg2+ binding site of the ε subunit. We then probed the effect of pH on the ATP binding affinity of the ε subunit from the C. thermarum F1Fo ATP synthase at various physiologically relevant pH values. We show that binding affinity changes 5.9 fold between pH 7.0, where binding is weakest, to pH 8.5 where it is strongest. Since the C. thermarum cytoplasm is pH 8.0 when it grows optimally, this correlates to the ε subunit being down due to ATP/Mg2+ affinity, and not being involved in blocking ATP hydrolysis. Here, we have experimentally correlated that the pH of the bacterial cytoplasm is of critical importance for ε subunit ATP affinity regulated by second-shell residues thus the function of the ε subunit changes with growth conditions.
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Affiliation(s)
- Alexander Krah
- Korea Institute for Advanced Study, School of Computational Sciences, Seoul, South Korea.,Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Timothy Vogelaar
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Sam I de Jong
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jolyon K Claridge
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Duncan G G McMillan
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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30
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Yakiyama Y. Molecular-Shape-Organized Stimuli-Responsive Functional Crystalline Systems. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.1036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yumi Yakiyama
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University
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31
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Bernardi P, Carraro M, Lippe G. The mitochondrial permeability transition: Recent progress and open questions. FEBS J 2022; 289:7051-7074. [PMID: 34710270 PMCID: PMC9787756 DOI: 10.1111/febs.16254] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/27/2021] [Indexed: 01/13/2023]
Abstract
Major progress has been made in defining the basis of the mitochondrial permeability transition, a Ca2+ -dependent permeability increase of the inner membrane that has puzzled mitochondrial research for almost 70 years. Initially considered an artefact of limited biological interest by most, over the years the permeability transition has raised to the status of regulator of mitochondrial ion homeostasis and of druggable effector mechanism of cell death. The permeability transition is mediated by opening of channel(s) modulated by matrix cyclophilin D, the permeability transition pore(s) (PTP). The field has received new impulse (a) from the hypothesis that the PTP may originate from a Ca2+ -dependent conformational change of F-ATP synthase and (b) from the reevaluation of the long-standing hypothesis that it originates from the adenine nucleotide translocator (ANT). Here, we provide a synthetic account of the structure of ANT and F-ATP synthase to discuss potential and controversial mechanisms through which they may form high-conductance channels; and review some intriguing findings from the wealth of early studies of PTP modulation that still await an explanation. We hope that this review will stimulate new experiments addressing the many outstanding problems, and thus contribute to the eventual solution of the puzzle of the permeability transition.
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Affiliation(s)
- Paolo Bernardi
- Department of Biomedical Sciences and CNR Neuroscience InstituteUniversity of PadovaItaly
| | - Michela Carraro
- Department of Biomedical Sciences and CNR Neuroscience InstituteUniversity of PadovaItaly
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32
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Mitochondrial ATP synthase c-subunit leak channel triggers cell death upon loss of its F 1 subcomplex. Cell Death Differ 2022; 29:1874-1887. [PMID: 35322203 PMCID: PMC9433415 DOI: 10.1038/s41418-022-00972-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial ATP synthase is vital not only for cellular energy production but also for energy dissipation and cell death. ATP synthase c-ring was suggested to house the leak channel of mitochondrial permeability transition (mPT), which activates during excitotoxic ischemic insult. In this present study, we purified human c-ring from both eukaryotic and prokaryotic hosts to biophysically characterize its channel activity. We show that purified c-ring forms a large multi-conductance, voltage-gated ion channel that is inhibited by the addition of ATP synthase F1 subcomplex. In contrast, dissociation of F1 from FO occurs during excitotoxic neuronal death suggesting that the F1 constitutes the gate of the channel. mPT is known to dissipate the osmotic gradient across the inner membrane during cell death. We show that ATP synthase c-subunit knock down (KD) prevents the osmotic change in response to high calcium and eliminates large conductance, Ca2+ and CsA sensitive channel activity of mPT. These findings elucidate the gating mechanism of the ATP synthase c-subunit leak channel (ACLC) and suggest how ACLC opening is regulated by cell stress in a CypD-dependent manner.
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33
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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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34
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Gerle C, Kishikawa JI, Yamaguchi T, Nakanishi A, Çoruh O, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. Structures of Multisubunit Membrane Complexes With the CRYO ARM 200. Microscopy (Oxf) 2022; 71:249-261. [PMID: 35861182 PMCID: PMC9535789 DOI: 10.1093/jmicro/dfac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Progress in structural membrane biology has been significantly accelerated by the ongoing ‘Resolution Revolution’ in cryo-electron microscopy (cryo-EM). In particular, structure determination by single-particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever-increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo-electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single-particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor lipopolysaccharide peptidoglycan ring (LP ring) from Salmonella enterica.
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Affiliation(s)
- Christoph Gerle
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,RIKEN SPring-8 Center, Life Science Research Infrastructure Group, Sayo-gun, Hyogo 679-5148, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Tomoko Yamaguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka, University, Ibaraki, Osaka 567-0047, Japan
| | - Orkun Çoruh
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,Institute of Science and Technology Austria, Klosterneuburg, 3400 Austria
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,JEOL Ltd., Akishima, Tokyo, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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35
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Courbon GM, Rubinstein JL. CryoEM Reveals the Complexity and Diversity of ATP Synthases. Front Microbiol 2022; 13:864006. [PMID: 35783400 PMCID: PMC9244403 DOI: 10.3389/fmicb.2022.864006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022] Open
Abstract
During respiration, adenosine triphosphate (ATP) synthases harness the electrochemical proton motive force (PMF) generated by the electron transport chain (ETC) to synthesize ATP. These macromolecular machines operate by a remarkable rotary catalytic mechanism that couples transmembrane proton translocation to rotation of a rotor subcomplex, and rotation to ATP synthesis. Initially, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cross-linking were the only ways to gain insights into the three-dimensional (3D) structures of ATP synthases and, in particular, provided ground-breaking insights into the soluble parts of the complex that explained the catalytic mechanism by which rotation is coupled to ATP synthesis. In contrast, early electron microscopy was limited to studying the overall shape of the assembly. However, advances in electron cryomicroscopy (cryoEM) have allowed determination of high-resolution structures, including the membrane regions of ATP synthases. These studies revealed the high-resolution structures of the remaining ATP synthase subunits and showed how these subunits work together in the intact macromolecular machine. CryoEM continues to uncover the diversity of ATP synthase structures across species and has begun to show how ATP synthases can be targeted by therapies to treat human diseases.
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Affiliation(s)
- Gautier M. Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON, Canada
- *Correspondence: John L. Rubinstein
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36
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Zhang X, Wang J, Juan Y, Yang H, Wei W, Zhao J. A novel fluorescence method for detection of phosphate anions based on porphyrin metalation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121136. [PMID: 35299095 DOI: 10.1016/j.saa.2022.121136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
In this work, a novel fluorescence method for the detection of phosphate anions (PO43-) was developed based on porphyrin metalation. Through catalysis by G-quadruplex (G4), Cu2+ could insert into the porphyrins to quench their fluorescence. G4 simultaneously improved the fluorescence of the porphyrins but not that of Cu2+-porphyrin. In the absence of PO43-, the porphyrins were metallized by Cu2+, and no fluorescence was observed. In the presence of PO43-, PO43- could coordinate with Cu2+ to prevent porphyrin metalation. Free porphyrin could bind with G4 to emit strong fluorescence. By comparing four common porphyrins, we found that G4 had the greatest effect on increasing the fluorescence intensity of N-methylmesoporphyrin IX (NMM). Thus, NMM/G4 was chosen for the design of a biosensor. Under optimal experimental conditions, this method showed high sensitivity and satisfactory selectivity for PO43- with a detection limit of 44 nM in a linear range of 0.01-1.0 μM. The recovery experiments showed recovery rates of 93.75-106.00%, suggesting a great potential for measuring PO43- in real samples.
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Affiliation(s)
- Xingping Zhang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; School of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Jiujun Wang
- School of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Yewen Juan
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; School of Life Sciences, Nanjing University, Nanjing, China
| | - Hualin Yang
- School of Life Science, Yangtze University, Jingzhou, Hubei, China.
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; School of Life Sciences, Nanjing University, Nanjing, China; Shenzhen Research Institute, Nanjing University, Shenzhen, China.
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China; Shenzhen Research Institute, Nanjing University, Shenzhen, China.
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37
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ATP synthesis in an ancient ATP synthase at low driving forces. Proc Natl Acad Sci U S A 2022; 119:e2201921119. [PMID: 35512103 DOI: 10.1073/pnas.2201921119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe ATP synthases of many anaerobic archaea have an unusual motor subunit c that otherwise is only found in eukaryotic V1VO ATPases. The evolutionary switch from synthase to hydrolase is thought to be caused by a doubling of the rotor subunit c, followed by a loss of the ion binding site. By purification and reconstitution of an ATP synthase with a V-type c subunit, we have unequivocally demonstrated, against expectations, the capability of such an enzyme to synthesize ATP at physiological relevant driving forces of 90 to 150 mV. This is the long-awaited answer to an eminent question in microbial energetics and physiology, especially for life near the thermodynamic limit of ATP synthesis.
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38
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Peil A, Xin L, Both S, Shen L, Ke Y, Weiss T, Zhan P, Liu N. DNA Assembly of Modular Components into a Rotary Nanodevice. ACS NANO 2022; 16:5284-5291. [PMID: 35286063 PMCID: PMC9047004 DOI: 10.1021/acsnano.1c10160] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The bacterial flagellar motor is a rotary machine composed of functional modular components, which can perform bidirectional rotations to control the migration behavior of the bacterial cell. It resembles a two-cogwheel gear system, which consists of small and large cogwheels with cogs at the edges to regulate rotations. Such gearset models provide elegant blueprints to design and build artificial nanomachinery with desired functionalities. In this work, we demonstrate DNA assembly of a structurally well-defined nanodevice, which can carry out programmable rotations powered by DNA fuels. Our rotary nanodevice consists of three modular components, small origami ring, large origami ring, and gold nanoparticles (AuNPs). They mimic the sun gear, ring gear, and planet gears in a planetary gearset accordingly. These modular components are self-assembled in a compact manner, such that they can work cooperatively to impart bidirectional rotations. The rotary dynamics is optically recorded using fluorescence spectroscopy in real time, given the sensitive distance-dependent interactions between the tethered fluorophores and AuNPs on the rings. The experimental results are well supported by the theoretical calculations.
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Affiliation(s)
- Andreas Peil
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| | - Ling Xin
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (L.X.)
| | - Steffen Both
- Fourth
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Luyao Shen
- Wallace
L. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322 United States
| | - Yonggang Ke
- Wallace
L. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322 United States
| | - Thomas Weiss
- Fourth
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Institute
of Physics, University of Graz, and NAWI
Graz, Universitätsplatz
5, 8010 Graz, Austria
| | - Pengfei Zhan
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (P.Z.)
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (N.L.)
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39
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Abstract
ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F1 motor and a proton-translocation-driven FO motor. The F1 and FO motors oppose each other’s action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F1 or proton translocation through FO, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F1, leading to catalysis. CryoEM of mitochondrial ATP synthase frozen during rotary catalysis reveals dramatic conformational changes in the peripheral stalk subcomplex, which enable the enzyme’s efficient synthesis of ATP.
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40
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Keskin Alkaç Z, Ahmet Korkak F, Dağoğlu G, Akdeniz İncili C, Dağoğlu Hark B, Tanyildizi S. Puerarin mitigates oxidative injuries, opening of mitochondrial permeability transition pores and pathological damage associated with liver and kidney in Xanthium strumarium-intoxicated rats. Toxicon 2022; 213:13-22. [PMID: 35427636 DOI: 10.1016/j.toxicon.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/09/2022]
Abstract
In this study, the therapeutic effects of puerarin on Xanthium strumarium toxicity, which can develop in many species and does not have a specific antidote, were investigated. A single dose of 100 g/kg X. strumarium seeds was administered by gavage to female Sprague-Dawley rats, 6 h following which 200 mg/kg puerarin was administered by the same route, with puerarin administration being repeated daily at the same time. After completing the application, the blood, liver and kidney tissues of the rats were examined. Further, the biochemical parameters, glucose, MDA, GSH, SOD, mitochondrial Ca2+ and mitochondrial permeability transition pore (mPTP) opening levels, apoptotic factors (TUNEL, Bax and Bcl-2), ATP synthase and histopathological changes of the experimental rats were examined. The results revealed that while the administration of X. strumarium resulted in increased blood AST, ALT, ALP, LDH, CK, BUN and creatinine levels, it decreased glucose levels. In addition, it increased the MDA levels in the tissues and significantly increased the oxidative stress levels by decreasing the GSH levels and SOD activity. X. strumarium caused an increase in the mitochondrial Ca2+ and mPTP opening levels. Moreover, it increased the immunohistochemically determined ATP synthase expression and histopathologically identified necrotic liver cell death rates. Owing to its antioxidant properties and inhibitory effects on mPTP opening, puerarin administered for therapeutic purposes decreased the oxidative damage caused by X. strumarium toxicity, blood biochemical parameter levels, mitochondrial Ca2+ levels, mPTP opening, ATP synthase expression and the percentage of necrotic cells. Hence, the reduction in the liver and kidney damage in X. strumarium toxicity by puerarin indicates its potential use as an antidote for X. strumarium poisoning.
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Affiliation(s)
- Zeliha Keskin Alkaç
- Pharmacology and Toxicology Department, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey.
| | - Fatih Ahmet Korkak
- Pharmacology and Toxicology Department, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey
| | - Gürdal Dağoğlu
- Pharmacology and Toxicology Department, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey
| | - Canan Akdeniz İncili
- Pathology Department, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey
| | - Betül Dağoğlu Hark
- Biostatistics and Medical Informatics Department, Faculty of Medicine, Firat University, Elazig, Turkey
| | - Sadettin Tanyildizi
- Pharmacology and Toxicology Department, Faculty of Veterinary Medicine, Firat University, Elazig, Turkey
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41
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Li Z, Xu X, Yu F, Fei J, Li Q, Dong M, Li J. Oriented Nanoarchitectonics of Bacteriorhodopsin for Enhancing ATP Generation in a F o F 1 -ATPase-Based Assembly System. Angew Chem Int Ed Engl 2022; 61:e202116220. [PMID: 35129265 DOI: 10.1002/anie.202116220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Indexed: 12/23/2022]
Abstract
Energy conversion plays an important role in the metabolism of photosynthetic organisms. Improving energy transformation by promoting a proton gradient has been a great challenge for a long time. In the present study, we realize a directional proton migration through the construction of oriented bacteriorhodopsin (BR) microcapsules coated by Fo F1 -ATPase molecular motors through layer-by-layer (LBL) assembly. The changes in the conformation of BR under illumination lead to proton transfer in a radial direction, which generates a higher proton gradient to drive the synthesis of adenosine triphosphate (ATP) by Fo F1 -ATPase. Furthermore, to promote the photosynthetic activity, optically matched quantum dots were introduced into the artificial coassembly system of BR and Fo F1 -ATPase. Such a design creates a new path for the use of light energy.
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Affiliation(s)
- Zibo Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Xia Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fanchen Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
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42
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Manoj KM, Bazhin NM, Tamagawa H, Jaeken L, Parashar A. The physiological role of complex V in ATP synthesis: Murzyme functioning is viable whereas rotary conformation change model is untenable. J Biomol Struct Dyn 2022; 41:3993-4012. [PMID: 35394896 DOI: 10.1080/07391102.2022.2060307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Complex V or FoF1-ATPase is a multimeric protein found in bioenergetic membranes of cells and organelles like mitochondria/chloroplasts. The popular perception on Complex V deems it as a reversible molecular motor, working bi-directionally (breaking or making ATP) via a conformation-change based chemiosmotic rotary ATP synthesis (CRAS) mechanism, driven by proton-gradients or trans-membrane potential (TMP). In continuance of our pursuits against the CRAS model of cellular bioenergetics, herein we demonstrate the validity of the murburn model based in diffusible reactive (oxygen) species (DRS/DROS). Supported by new in silico derived data (that there are ∼12 adenosine nucleotide binding sites on the F1 bulb and not merely 3 sites, as perceived earlier), available structural information, known experimental observations, and thermodynamic/kinetic considerations (that de-solvation of protons from hydronium ions is facile), we deduce that Complex V serves as a physiological chemostat and a murzyme (enzyme working via murburn scheme, employing DRS). That is- Complex V uses ATP (via consumption at ε or proteins of F1 module) as a Michaelis-Menten substrate to serve as a pH-stat by inletting protons via the c-ring of Fo module. Physiologically, Complex V also functions as a murzyme by presenting ADP/Pi (or their reaction intermediates) on the αβ bulb, thereby enabling greater opportunities for DRS/proton-assisted ATP formation. Thus, the murburn paradigm succeeds the CRAS hypothesis for explaining the role of oxygen in mitochondrial physiologies of oxidative phosphorylation, thermogenesis, TMP and homeostasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- Biochemistry Department, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
| | - Nikolai Mikhailovich Bazhin
- Environmental Chemistry Department, Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Laurent Jaeken
- Industrial Sciences and Technology, Karel de Grote University College, Antwerp University Association, Hoboken, Belgium
| | - Abhinav Parashar
- Biochemistry Department, Satyamjayatu: The Science & Ethics Foundation, Palakkad, Kerala, India
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43
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Vlasov AV, Osipov SD, Bondarev NA, Uversky VN, Borshchevskiy VI, Yanyushin MF, Manukhov IV, Rogachev AV, Vlasova AD, Ilyinsky NS, Kuklin AI, Dencher NA, Gordeliy VI. ATP synthase F OF 1 structure, function, and structure-based drug design. Cell Mol Life Sci 2022; 79:179. [PMID: 35253091 PMCID: PMC11072866 DOI: 10.1007/s00018-022-04153-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
ATP synthases are unique rotatory molecular machines that supply biochemical reactions with adenosine triphosphate (ATP)-the universal "currency", which cells use for synthesis of vital molecules and sustaining life. ATP synthases of F-type (FOF1) are found embedded in bacterial cellular membrane, in thylakoid membranes of chloroplasts, and in mitochondrial inner membranes in eukaryotes. The main functions of ATP synthases are control of the ATP synthesis and transmembrane potential. Although the key subunits of the enzyme remain highly conserved, subunit composition and structural organization of ATP synthases and their assemblies are significantly different. In addition, there are hypotheses that the enzyme might be involved in the formation of the mitochondrial permeability transition pore and play a role in regulation of the cell death processes. Dysfunctions of this enzyme lead to numerous severe disorders with high fatality levels. In our review, we focus on FOF1-structure-based approach towards development of new therapies by using FOF1 structural features inherited by the representatives of this enzyme family from different taxonomy groups. We analyzed and systematized the most relevant information about the structural organization of FOF1 to discuss how this approach might help in the development of new therapies targeting ATP synthases and design tools for cellular bioenergetics control.
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Affiliation(s)
- Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Stepan D Osipov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Nikolay A Bondarev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mikhail F Yanyushin
- Institute of Basic Biological Problems, Russian Academy of Sciences, 142290, Pushchino, Moscow region, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Andrey V Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Alexandr I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Norbert A Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Physical Biochemistry, Department Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany.
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027, Grenoble, France.
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44
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Li Z, Xu X, Yu F, Fei J, Li Q, Dong M, Li J. Oriented Nanoarchitectonics of Bacteriorhodopsin for Enhancing ATP Generation in a F
o
F
1
‐ATPase‐Based Assembly System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zibo Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education School of Chemistry and Chemical Engineering Shandong University Jinan 250100 China
| | - Xia Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Fanchen Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education School of Chemistry and Chemical Engineering Shandong University Jinan 250100 China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C 8000 Denmark
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
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45
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Lu S, Huang M, Huang G, Guo Q, Li H, Deng J, Zhang C, Yu Y. Two 'braking mechanisms' for tin phthalocyanine molecular rotors on dipolar iron oxide surfaces. NANOSCALE ADVANCES 2022; 4:1213-1219. [PMID: 36131761 PMCID: PMC9417875 DOI: 10.1039/d1na00588j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/10/2021] [Indexed: 06/15/2023]
Abstract
Manipulation of artificial molecular rotors/motors is a key issue in the field of molecular nanomachines. Here we assemble non-planar SnPc molecules on an FeO film to form two kinds of rotors with different apparent morphologies, rotational speeds and stabilities. Both kinds of rotors can switch to each other via external field stimulation and the switch depends on the polarity of the applied bias voltage. Furthermore, we reveal that the molecular fragment has a great influence on the motions of molecules. Combining scanning tunneling microscopy and DFT calculations, two braking mechanisms are addressed for molecular rotors. One is the transformation of adsorption configurations under the external electric field stimulus that enables the molecular rotor to stop/restart its rotation. The other is the introduction of embedded molecular fragments that act as a brake pad and can stop the molecular rotation. We find that the rotation can be recovered by separating the molecule from the fragments. Our study suggests a good system for manipulating molecular rotors' properties in nanophysics and has important value for the design of controllable molecular machines.
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Affiliation(s)
- Shuangzan Lu
- Department of Physics, Faculty of Physics and Electronic Sciences, Hubei University Wuhan 430062 China
- School of Physics and Technology, Wuhan University Wuhan 430072 China
| | - Min Huang
- Department of Physics, Faculty of Physics and Electronic Sciences, Hubei University Wuhan 430062 China
| | - Guodong Huang
- Department of Physics, Faculty of Physics and Electronic Sciences, Hubei University Wuhan 430062 China
| | - Qinmin Guo
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology Wuhan 430081 China
| | - Hongxing Li
- Hunan Provincial Key Laboratory of Flexible Electronic Materials Genome Engineering, Changsha University of Science and Technology Changsha 410114 China
| | - Jinghao Deng
- School of Physics and Technology, Wuhan University Wuhan 430072 China
| | - Chendong Zhang
- School of Physics and Technology, Wuhan University Wuhan 430072 China
| | - Yinghui Yu
- Department of Physics, Faculty of Physics and Electronic Sciences, Hubei University Wuhan 430062 China
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46
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Vermaas JV, Mayne CG, Shinn E, Tajkhorshid E. Assembly and Analysis of Cell-Scale Membrane Envelopes. J Chem Inf Model 2022; 62:602-617. [PMID: 34910495 PMCID: PMC8903035 DOI: 10.1021/acs.jcim.1c01050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Christopher G. Mayne
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Shinn
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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47
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Ebanks B, Chakrabarti L. Mitochondrial ATP Synthase is a Target of Oxidative Stress in Neurodegenerative Diseases. Front Mol Biosci 2022; 9:854321. [PMID: 35237666 PMCID: PMC8882969 DOI: 10.3389/fmolb.2022.854321] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial ATP synthase is responsible for the production of cellular ATP, and it does so by harnessing the membrane potential of the mitochondria that is produced by the sequential oxidation of select cellular metabolites. Since the structural features of ATP synthase were first resolved nearly three decades ago, significant progress has been made in understanding its role in health and disease. Mitochondrial dysfunction is common to neurodegeneration, with elevated oxidative stress a hallmark of this dysfunction. The patterns of this oxidative stress, including molecular targets and the form of oxidative modification, can vary widely. In this mini review we discuss the oxidative modifications of ATP synthase that have been observed in Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease. Oxidative modifications of ATP synthase in Alzheimer’s disease are well-documented, and there is a growing body of knowledge on the subject in Parkinson’s disease. The consideration of ATP synthase as a pharmacological target in a variety of diseases underlines the importance of understanding these modifications, both as a potential target, and also as inhibitors of any pharmacological intervention.
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Affiliation(s)
- Brad Ebanks
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
- *Correspondence: Brad Ebanks,
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Nottingham, United Kingdom
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48
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Chiang JC, Chen WM, Newman C, Chen BPC, Lee H. Lysophosphatidic Acid Receptor 3 Promotes Mitochondrial Homeostasis against Oxidative Stress: Potential Therapeutic Approaches for Hutchinson–Gilford Progeria Syndrome. Antioxidants (Basel) 2022; 11:antiox11020351. [PMID: 35204233 PMCID: PMC8869156 DOI: 10.3390/antiox11020351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 02/04/2023] Open
Abstract
Lysophosphatidic acid (LPA) is a growth factor-like lipid mediator that regulates various physiological functions via activation of multiple LPA G protein-coupled receptors. We previously reported that LPA suppresses oxidative stress in premature aging Hutchinson-Gilford progeria syndrome (HGPS) patient fibroblasts via its type 3 receptor (LPA3). Mitochondria have been suggested to be the primary origin of oxidative stress via the overproduction of reactive oxygen species (ROS). Mitochondria are responsible for producing ATP through oxidative phosphorylation (OXPHOS) and have a calcium buffering capacity for the cell. Defects in mitochondria will lead to declined antioxidant capacity and cell apoptosis. Therefore, we aim to demonstrate the regulatory role of LPA3 in mitochondrial homeostasis. siRNA-mediated depletion of LPA3 leads to the depolarization of mitochondrial potential (ΔΨm) and cellular ROS accumulation. In addition, the depletion of LPA3 enhances cisplatin-induced cytochrome C releasing. This indicates that LPA3 is essential to suppress the mitochondrial apoptosis pathway. LPA3 is also shown to improve mitochondrial ADP-ATP exchange by enhancing the protein level of ANT2. On the other hand, LPA3 regulates calcium uptake from the ER to mitochondria via the IP3R1-VDAC1 channel. Moreover, activation of LPA3 by selective agonist OMPT rescues mitochondrial homeostasis of H2O2-induced oxidative stress cells and HGPS patient fibroblasts by improving mitochondrial ΔΨm and OXPHOS. In summary, our findings imply that LPA3 acts as the gatekeeper for mitochondrial healthiness to maintain cell youth. Furthermore, LPA3 can be a promising therapeutic target to prevent mitochondrial oxidative stress in aging and HGPS.
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Affiliation(s)
- Jui-Chung Chiang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.-C.C.); (W.-M.C.); (C.N.)
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Min Chen
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.-C.C.); (W.-M.C.); (C.N.)
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ciara Newman
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.-C.C.); (W.-M.C.); (C.N.)
| | - Benjamin P. C. Chen
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.-C.C.); (W.-M.C.); (C.N.)
- Correspondence: (B.P.C.C.); (H.L.); Tel.: +1-214-648-1263 (B.P.C.C.); +886-2-3366-2499 (H.L.)
| | - Hsinyu Lee
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Correspondence: (B.P.C.C.); (H.L.); Tel.: +1-214-648-1263 (B.P.C.C.); +886-2-3366-2499 (H.L.)
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49
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Mitome N, Kubo S, Ohta S, Takashima H, Shigefuji Y, Niina T, Takada S. Cooperation among c-subunits of F oF 1-ATP synthase in rotation-coupled proton translocation. eLife 2022; 11:69096. [PMID: 35107420 PMCID: PMC8809890 DOI: 10.7554/elife.69096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 12/21/2021] [Indexed: 01/23/2023] Open
Abstract
In FoF1-ATP synthase, proton translocation through Fo drives rotation of the c-subunit oligomeric ring relative to the a-subunit. Recent studies suggest that in each step of the rotation, key glutamic acid residues in different c-subunits contribute to proton release to and proton uptake from the a-subunit. However, no studies have demonstrated cooperativity among c-subunits toward FoF1-ATP synthase activity. Here, we addressed this using Bacillus PS3 ATP synthase harboring a c-ring with various combinations of wild-type and cE56D, enabled by genetically fused single-chain c-ring. ATP synthesis and proton pump activities were decreased by a single cE56D mutation and further decreased by double cE56D mutations. Moreover, activity further decreased as the two mutation sites were separated, indicating cooperation among c-subunits. Similar results were obtained for proton transfer-coupled molecular simulations. The simulations revealed that prolonged proton uptake in mutated c-subunits is shared between two c-subunits, explaining the cooperation observed in biochemical assays. Cells need to be able to store and transfer energy to fuel their various activities. To do this, they produce a small molecule called ATP to carry the energy, which is then released when the ATP is broken down. An enzyme found in plants, animals and bacteria, called FoF1 ATP synthase, can both create and use ATP. When it does this, protons, or positive hydrogen ions, are transported across cellular boundaries called membranes. The region of the enzyme that is responsible for pumping the protons contains different parts known as the c-ring and the a-subunit. The movement of protons drives the c-ring to rotate relative to the a-subunit, which leads to producing ATP. Previous research using simulations and the protein structures found there are two or three neighbouring amino acids in the c-ring that face the a-subunit, suggesting that these amino acids act together to drive the rotation. To test this hypothesis, Mitome et al. mutated these amino acids to examine the effect on the enzyme’s ability to produce ATP. A single mutation reduced the production of ATP, which decreased even further with mutations in two of the amino acids. The extent of this decrease depended on the distance between the two mutations in the c-ring. Simulations of these changes also found similar results. This indicates there is coordination between different parts of the c-ring to increase the rate of ATP production. This study offers new insights into the molecular processes controlling ATP synthesis and confirms previous theoretical research. This will interest specialists in bioenergetics because it addresses a fundamental biological question with broad impact.
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Affiliation(s)
- Noriyo Mitome
- Faculty of Education, Tokoha University, Shizuoka, Japan.,Department of Chemistry and Biochemistry, National Institute of Technology, Numazu College, Numazu, Japan.,Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Ube, Japan
| | - Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Sumie Ohta
- Department of Chemistry and Biochemistry, National Institute of Technology, Numazu College, Numazu, Japan
| | - Hikaru Takashima
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Ube, Japan
| | - Yuto Shigefuji
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Ube, Japan
| | - Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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50
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Marciniak A, Chodnicki P, Hossain KA, Slabonska J, Czub J. Determinants of Directionality and Efficiency of the ATP Synthase F o Motor at Atomic Resolution. J Phys Chem Lett 2022; 13:387-392. [PMID: 34985899 PMCID: PMC8762653 DOI: 10.1021/acs.jpclett.1c03358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 05/27/2023]
Abstract
Fo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor's directionality naturally arises from the interplay between intraprotein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site, and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the Fo motor with previous functional and single-molecule data.
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Affiliation(s)
- Antoni Marciniak
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Pawel Chodnicki
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Kazi A Hossain
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Joanna Slabonska
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department
of Physical Chemistry, Gdansk University
of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
- BioTechMed
Center, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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