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Lhuissier C, Desquiret-Dumas V, Girona A, Alban J, Faure J, Cassereau J, Codron P, Lenaers G, Baris OR, Gueguen N, Chevrollier A. Mitochondrial F0F1-ATP synthase governs the induction of mitochondrial fission. iScience 2024; 27:109808. [PMID: 38741710 PMCID: PMC11089353 DOI: 10.1016/j.isci.2024.109808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/22/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Mitochondrial dynamics is a process that balances fusion and fission events, the latter providing a mechanism for segregating dysfunctional mitochondria. Fission is controlled by the mitochondrial membrane potential (ΔΨm), optic atrophy 1 (OPA1) cleavage, and DRP1 recruitment. It is thought that this process is closely linked to the activity of the mitochondrial respiratory chain (MRC). However, we report here that MRC inhibition does not decrease ΔΨm nor increase fission, as evidenced by hyperconnected mitochondria. Conversely, blocking F0F1-ATP synthase activity induces fragmentation. We show that the F0F1-ATP synthase is sensing the inhibition of MRC activity by immediately promoting its reverse mode of action to hydrolyze matrix ATP and restoring ΔΨm, thus preventing fission. While this reverse mode is expected to be inhibited by the ATPase inhibitor ATPIF1, we show that this sensing is independent of this factor. We have unraveled an unexpected role of F0F1-ATP synthase in controlling the induction of fission by sensing and maintaining ΔΨm.
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Affiliation(s)
- Charlène Lhuissier
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
| | - Valérie Desquiret-Dumas
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
- Departments of Biochemistry and Molecular Biology, University Hospital Angers, Angers, France
| | - Anaïs Girona
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
| | - Jennifer Alban
- Departments of Biochemistry and Molecular Biology, University Hospital Angers, Angers, France
| | - Justine Faure
- Departments of Biochemistry and Molecular Biology, University Hospital Angers, Angers, France
| | - Julien Cassereau
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
- Department of Neurology, Angers University Hospital, Angers, France
| | - Philippe Codron
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
- Department of Neurology, Angers University Hospital, Angers, France
| | - Guy Lenaers
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
- Department of Neurology, Angers University Hospital, Angers, France
| | - Olivier R. Baris
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
| | - Naïg Gueguen
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
- Departments of Biochemistry and Molecular Biology, University Hospital Angers, Angers, France
| | - Arnaud Chevrollier
- University Angers, MitoLab Team, MitoVasc Unit, CNRS UMR6015, INSERM U1083, SFR ICAT, Angers, France
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2
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Blanc FEC, Hummer G. Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. Proc Natl Acad Sci U S A 2024; 121:e2314199121. [PMID: 38451940 PMCID: PMC10945847 DOI: 10.1073/pnas.2314199121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/10/2024] [Indexed: 03/09/2024] Open
Abstract
Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of adenosine triphosphate (ATP). Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.
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Affiliation(s)
- Florian E. C. Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main60438, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main60438, Germany
- Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main60438, Germany
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3
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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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4
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Yasuda S, Hayashi T, Murata T, Kinoshita M. Physical pictures of rotation mechanisms of F 1- and V 1-ATPases: Leading roles of translational, configurational entropy of water. Front Mol Biosci 2023; 10:1159603. [PMID: 37363397 PMCID: PMC10288849 DOI: 10.3389/fmolb.2023.1159603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
We aim to develop a theory based on a concept other than the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex. Experimental results conflicting with the chemo-mechanical coupling have recently emerged. We claim that the system comprises not only the protein complex but also the aqueous solution in which the protein complex is immersed and the system performs essentially no mechanical work. We perform statistical-mechanical analyses on V1-ATPase (the A3B3DF complex) for which crystal structures in more different states are experimentally known than for F1-ATPase (the α3β3γ complex). Molecular and atomistic models are employed for water and the structure of V1-ATPase, respectively. The entropy originating from the translational displacement of water molecules in the system is treated as a pivotal factor. We find that the packing structure of the catalytic dwell state of V1-ATPase is constructed by the interplay of ATP bindings to two of the A subunits and incorporation of the DF subunit. The packing structure represents the nonuniformity with respect to the closeness of packing of the atoms in constituent proteins and protein interfaces. The physical picture of rotation mechanism of F1-ATPase recently constructed by Kinoshita is examined, and common points and differences between F1- and V1-ATPases are revealed. An ATP hydrolysis cycle comprises binding of ATP to the protein complex, hydrolysis of ATP into ADP and Pi in it, and dissociation of ADP and Pi from it. During each cycle, the chemical compounds bound to the three A or β subunits and the packing structure of the A3B3 or α3β3 complex are sequentially changed, which induces the unidirectional rotation of the central shaft for retaining the packing structure of the A3B3DF or α3β3γ complex stabilized for almost maximizing the water entropy. The torque driving the rotation is generated by water with no input of chemical free energy. The presence of ATP is indispensable as a trigger of the torque generation. The ATP hydrolysis or synthesis reaction is tightly coupled to the rotation of the central shaft in the normal or inverse direction through the water-entropy effect.
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Affiliation(s)
- Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba, Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology and Art and Sports Sciences, Faculty of Engineering, Niigata University, Niigata, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba, Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
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Sebők-Nagy K, Blastyák A, Juhász G, Páli T. Reversible binding of divalent cations to Ductin protein assemblies-A putative new regulatory mechanism of membrane traffic processes. Front Mol Biosci 2023; 10:1195010. [PMID: 37228584 PMCID: PMC10203432 DOI: 10.3389/fmolb.2023.1195010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Ductins are a family of homologous and structurally similar membrane proteins with 2 or 4 trans-membrane alpha-helices. The active forms of the Ductins are membranous ring- or star-shaped oligomeric assemblies and they provide various pore, channel, gap-junction functions, assist in membrane fusion processes and also serve as the rotor c-ring domain of V-and F-ATPases. All functions of the Ductins have been reported to be sensitive to the presence of certain divalent metal cations (Me2+), most frequently Cu2+ or Ca2+ ions, for most of the better known members of the family, and the mechanism of this effect is not yet known. Given that we have earlier found a prominent Me2+ binding site in a well-characterised Ductin protein, we hypothesise that certain divalent cations can structurally modulate the various functions of Ductin assemblies via affecting their stability by reversible non-covalent binding to them. A fine control of the stability of the assembly ranging from separated monomers through a loosely/weakly to tightly/strongly assembled ring might render precise regulation of Ductin functions possible. The putative role of direct binding of Me2+ to the c-ring subunit of active ATP hydrolase in autophagy and the mechanism of Ca2+-dependent formation of the mitochondrial permeability transition pore are also discussed.
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Affiliation(s)
- Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gábor Juhász
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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6
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F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:ijms24065417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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7
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Parkin D, Takano M. Coulombic Organization in Membrane-Embedded Rotary Motor of ATP Synthase. J Phys Chem B 2023; 127:1552-1562. [PMID: 36734508 DOI: 10.1021/acs.jpcb.2c07875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The electrochemical potential difference of protons across the membrane is used to synthesize ATP through the proton-motive rotatory motion of the membrane-embedded region of ATP synthase called Fo. In this study, we illuminate the unsolved proton-motive rotary mechanism of Fo on the basis of atomistic simulation with full description of protein, lipid, and water molecules, and highlight the underlying Coulombic design. We first show that a water channel is spontaneously formed at the interfacial region between the rotor (c-ring) and the stator (a-subunit). The observed water channel is a full channel penetrating the membrane, but a Coulomb barrier by a strictly conserved arginine of the a-subunit dominates at the midpoint of the full channel, preventing proton leakage. Our molecular dynamics simulation further demonstrates that the Coulomb attraction between the arginine and the essential glutamic acid of the c-subunit drives the c-ring rotation. We finally illustrate that the charge-state changes of the glutamic acids, enabled by the electrochemical potential difference of proton and the thermal motion, can produce unidirectional rotation of the c-ring.
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Affiliation(s)
- Dan Parkin
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo169-8555, Japan
| | - Mitsunori Takano
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo169-8555, Japan.,Department of Pure and Applied Physics, Waseda University, 3-8-1 Okubo, Shinjuku-Ku, Tokyo169-8555, Japan
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8
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Biou V. Lipid-membrane protein interaction visualised by cryo-EM: A review. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184068. [PMID: 36216098 DOI: 10.1016/j.bbamem.2022.184068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Membrane proteins reside at interfaces between aqueous and lipid media and solving their molecular structure relies most of the time on removing them from the membrane using detergent. Luckily, this solubilization process does not strip them from all the associated lipids and single-particle cryo-transmission electron microscopy (SP-TEM) has proved a very good tool to visualise both protein high-resolution structure and, often, many of its associated lipids. In this review, we observe membrane protein structures from the Protein DataBank and their associated maps in the Electron Microscopy DataBase and determine how the SP-TEM maps allow lipid visualization, the type of binding sites, the influence of symmetry, resolution and other factors. We illustrate lipid visualization around and inside the protein core, show that some lipid bilayers in the core can be shifted with respect to the membrane and how some proteins can actively bend the lipid bilayer that binds to them. We conclude that resolution improvement in SP-TEM will likely enable many more discoveries regarding the role of lipids bound to proteins.
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Affiliation(s)
- Valérie Biou
- Université de Paris, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique, F-75005 Paris, France.
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9
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Kulke M, Vermaas JV. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:6161-6171. [PMID: 36129782 DOI: 10.1021/acs.jctc.2c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on finite-sized systems in order to map onto computational resources. To minimize artifacts arising from finite-sized simulation systems, it is common practice for MD simulations to be performed with periodic boundary conditions (PBCs). However, in order to calculate specific physical properties, such as mean square displacements to calculate diffusion coefficients, continuous particle trajectories where the atomic movements are continuous and do not jump between cell faces are required. In these cases, modifying atomic coordinates through unwrapping schemes is an essential post-processing tool to remove these jumps. Here, two established trajectory unwrapping schemes are applied to 1 μs wrapped trajectories for a small water box and lysozyme in water. The existing schemes can result in spurious diffusion coefficients, long bonds within unwrapped molecules, and inconsistent atomic coordinates when coordinates are rewrapped after unwrapping. We determine that prior unwrapping schemes do not account for changing periodic box dimensions and introduce an additional correction term to the existing displacement unwrapping scheme to correct for these artifacts. We also demonstrate that the resulting algorithm is a hybrid between the existing heuristic and displacement unwrapping schemes. After treatment using this new unwrapping scheme, molecular geometries are correct even after long simulations. In anticipation for longer MD trajectories, we develop implementations for this new scheme in multiple PBC handling tools.
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Affiliation(s)
- Martin Kulke
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, Michigan 48824, United States
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, Michigan 48824, United States
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10
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Strong proton transfer from phenolic ring to imine functionality in 1D azido and dicyanamido bridged Mn(II) coordination polymers: Synthesis, crystal structure and magnetic studies. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Todokoro Y, Kang SJ, Suzuki T, Ikegami T, Kainosho M, Yoshida M, Fujiwara T, Akutsu H. Chemical Conformation of the Essential Glutamate Site of the c-Ring within Thermophilic Bacillus F oF 1-ATP Synthase Determined by Solid-State NMR Based on its Isolated c-Ring Structure. J Am Chem Soc 2022; 144:14132-14139. [PMID: 35905443 DOI: 10.1021/jacs.2c03580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton translocation through the membrane-embedded Fo component of F-type ATP synthase (FoF1) is facilitated by the rotation of the Fo c-subunit ring (c-ring), carrying protons at essential acidic amino acid residues. Cryo-electron microscopy (Cryo-EM) structures of FoF1 suggest a unique proton translocation mechanism. To elucidate it based on the chemical conformation of the essential acidic residues of the c-ring in FoF1, we determined the structure of the isolated thermophilic Bacillus Fo (tFo) c-ring, consisting of 10 subunits, in membranes by solid-state NMR. This structure contains a distinct proton-locking conformation, wherein Asn23 (cN23) CγO and Glu56 (cE56) CδOH form a hydrogen bond in a closed form. We introduced stereo-array-isotope-labeled (SAIL) Glu and Asn into the tFoc-ring to clarify the chemical conformation of these residues in tFoF1-ATP synthase (tFoF1). Two well-separated 13C signals could be detected for cN23 and cE56 in a 505 kDa membrane protein complex, respectively, thereby suggesting the presence of two distinct chemical conformations. Based on the signal intensity and structure of the tFoc-ring and tFoF1, six pairs of cN23 and cE56 surrounded by membrane lipids take the closed form, whereas the other four in the a-c interface employ the deprotonated open form at a proportion of 87%. This indicates that the a-c interface is highly hydrophilic. The pKa values of the four cE56 residues in the a-c interface were estimated from the cN23 signal intensity in the open and closed forms and distribution of polar residues around each cE56. The results favor a rotation of the c-ring for ATP synthesis.
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Affiliation(s)
- Yasuto Todokoro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Technical Support Division, School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Su-Jin Kang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-Gu, Seoul 151-742, Republic of Korea.,College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Toshiharu Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama 226-0026, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masatsune Kainosho
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masasuke Yoshida
- Department of Molecular Bioscience, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-Gu, Seoul 151-742, Republic of Korea.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
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12
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Kubo S, Takada S. Rotational Mechanism of FO Motor in the F-Type ATP Synthase Driven by the Proton Motive Force. Front Microbiol 2022; 13:872565. [PMID: 35783438 PMCID: PMC9243769 DOI: 10.3389/fmicb.2022.872565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
In FOF1 ATP synthase, driven by the proton motive force across the membrane, the FO motor rotates the central rotor and induces conformational changes in the F1 motor, resulting in ATP synthesis. Recently, many near-atomic resolution structural models have been obtained using cryo-electron microscopy. Despite high resolution, however, static information alone cannot elucidate how and where the protons pass through the FO and how proton passage is coupled to FO rotation. Here, we review theoretical and computational studies based on FO structure models. All-atom molecular dynamics (MD) simulations elucidated changes in the protonation/deprotonation of glutamate—the protein-carrier residue—during rotation and revealed the protonation states that form the “water wire” required for long-range proton hopping. Coarse-grained MD simulations unveiled a free energy surface based on the protonation state and rotational angle of the rotor. Hybrid Monte Carlo and MD simulations showed how proton transfer is coupled to rotation.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- *Correspondence: Shintaroh Kubo
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- Shoji Takada
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13
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Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Molecules 2022; 27:3494. [PMID: 35684429 PMCID: PMC9182050 DOI: 10.3390/molecules27113494] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial diseases (MDs) may result from mutations affecting nuclear or mitochondrial genes, encoding mitochondrial proteins, or non-protein-coding mitochondrial RNA. Despite the great variability of affected genes, in the most severe cases, a neuromuscular and neurodegenerative phenotype is observed, and no specific therapy exists for a complete recovery from the disease. The most used treatments are symptomatic and based on the administration of antioxidant cocktails combined with antiepileptic/antipsychotic drugs and supportive therapy for multiorgan involvement. Nevertheless, the real utility of antioxidant cocktail treatments for patients affected by MDs still needs to be scientifically demonstrated. Unfortunately, clinical trials for antioxidant therapies using α-tocopherol, ascorbate, glutathione, riboflavin, niacin, acetyl-carnitine and coenzyme Q have met a limited success. Indeed, it would be expected that the employed antioxidants can only be effective if they are able to target the specific mechanism, i.e., involving the central and peripheral nervous system, responsible for the clinical manifestations of the disease. Noteworthily, very often the phenotypes characterizing MD patients are associated with mutations in proteins whose function does not depend on specific cofactors. Conversely, the administration of the antioxidant cocktails might determine the suppression of endogenous oxidants resulting in deleterious effects on cell viability and/or toxicity for patients. In order to avoid toxicity effects and before administering the antioxidant therapy, it might be useful to ascertain the blood serum levels of antioxidants and cofactors to be administered in MD patients. It would be also worthwhile to check the localization of mutations affecting proteins whose function should depend (less or more directly) on the cofactors to be administered, for estimating the real need and predicting the success of the proposed cofactor/antioxidant-based therapy.
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Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Guido Primiano
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Albina Tummolo
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Lucas Cafferati Beltrame
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Gianluigi La Piana
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Noemi Sgobba
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Giulia Paterno
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Domenico Marzulli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Serenella Servidei
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Giuseppe Petrosillo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Giovanni Lentini
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
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14
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Tan C, Jung J, Kobayashi C, Torre DUL, Takada S, Sugita Y. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput Biol 2022; 18:e1009578. [PMID: 35381009 PMCID: PMC9012402 DOI: 10.1371/journal.pcbi.1009578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/15/2022] [Accepted: 03/26/2022] [Indexed: 12/28/2022] Open
Abstract
Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynamics (MD) simulations with CG models, unified treatments of proteins and nucleic acids, as well as efficient parallel computations, are indispensable. In the GENESIS MD software, we implement several residue-level CG models, covering structure-based and context-based potentials for both well-folded biomolecules and intrinsically disordered regions. An amino acid residue in protein is represented as a single CG particle centered at the Cα atom position, while a nucleotide in RNA or DNA is modeled with three beads. Then, a single CG particle represents around ten heavy atoms in both proteins and nucleic acids. The input data in CG MD simulations are treated as GROMACS-style input files generated from a newly developed toolbox, GENESIS-CG-tool. To optimize the performance in CG MD simulations, we utilize multiple neighbor lists, each of which is attached to a different nonbonded interaction potential in the cell-linked list method. We found that random number generations for Gaussian distributions in the Langevin thermostat are one of the bottlenecks in CG MD simulations. Therefore, we parallelize the computations with message-passing-interface (MPI) to improve the performance on PC clusters or supercomputers. We simulate Herpes simplex virus (HSV) type 2 B-capsid and chromatin models containing more than 1,000 nucleosomes in GENESIS as examples of large-scale biomolecular simulations with residue-level CG models. This framework extends accessible spatial and temporal scales by multi-scale simulations to study biologically relevant phenomena, such as genome-scale chromatin folding or phase-separated membrane-less condensations.
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Affiliation(s)
- Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Diego Ugarte La Torre
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
- * E-mail:
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15
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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: 2] [Impact Index Per Article: 1.0] [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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16
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17
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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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18
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Krah A, Grüber G, Bond PJ. Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase. Curr Res Struct Biol 2022; 4:278-284. [PMID: 36186842 PMCID: PMC9516385 DOI: 10.1016/j.crstbi.2022.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/13/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB), the deadly disease caused by Mycobacterium tuberculosis (Mtb), kills more people worldwide than any other bacterial infectious disease. There has been a recent resurgence of TB drug discovery activities, resulting in the identification of a number of novel enzyme inhibitors. Many of these inhibitors target the electron transport chain complexes and the F1FO-ATP synthase; these enzymes represent new target spaces for drug discovery, since the generation of ATP is essential for the bacterial pathogen's physiology, persistence, and pathogenicity. The anti-TB drug bedaquiline (BDQ) targets the Mtb F-ATP synthase and is used as salvage therapy against this disease. Medicinal chemistry efforts to improve the physio-chemical properties of BDQ resulted in the discovery of 3,5-dialkoxypyridine (DARQ) analogs to which TBAJ-876 belongs. TBAJ-876, a clinical development candidate, shows attractive in vitro and in vivo antitubercular activity. Both BDQ and TBAJ-876 inhibit the mycobacterial F1FO-ATP synthase by stopping rotation of the c-ring turbine within the FO domain, thereby preventing proton translocation and ATP synthesis to occur. While structural data for the BDQ bound state are available, no structural information about TBAJ-876 binding have been described. In this study, we show how TBAJ-876 binds to the FO domain of the M. smegmatis F1FO-ATP synthase. We further calculate the binding free energy of both drugs bound to their target and predict an increased affinity of TBAJ-876 for the FO domain. This approach will be useful in future efforts to design new and highly potent DARQ analogs targeting F-ATP synthases of Mtb, nontuberculosis mycobacteria (NTM) as well as the M. leprosis complex. BDQ inhibits mycobacterial F-ATP synthase. TBAJ-876 is a BDQ analogue with improved affinity for the enzyme. Simulations help to structurally clarify the FO domain binding sites of TBAJ-876. Insights will help guide development of multidrug-resistant tuberculosis drugs.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore
- Corresponding author.
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
- Corresponding author. Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore.
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19
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Katyal G, Ebanks B, Lucassen M, Papetti C, Chakrabarti L. Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish. PLoS One 2021; 16:e0245822. [PMID: 34613983 PMCID: PMC8494342 DOI: 10.1371/journal.pone.0245822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial changes such as tight coupling of the mitochondria have facilitated sustained oxygen and respiratory activity in haemoglobin-less icefish of the Channichthyidae family. We aimed to characterise features in the sequence and structure of the proteins directly involved in proton transport, which have potential physiological implications. ATP synthase subunit a (ATP6) and subunit 8 (ATP8) are proteins that function as part of the F0 component (proton pump) of the F0F1complex. Both proteins are encoded by the mitochondrial genome and involved in oxidative phosphorylation. To explore mitochondrial sequence variation for ATP6 and ATP8 we analysed sequences from C. gunnari and C. rastrospinosus and compared them with their closely related red-blooded species and eight other vertebrate species. Our comparison of the amino acid sequence of these proteins reveals important differences that could underlie aspects of the unique physiology of the icefish. In this study we find that changes in the sequence of subunit a of the icefish C. gunnari at position 35 where there is a hydrophobic alanine which is not seen in the other notothenioids we analysed. An amino acid change of this type is significant since it may have a structural impact. The biology of the haemoglobin-less icefish is necessarily unique and any insights about these animals will help to generate a better overall understanding of important physiological pathways.
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Affiliation(s)
- Gunjan Katyal
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Brad Ebanks
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | | | | | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Nottingham, United Kingdom
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20
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Kubo S, Yang SK, Black CS, Dai D, Valente-Paterno M, Gaertig J, Ichikawa M, Bui KH. Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM. EMBO Rep 2021; 22:e52911. [PMID: 34338432 PMCID: PMC8419702 DOI: 10.15252/embr.202152911] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/15/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | - Shun Kai Yang
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | - Corbin S Black
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | - Daniel Dai
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
| | | | - Jacek Gaertig
- Department of Cellular BiologyUniversity of GeorgiaAthensGAUSA
| | - Muneyoshi Ichikawa
- Division of Biological ScienceGraduate School of Science and TechnologyNara Institute of Science and TechnologyIkomaJapan
- PRESTOJapan Science and Technology AgencyKawaguchiJapan
| | - Khanh Huy Bui
- Department of Anatomy and Cell BiologyMcGill UniversityMontréalQCCanada
- Centre de Recherche en Biologie StructuraleMcGill UniversityMontréalQCCanada
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21
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Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor. Proc Natl Acad Sci U S A 2021; 118:2101144118. [PMID: 34244431 PMCID: PMC8285958 DOI: 10.1073/pnas.2101144118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Dynamin is a protein that is a central player in endocytosis, a process that mediates the entry of diverse particles into cells, from nutrients to viruses. Dynamin’s primary activity is to use guanosine triphosphate as fuel to constrict and cut membrane tubes. Key quantitative aspects of its function remain yet unclear. In this work, we determine the strength of an individual dynamin motor. Then, by building a detailed computational model resolving individual motors, we demonstrate that dynamin produces sufficient force to tightly constrict a membrane tube when most of its motors are simultaneously cooperating. Hence, we quantitatively validate the prevailing constriction-by-ratchet model for nature’s strongest torque-generating motor: the dynamin “nanomuscle.” Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful enough stroke is produced and how the motor modules would cooperate in the constriction process. Here, we characterized the dynamin motor modules by single-molecule Förster resonance energy transfer (smFRET) and found strong nucleotide-dependent conformational preferences. Integrating smFRET with molecular dynamics simulations allowed us to estimate the forces generated in a power stroke. Subsequently, the quantitative force data and the measured kinetics of the GTPase cycle were incorporated into a model including both a dynamin filament, with explicit motor cross-bridges, and a realistic deformable membrane template. In our simulations, collective constriction of the membrane by dynamin motor modules, based on the ratchet mechanism, is directly reproduced and analyzed. Functional parallels between the dynamin system and actomyosin in the muscle are seen. Through concerted action of the motors, tight membrane constriction to the hemifission radius can be reached. Our experimental and computational study provides an example of how collective motor action in megadalton molecular assemblies can be approached and explicitly resolved.
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22
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The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain. Int J Biol Macromol 2021; 186:54-70. [PMID: 34237360 DOI: 10.1016/j.ijbiomac.2021.06.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022]
Abstract
Lactoferrin (Lf), a bioactive milk protein, exhibits strong anticancer and antifungal activities. The search for Lf targets and mechanisms of action is of utmost importance to enhance its effective applications. A common feature among Lf-treated cancer and fungal cells is the inhibition of a proton pump called V-ATPase. Lf-driven V-ATPase inhibition leads to cytosolic acidification, ultimately causing cell death of cancer and fungal cells. Given that a detailed elucidation of how Lf and V-ATPase interact is still missing, herein we aimed to fill this gap by employing a five-stage computational approach. Molecular dynamics simulations of both proteins were performed to obtain a robust sampling of their conformational landscape, followed by clustering, which allowed retrieving representative structures, to then perform protein-protein docking. Subsequently, molecular dynamics simulations of the docked complexes and free binding energy calculations were carried out to evaluate the dynamic binding process and build a final ranking based on the binding affinities. Detailed atomist analysis of the top ranked complexes clearly indicates that Lf binds to the V1 cytosolic domain of V-ATPase. Particularly, our data suggest that Lf binds to the interfaces between A/B subunits, where the ATP hydrolysis occurs, thus inhibiting this process. The free energy decomposition analysis further identified key binding residues that will certainly aid in the rational design of follow-up experimental studies, hence bridging computational and experimental biochemistry.
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23
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Almendro-Vedia V, Natale P, Valdivieso González D, Lillo MP, Aragones JL, López-Montero I. How rotating ATP synthases can modulate membrane structure. Arch Biochem Biophys 2021; 708:108939. [PMID: 34052190 DOI: 10.1016/j.abb.2021.108939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
F1Fo-ATP synthase (ATP synthase) is a central membrane protein that synthetizes most of the ATP in the cell through a rotational movement driven by a proton gradient across the hosting membrane. In mitochondria, ATP synthases can form dimers through specific interactions between some subunits of the protein. The dimeric form of ATP synthase provides the protein with a spontaneous curvature that sustain their arrangement at the rim of the high-curvature edges of mitochondrial membrane (cristae). Also, a direct interaction with cardiolipin, a lipid present in the inner mitochondrial membrane, induces the dimerization of ATP synthase molecules along cristae. The deletion of those biochemical interactions abolishes the protein dimerization producing an altered mitochondrial function and morphology. Mechanically, membrane bending is one of the key deformation modes by which mitochondrial membranes can be shaped. In particular, bending rigidity and spontaneous curvature are important physical factors for membrane remodelling. Here, we discuss a complementary mechanism whereby the rotatory movement of the ATP synthase might modify the mechanical properties of lipid bilayers and contribute to the formation and regulation of the membrane invaginations.
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Affiliation(s)
- Víctor Almendro-Vedia
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - Paolo Natale
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - David Valdivieso González
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - M Pilar Lillo
- Departamento Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Juan L Aragones
- Departamento de Física Teórica de la Materia Condensada, Instituto Nicolás Cabrera and Condensed Matter Physics Centre (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Iván López-Montero
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain.
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Woo J, Cho H, Seol Y, Kim SH, Park C, Yousefian-Jazi A, Hyeon SJ, Lee J, Ryu H. Power Failure of Mitochondria and Oxidative Stress in Neurodegeneration and Its Computational Models. Antioxidants (Basel) 2021; 10:antiox10020229. [PMID: 33546471 PMCID: PMC7913624 DOI: 10.3390/antiox10020229] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
The brain needs more energy than other organs in the body. Mitochondria are the generator of vital power in the living organism. Not only do mitochondria sense signals from the outside of a cell, but they also orchestrate the cascade of subcellular events by supplying adenosine-5′-triphosphate (ATP), the biochemical energy. It is known that impaired mitochondrial function and oxidative stress contribute or lead to neuronal damage and degeneration of the brain. This mini-review focuses on addressing how mitochondrial dysfunction and oxidative stress are associated with the pathogenesis of neurodegenerative disorders including Alzheimer’s disease, amyotrophic lateral sclerosis, Huntington’s disease, and Parkinson’s disease. In addition, we discuss state-of-the-art computational models of mitochondrial functions in relation to oxidative stress and neurodegeneration. Together, a better understanding of brain disease-specific mitochondrial dysfunction and oxidative stress can pave the way to developing antioxidant therapeutic strategies to ameliorate neuronal activity and prevent neurodegeneration.
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Affiliation(s)
- JunHyuk Woo
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
- Department of Physics and Astronomy and Center for Theoretical Physics, Seoul National University, Seoul 08826, Korea
| | - Hyesun Cho
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
| | - YunHee Seol
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
| | - Soon Ho Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
| | - Chanhyeok Park
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
| | - Ali Yousefian-Jazi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
| | - Seung Jae Hyeon
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
| | - Junghee Lee
- Department of Neurology, Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA 02118, USA;
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Hoon Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.W.); (H.C.); (Y.S.); (S.H.K.); (C.P.); (A.Y.-J.); (S.J.H.)
- Department of Neurology, Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA 02118, USA;
- Correspondence:
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