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Oot RA, Wilkens S. Human V-ATPase function is positively and negatively regulated by TLDc proteins. Structure 2024; 32:989-1000.e6. [PMID: 38593795 DOI: 10.1016/j.str.2024.03.009] [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: 11/09/2023] [Revised: 02/23/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Proteins that contain a highly conserved TLDc domain (Tre2/Bub2/Cdc16 LysM domain catalytic) offer protection against oxidative stress and are widely implicated in neurological health and disease. How this family of proteins exerts their function, however, is poorly understood. We have recently found that the yeast TLDc protein, Oxr1p, inhibits the proton pumping vacuolar ATPase (V-ATPase) by inducing disassembly of the pump. While loss of TLDc protein function in mammals shares disease phenotypes with V-ATPase defects, whether TLDc proteins impact human V-ATPase activity directly is unclear. Here we examine the effects of five human TLDc proteins, TLDC2, NCOA7, OXR1, TBC1D24, and mEAK7 on the activity of the human V-ATPase. We find that while TLDC2, TBC1D24, and the TLDc domains of OXR1 and NCOA7 inhibit V-ATPase by inducing enzyme disassembly, mEAK7 activates the pump. The data thus shed new light both on mammalian TLDc protein function and V-ATPase regulation.
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Affiliation(s)
- Rebecca A Oot
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| | - Stephan Wilkens
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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2
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Bindschedler A, Schmuckli-Maurer J, Buchser S, Fischer TD, Wacker R, Davalan T, Brunner J, Heussler VT. LC3B labeling of the parasitophorous vacuole membrane of Plasmodium berghei liver stage parasites depends on the V-ATPase and ATG16L1. Mol Microbiol 2024; 121:1095-1111. [PMID: 38574236 DOI: 10.1111/mmi.15259] [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: 04/05/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
The protozoan parasite Plasmodium, the causative agent of malaria, undergoes an obligatory stage of intra-hepatic development before initiating a blood-stage infection. Productive invasion of hepatocytes involves the formation of a parasitophorous vacuole (PV) generated by the invagination of the host cell plasma membrane. Surrounded by the PV membrane (PVM), the parasite undergoes extensive replication. During intracellular development in the hepatocyte, the parasites provoke the Plasmodium-associated autophagy-related (PAAR) response. This is characterized by a long-lasting association of the autophagy marker protein, and ATG8 family member, LC3B with the PVM. LC3B localization at the PVM does not follow the canonical autophagy pathway since upstream events specific to canonical autophagy are dispensable. Here, we describe that LC3B localization at the PVM of Plasmodium parasites requires the V-ATPase and its interaction with ATG16L1. The WD40 domain of ATG16L1 is crucial for its recruitment to the PVM. Thus, we provide new mechanistic insight into the previously described PAAR response targeting Plasmodium liver stage parasites.
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Affiliation(s)
- Annina Bindschedler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Sophie Buchser
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Tara D Fischer
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Rahel Wacker
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Tim Davalan
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jessica Brunner
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Volker T Heussler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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3
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Peterson A, Baskett C, Ratcliff WC, Burnetti A. Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Curr Biol 2024; 34:648-654.e3. [PMID: 38218181 DOI: 10.1016/j.cub.2023.12.044] [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: 04/20/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
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Affiliation(s)
- Autumn Peterson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Carina Baskett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
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4
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Wilkens S, Khan MM, Knight K, Oot R. Tender love and disassembly: How a TLDc domain protein breaks the V-ATPase. Bioessays 2023; 45:e2200251. [PMID: 37183929 PMCID: PMC10392918 DOI: 10.1002/bies.202200251] [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: 12/31/2022] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Vacuolar ATPases (V-ATPases, V1 Vo -ATPases) are rotary motor proton pumps that acidify intracellular compartments, and, when localized to the plasma membrane, the extracellular space. V-ATPase is regulated by a unique process referred to as reversible disassembly, wherein V1 -ATPase disengages from Vo proton channel in response to diverse environmental signals. Whereas the disassembly step of this process is ATP dependent, the (re)assembly step is not, but requires the action of a heterotrimeric chaperone referred to as the RAVE complex. Recently, an alternative pathway of holoenzyme disassembly was discovered that involves binding of Oxidation Resistance 1 (Oxr1p), a poorly characterized protein implicated in oxidative stress response. Unlike conventional reversible disassembly, which depends on enzyme activity, Oxr1p induced dissociation can occur in absence of ATP. Yeast Oxr1p belongs to the family of TLDc domain containing proteins that are conserved from yeast to mammals, and have been implicated in V-ATPase function in a variety of tissues. This brief perspective summarizes what we know about the molecular mechanisms governing both reversible (ATP dependent) and Oxr1p driven (ATP independent) V-ATPase dissociation into autoinhibited V1 and Vo subcomplexes.
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Affiliation(s)
- Stephan Wilkens
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Md. Murad Khan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Kassidy Knight
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Rebecca Oot
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
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5
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Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K. Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding. J Biol Chem 2023; 299:102884. [PMID: 36626983 PMCID: PMC9971907 DOI: 10.1016/j.jbc.2023.102884] [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: 10/25/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FoF1 ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of FoF1, where the overall structure of the F1 domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.
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Affiliation(s)
- Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Jun-ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan,Institute for Protein Research, Osaka University, Osaka Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
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Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between V o and V 1 motors. Proc Natl Acad Sci U S A 2022; 119:e2210204119. [PMID: 36215468 PMCID: PMC9586324 DOI: 10.1073/pnas.2210204119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
V-ATPases are ion pumps consisting of two rotary motor proteins, Vo and V1, that actively transport ions across the cell membrane using the chemical energy of ATP. To understand how V-ATPases transduce the energy in the presence of a structural symmetry mismatch between Vo and V1, we simultaneously visualized the rotational pauses and forward and backward steps of Vo and V1 coupled with ion transport and ATP hydrolysis reactions, respectively. Our results suggest that V-ATPases with multiple peripheral stalks are more rigidly coupled than F-ATPases that have only one peripheral stalk and work as ATP synthases. Our high-speed/high-precision single-molecule imaging of rotary ATPases in action will pave the way for a comprehensive understanding of their energy transduction mechanisms. V-ATPases are rotary motor proteins that convert the chemical energy of ATP into the electrochemical potential of ions across cell membranes. V-ATPases consist of two rotary motors, Vo and V1, and Enterococcus hirae V-ATPase (EhVoV1) actively transports Na+ in Vo (EhVo) by using torque generated by ATP hydrolysis in V1 (EhV1). Here, we observed ATP-driven stepping rotation of detergent-solubilized EhVoV1 wild-type, aE634A, and BR350K mutants under various Na+ and ATP concentrations ([Na+] and [ATP], respectively) by using a 40-nm gold nanoparticle as a low-load probe. When [Na+] was low and [ATP] was high, under the condition that only Na+ binding to EhVo is rate limiting, wild-type and aE634A exhibited 10 pausing positions reflecting 10-fold symmetry of the EhVo rotor and almost no backward steps. Duration time before the forward steps was inversely proportional to [Na+], confirming that Na+ binding triggers the steps. When both [ATP] and [Na+] were low, under the condition that both Na+ and ATP bindings are rate limiting, aE634A exhibited 13 pausing positions reflecting 10- and 3-fold symmetries of EhVo and EhV1, respectively. The distribution of duration time before the forward step was fitted well by the sum of two exponential decay functions with distinct time constants. Furthermore, occasional backward steps smaller than 36° were observed. Small backward steps were also observed during three long ATP cleavage pauses of BR350K. These results indicate that EhVo and EhV1 do not share pausing positions, Na+ and ATP bindings occur at different angles, and the coupling between EhVo and EhV1 has a rigid component.
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7
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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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8
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Rotor subunits adaptations in ATP synthases from photosynthetic organisms. Biochem Soc Trans 2021; 49:541-550. [PMID: 33890627 PMCID: PMC8106487 DOI: 10.1042/bst20190936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 11/17/2022]
Abstract
Driven by transmembrane electrochemical ion gradients, F-type ATP synthases are the primary source of the universal energy currency, adenosine triphosphate (ATP), throughout all domains of life. The ATP synthase found in the thylakoid membranes of photosynthetic organisms has some unique features not present in other bacterial or mitochondrial systems. Among these is a larger-than-average transmembrane rotor ring and a redox-regulated switch capable of inhibiting ATP hydrolysis activity in the dark by uniquely adapted rotor subunit modifications. Here, we review recent insights into the structure and mechanism of ATP synthases specifically involved in photosynthesis and explore the cellular physiological consequences of these adaptations at short and long time scales.
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9
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Feng Y, Ovalle M, Seale JSW, Lee CK, Kim DJ, Astumian RD, Stoddart JF. Molecular Pumps and Motors. J Am Chem Soc 2021; 143:5569-5591. [PMID: 33830744 DOI: 10.1021/jacs.0c13388] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pumps and motors are essential components of the world as we know it. From the complex proteins that sustain our cells, to the mechanical marvels that power industries, much we take for granted is only possible because of pumps and motors. Although molecular pumps and motors have supported life for eons, it is only recently that chemists have made progress toward designing and building artificial forms of the microscopic machinery present in nature. The advent of artificial molecular machines has granted scientists an unprecedented level of control over the relative motion of components of molecules through the development of kinetically controlled, away-from-thermodynamic equilibrium chemistry. We outline the history of pumps and motors, focusing specifically on the innovations that enable the design and synthesis of the artificial molecular machines central to this Perspective. A key insight connecting biomolecular and artificial molecular machines is that the physical motions by which these machines carry out their function are unambiguously in mechanical equilibrium at every instant. The operation of molecular motors and pumps can be described by trajectory thermodynamics, a theory based on the work of Onsager, which is grounded on the firm foundation of the principle of microscopic reversibility. Free energy derived from thermodynamically non-equilibrium reactions kinetically favors some reaction pathways over others. By designing molecules with kinetic asymmetry, one can engineer potential landscapes to harness external energy to drive the formation and maintenance of geometries of component parts of molecules away-from-equilibrium, that would be impossible to achieve by standard synthetic approaches.
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Affiliation(s)
- Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Marco Ovalle
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - James S W Seale
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Christopher K Lee
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dong Jun Kim
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - R Dean Astumian
- Department of Physics, University of Maine, Orono, Maine 04469, United States
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.,Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
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10
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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11
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Wittig S, Ganzella M, Barth M, Kostmann S, Riedel D, Pérez-Lara Á, Jahn R, Schmidt C. Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes. Nat Commun 2021; 12:858. [PMID: 33558502 PMCID: PMC7870876 DOI: 10.1038/s41467-021-21102-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/18/2020] [Indexed: 02/08/2023] Open
Abstract
Synaptic vesicles are storage organelles for neurotransmitters. They pass through a trafficking cycle and fuse with the pre-synaptic membrane when an action potential arrives at the nerve terminal. While molecular components and biophysical parameters of synaptic vesicles have been determined, our knowledge on the protein interactions in their membranes is limited. Here, we apply cross-linking mass spectrometry to study interactions of synaptic vesicle proteins in an unbiased approach without the need for specific antibodies or detergent-solubilisation. Our large-scale analysis delivers a protein network of vesicle sub-populations and functional assemblies including an active and an inactive conformation of the vesicular ATPase complex as well as non-conventional arrangements of the luminal loops of SV2A, Synaptophysin and structurally related proteins. Based on this network, we specifically target Synaptobrevin-2, which connects with many proteins, in different approaches. Our results allow distinction of interactions caused by 'crowding' in the vesicle membrane from stable interaction modules.
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Affiliation(s)
- Sabine Wittig
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marcelo Ganzella
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marie Barth
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Susann Kostmann
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dietmar Riedel
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ángel Pérez-Lara
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Reinhard Jahn
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
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12
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Abstract
ATP synthase is an essential enzyme found in all known forms of life, generating the majority of cellular energy via a rotary catalytic mechanism. Here, we describe the in-depth methods for expression, purification, and functional assessment of E. coli ATP synthase.
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13
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Kabra R, Singh S. Transporter proteins and its implication in human diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 124:1-21. [PMID: 33632463 DOI: 10.1016/bs.apcsb.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Drug transporters, classified in various ways like efflux transporters and influx transporters; secretory transporters and absorptive transporters; ATP-driven transporters and Solute Linked Carrier (SLC) transporters are of great importance while studying pharmacokinetics. They have impeccable roles in the drug discovery process of infectious diseases. Many of these find a pivotal role in synthetic antimicrobial peptides. The chapter briefly elucidates the varied types and their significance.
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Affiliation(s)
- Ritika Kabra
- National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Shailza Singh
- National Centre for Cell Science, SP Pune University Campus, Pune, India.
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14
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Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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15
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Hu L, Wang N, Lim YD, Miao J. Chemical reaction dependency, magnetic field and surfactant effects on the propulsion of disk‐like micromotor and its application for
E. coli
transportation. NANO SELECT 2020. [DOI: 10.1002/nano.202000024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering Nanyang Technological University Nanyang 639798 Singapore
| | - Nan Wang
- Department of Science and Math Singapore University of Technology and Design Singapore 487372 Singapore
| | - Yu Dian Lim
- Centre for Micro‐/Nano‐electronics (NOVITAS), School of Electrical and Electronics Engineering Nanyang Technological University Nanyang 639798 Singapore
| | - Jianmin Miao
- School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 P. R. China
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16
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Krasnoselska GO, Meier T. Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase. Methods Mol Biol 2019; 1805:51-71. [PMID: 29971712 DOI: 10.1007/978-1-4939-8556-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
F-type adenosine triphosphate (ATP) synthase is a membrane-bound macromolecular complex, which is responsible for the synthesis of ATP, the universal energy source in living cells. This enzyme uses the proton- or sodium-motive force to power ATP synthesis by a unique rotary mechanism and can also operate in reverse, ATP hydrolysis, to generate ion gradients across membranes. The F1Fo-ATP synthases from bacteria consist of eight different structural subunits, forming a complex of ∼550 kDa in size. In the bacterium Ilyobacter tartaricus the ATP synthase has the stoichiometry α3β3γδεab2c11. This chapter describes a wet-lab working protocol for the purification of several tens of milligrams of pure, heterologously (E. coli-)produced I. tartaricus Na+-driven F1Fo-ATP synthase and its subsequent efficient reconstitution into proteoliposomes. The methods are useful for a broad range of subsequent biochemical and biotechnological applications.
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Affiliation(s)
- Ganna O Krasnoselska
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Department of Life Sciences, Imperial College London, London, UK.
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17
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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18
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Mendoza-Hoffmann F, Zarco-Zavala M, Ortega R, García-Trejo JJ. Control of rotation of the F1FO-ATP synthase nanomotor by an inhibitory α-helix from unfolded ε or intrinsically disordered ζ and IF1 proteins. J Bioenerg Biomembr 2018; 50:403-424. [DOI: 10.1007/s10863-018-9773-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022]
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19
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Hu L, Rehman S, Tao K, Miao J. Characterization on Three-Dimensional Trajectory of Disk-Like Gold-Nickel-Platinum Nanomotor Using Digital Holographic Imaging. ChemistrySelect 2018. [DOI: 10.1002/slct.201801534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering; Nanyang Technological University, 50 Nanyang Avenue; Singapore 639798
| | - Shakil Rehman
- Singapore-MIT Alliance for Research and Technology (SMART), 1 CREATE Way; Singapore 138602
| | - Kai Tao
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering; Northwestern Polytechnical University, Xi'an; China 710072
| | - Jianmin Miao
- School of Mechanical and Aerospace Engineering; Nanyang Technological University, 50 Nanyang Avenue; Singapore 639798
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20
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Colina-Tenorio L, Dautant A, Miranda-Astudillo H, Giraud MF, González-Halphen D. The Peripheral Stalk of Rotary ATPases. Front Physiol 2018; 9:1243. [PMID: 30233414 PMCID: PMC6131620 DOI: 10.3389/fphys.2018.01243] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022] Open
Abstract
Rotary ATPases are a family of enzymes that are thought of as molecular nanomotors and are classified in three types: F, A, and V-type ATPases. Two members (F and A-type) can synthesize and hydrolyze ATP, depending on the energetic needs of the cell, while the V-type enzyme exhibits only a hydrolytic activity. The overall architecture of all these enzymes is conserved and three main sectors are distinguished: a catalytic core, a rotor and a stator or peripheral stalk. The peripheral stalks of the A and V-types are highly conserved in both structure and function, however, the F-type peripheral stalks have divergent structures. Furthermore, the peripheral stalk has other roles beyond its stator function, as evidenced by several biochemical and recent structural studies. This review describes the information regarding the organization of the peripheral stalk components of F, A, and V-ATPases, highlighting the key differences between the studied enzymes, as well as the different processes in which the structure is involved.
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Affiliation(s)
- Lilia Colina-Tenorio
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alain Dautant
- CNRS, UMR5095, IBGC, Bordeaux, France.,Energy Transducing Systems and Mitochondrial Morphology, Université de Bordeaux, Bordeaux, France
| | - Héctor Miranda-Astudillo
- Genetics and Physiology of Microalgae, InBios, PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Marie-France Giraud
- CNRS, UMR5095, IBGC, Bordeaux, France.,Energy Transducing Systems and Mitochondrial Morphology, Université de Bordeaux, Bordeaux, France
| | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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21
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Structure and dynamics of rotary V 1 motor. Cell Mol Life Sci 2018; 75:1789-1802. [PMID: 29387903 PMCID: PMC5910484 DOI: 10.1007/s00018-018-2758-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/25/2017] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
Abstract
Rotary ATPases are unique rotary molecular motors that function as energy conversion machines. Among all known rotary ATPases, F1-ATPase is the best characterized rotary molecular motor. There are many high-resolution crystal structures and the rotation dynamics have been investigated in detail by extensive single-molecule studies. In contrast, knowledge on the structure and rotation dynamics of V1-ATPase, another rotary ATPase, has been limited. However, recent high-resolution structural studies and single-molecule studies on V1-ATPase have provided new insights on how the catalytic sites in this molecular motor change its conformation during rotation driven by ATP hydrolysis. In this review, we summarize recent information on the structural features and rotary dynamics of V1-ATPase revealed from structural and single-molecule approaches and discuss the possible chemomechanical coupling scheme of V1-ATPase with a focus on differences between rotary molecular motors.
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22
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Sánchez-Vásquez L, González-Halphen D. TOPOLOGÍA Y FUNCIÓN DE LAS SUBUNIDADES INTRÍNSECAS DE LA MEMBRANA DE LAS F 1 F O -ATP SINTASA MITOCONDRIALES. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2017. [DOI: 10.1016/j.recqb.2017.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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23
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Sharma S, Wilkens S. Biolayer interferometry of lipid nanodisc-reconstituted yeast vacuolar H + -ATPase. Protein Sci 2017; 26:1070-1079. [PMID: 28241399 DOI: 10.1002/pro.3143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023]
Abstract
Vacuolar H+ -ATPase (V-ATPase) is a large, multisubunit membrane protein complex responsible for the acidification of subcellular compartments and the extracellular space. V-ATPase activity is regulated by reversible disassembly, resulting in cytosolic V1 -ATPase and membrane-integral V0 proton channel sectors. Reversible disassembly is accompanied by transient interaction with cellular factors and assembly chaperones. Quantifying protein-protein interactions involving membrane proteins, however, is challenging. Here we present a novel method to determine kinetic constants of membrane protein-protein interactions using biolayer interferometry (BLI). Yeast vacuoles are solubilized, vacuolar proteins are reconstituted into lipid nanodiscs with native vacuolar lipids and biotinylated membrane scaffold protein (MSP) followed by affinity purification of nanodisc-reconstituted V-ATPase (V1 V0 ND). We show that V1 V0 ND can be immobilized on streptavidin-coated BLI sensors to quantitate binding of a pathogen derived inhibitor and to measure the kinetics of nucleotide dependent enzyme dissociation.
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Affiliation(s)
- Stuti Sharma
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, Syracuse, New York, 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, Syracuse, New York, 13210
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24
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Schulz S, Wilkes M, Mills DJ, Kühlbrandt W, Meier T. Molecular architecture of the N-type ATPase rotor ring from Burkholderia pseudomallei. EMBO Rep 2017; 18:526-535. [PMID: 28283532 PMCID: PMC5376962 DOI: 10.15252/embr.201643374] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 11/09/2022] Open
Abstract
The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N‐type rotary ATPase, in addition to an operon for a regular F‐type rotary ATPase. The molecular architecture of N‐type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N1No‐type ATPase and investigated the structure and ion specificity of its membrane‐embedded c‐ring rotor by single‐particle electron cryo‐microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low‐density, low‐CMC detergent LDAO was optimal in terms of map quality and resolution. The cryoEM map of the c‐ring at 6.1 Å resolution reveals a heptadecameric oligomer with a molecular mass of ~141 kDa. Biochemical measurements indicate that the c17 ring is H+ specific, demonstrating that the ATPase is proton‐coupled. The c17 ring stoichiometry results in a very high ion‐to‐ATP ratio of 5.7. We propose that this N‐ATPase is a highly efficient proton pump that helps these melioidosis‐causing bacteria to survive in the hostile, acidic environment of phagosomes.
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Affiliation(s)
- Sarah Schulz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Martin Wilkes
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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25
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Schmidt C, Beilsten-Edmands V, Mohammed S, Robinson CV. Acetylation and phosphorylation control both local and global stability of the chloroplast F 1 ATP synthase. Sci Rep 2017; 7:44068. [PMID: 28276484 PMCID: PMC5343439 DOI: 10.1038/srep44068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/03/2017] [Indexed: 12/14/2022] Open
Abstract
ATP synthases (ATPases) are enzymes that produce ATP and control the pH in the cell or cellular compartments. While highly conserved over different species, ATPases are structurally well-characterised but the existence and functional significance of many post-translational modifications (PTMs) is not well understood. We combined a range of mass spectrometric techniques to unravel the location and extent of PTMs in the chloroplast ATP synthase (cATPase) purified from spinach leaves. We identified multiple phosphorylation and acetylation sites and found that both modifications stabilise binding of ε and δ subunits. Comparing cross-linking of naturally modified cATPase with the in vitro deacetylated enzyme revealed a major conformational change in the ε subunit in accord with extended and folded forms of the subunit. Locating modified residues within the catalytic head we found that phosphorylated and acetylated residues are primarily on α/β and β/α interfaces respectively. By aligning along different interfaces the higher abundance acetylated residues are proximal to the regulatory sites while the lower abundance phosphorylation sites are more densely populated at the catalytic sites. We propose that modifications in the catalytic head, together with the conformational change in subunit ε, work in synergy to fine-tune the enzyme during adverse conditions.
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Affiliation(s)
- Carla Schmidt
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - Shabaz Mohammed
- Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
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26
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Sobti M, Smits C, Wong AS, Ishmukhametov R, Stock D, Sandin S, Stewart AG. Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states. eLife 2016; 5. [PMID: 28001127 PMCID: PMC5214741 DOI: 10.7554/elife.21598] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022] Open
Abstract
A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s ε subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides. DOI:http://dx.doi.org/10.7554/eLife.21598.001 ATP synthase is a biological motor that produces a molecule called adenosine tri-phosphate (ATP for short), which acts as the major store of chemical energy in cells. A single molecule of ATP contains three phosphate groups: the cell can remove one of these phosphates to make a molecule called adenosine di-phosphate (ADP) and release energy to drive a variety of biological processes. ATP synthase sits in the membranes that separate cell compartments or form barriers around cells. When cells break down food they transport hydrogen ions across these membranes so that each side of the membrane has a different level (or “concentration”) of hydrogen ions. Movement of hydrogen ions from an area with a high concentration to a low concentration causes ATP synthase to rotate like a turbine. This rotation of the enzyme results in ATP synthase adding a phosphate group to ADP to make a new molecule of ATP. In certain conditions cells need to switch off the ATP synthase and this is done by changing the shape of the central shaft in a process called autoinhibition, which blocks the rotation. The ATP synthase from a bacterium known as E. coli – which is commonly found in the human gut –has been used as a model to study how this biological motor works. However, since the precise details of the three-dimensional structure of ATP synthase have remained unclear it has been difficult to interpret the results of these studies. Sobti et al. used a technique called Cryo-electron microscopy to investigate the structure of ATP synthase from E. coli. This made it possible to develop a three-dimensional model of the ATP synthase in its autoinhibited form. The structural data could also be split into three distinct shapes that relate to dwell points in the rotation of the motor where the rotation has been inhibited. These models further our understanding of ATP synthases and provide a template to understand the findings of previous studies. Further work will be needed to understand this essential biological process at the atomic level in both its inhibited and uninhibited form. This will reveal the inner workings of a marvel of the natural world and may also lead to the discovery of new antibiotics against related bacteria that cause diseases in humans. DOI:http://dx.doi.org/10.7554/eLife.21598.002
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Affiliation(s)
- Meghna Sobti
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Callum Smits
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Andrew Sw Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Robert Ishmukhametov
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniela Stock
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Sara Sandin
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Faculty of Medicine, The University of New South Wales, Sydney, Australia
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27
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Sielaff H, Martin J, Singh D, Biuković G, Grüber G, Frasch WD. Power Stroke Angular Velocity Profiles of Archaeal A-ATP Synthase Versus Thermophilic and Mesophilic F-ATP Synthase Molecular Motors. J Biol Chem 2016; 291:25351-25363. [PMID: 27729450 PMCID: PMC5207238 DOI: 10.1074/jbc.m116.745240] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/03/2016] [Indexed: 01/21/2023] Open
Abstract
The angular velocities of ATPase-dependent power strokes as a function of the rotational position for the A-type molecular motor A3B3DF, from the Methanosarcina mazei Gö1 A-ATP synthase, and the thermophilic motor α3β3γ, from Geobacillus stearothermophilus (formerly known as Bacillus PS3) F-ATP synthase, are resolved at 5 μs resolution for the first time. Unexpectedly, the angular velocity profile of the A-type was closely similar in the angular positions of accelerations and decelerations to the profiles of the evolutionarily distant F-type motors of thermophilic and mesophilic origins, and they differ only in the magnitude of their velocities. M. mazei A3B3DF power strokes occurred in 120° steps at saturating ATP concentrations like the F-type motors. However, because ATP-binding dwells did not interrupt the 120° steps at limiting ATP, ATP binding to A3B3DF must occur during the catalytic dwell. Elevated concentrations of ADP did not increase dwells occurring 40° after the catalytic dwell. In F-type motors, elevated ADP induces dwells 40° after the catalytic dwell and slows the overall velocity. The similarities in these power stroke profiles are consistent with a common rotational mechanism for A-type and F-type rotary motors, in which the angular velocity is limited by the rotary position at which ATP binding occurs and by the drag imposed on the axle as it rotates within the ring of stator subunits.
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Affiliation(s)
- Hendrik Sielaff
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - James Martin
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 and
| | - Dhirendra Singh
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Goran Biuković
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Gerhard Grüber
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Wayne D Frasch
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 and
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28
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Hu L, Miao J, Grüber G. Disk-like nanojets with steerable trajectory using platinum nozzle nanoengines. RSC Adv 2016. [DOI: 10.1039/c5ra24202a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nanojets with one off-center platinum nozzle nanoengine can propel forward circularly, while the nanojets with two identically and symmetrically distributed platinum nozzle nanoengines are capable of moving forward in a linear way.
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Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore
| | - Jianmin Miao
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore
| | - Gerhard Grüber
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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29
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Couoh-Cardel S, Milgrom E, Wilkens S. Affinity Purification and Structural Features of the Yeast Vacuolar ATPase Vo Membrane Sector. J Biol Chem 2015; 290:27959-71. [PMID: 26416888 DOI: 10.1074/jbc.m115.662494] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/27/2022] Open
Abstract
The membrane sector (Vo) of the proton pumping vacuolar ATPase (V-ATPase, V1Vo-ATPase) from Saccharomyces cerevisiae was purified to homogeneity, and its structure was characterized by EM of single molecules and two-dimensional crystals. Projection images of negatively stained Vo two-dimensional crystals showed a ring-like structure with a large asymmetric mass at the periphery of the ring. A cryo-EM reconstruction of Vo from single-particle images showed subunits a and d in close contact on the cytoplasmic side of the proton channel. A comparison of three-dimensional reconstructions of free Vo and Vo as part of holo V1Vo revealed that the cytoplasmic N-terminal domain of subunit a (aNT) must undergo a large conformational change upon enzyme disassembly or (re)assembly from Vo, V1, and subunit C. Isothermal titration calorimetry using recombinant subunit d and aNT revealed that the two proteins bind each other with a Kd of ~5 μm. Treatment of the purified Vo sector with 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] resulted in selective release of subunit d, allowing purification of a VoΔd complex. Passive proton translocation assays revealed that both Vo and VoΔd are impermeable to protons. We speculate that the structural change in subunit a upon release of V1 from Vo during reversible enzyme dissociation plays a role in blocking passive proton translocation across free Vo and that the interaction between aNT and d seen in free Vo functions to stabilize the Vo sector for efficient reassembly of V1Vo.
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Affiliation(s)
- Sergio Couoh-Cardel
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Elena Milgrom
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Stephan Wilkens
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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30
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Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase. Proc Natl Acad Sci U S A 2015; 112:10720-5. [PMID: 26261344 DOI: 10.1073/pnas.1500691112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We combine molecular simulations and mechanical modeling to explore the mechanism of energy conversion in the coupled rotary motors of FoF1-ATP synthase. A torsional viscoelastic model with frictional dissipation quantitatively reproduces the dynamics and energetics seen in atomistic molecular dynamics simulations of torque-driven γ-subunit rotation in the F1-ATPase rotary motor. The torsional elastic coefficients determined from the simulations agree with results from independent single-molecule experiments probing different segments of the γ-subunit, which resolves a long-lasting controversy. At steady rotational speeds of ∼ 1 kHz corresponding to experimental turnover, the calculated frictional dissipation of less than k(B)T per rotation is consistent with the high thermodynamic efficiency of the fully reversible motor. Without load, the maximum rotational speed during transitions between dwells is reached at ∼ 1 MHz. Energetic constraints dictate a unique pathway for the coupled rotations of the Fo and F1 rotary motors in ATP synthase, and explain the need for the finer stepping of the F1 motor in the mammalian system, as seen in recent experiments. Compensating for incommensurate eightfold and threefold rotational symmetries in Fo and F1, respectively, a significant fraction of the external mechanical work is transiently stored as elastic energy in the γ-subunit. The general framework developed here should be applicable to other molecular machines.
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Takeuchi J, Ohkubo A, Yuasa H. A ring-flippable sugar as a stimuli-responsive component of liposomes. Chem Asian J 2015; 10:586-94. [PMID: 25573604 DOI: 10.1002/asia.201403271] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Indexed: 11/07/2022]
Abstract
For the development of a liposome that takes in and out a drug in response to stimuli, 2,4-diaminoxylose (Xyl), which allows stimuli-responsive conformational switches between (4)C1 and (1)C4, was incorporated into a lipid structure: Xyl derivatives with C8 and C16 methylene chains at the 1,3-positions (C8Xyl and C16Xyl) were synthesized. (1)H NMR spectroscopy indicates that the addition of Zn(2+) and then H(+) induces conformational switches from the chair ((4)C1) to the reverse chair ((1)C4) and (1)C4-to-(4)C1, respectively, at Xyl; this leads to transformation of the lipids between linear and bent structures. Osmotic pressure and electron microscopy studies demonstrate that C8Xyl in water forms spherical solid aggregates (C8Xyl-Zn), which are converted into liposomes (C8Xyl+Zn) upon the addition of Zn(2+), and C16Xyl forms liposomes regardless of the presence of Zn(2+). The aggregates of C8Xyl±Zn incorporated a fluorophore and only C8Xyl+Zn released the content upon the addition of HCl. This study shows that Xyl could be a stimuli-responsive component of a liposome.
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Affiliation(s)
- Junji Takeuchi
- Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259J2-10, Nagatsutacho, Midoriku, Yokohama 226-8501 (Japan)
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Grüber G, Manimekalai MSS, Mayer F, Müller V. ATP synthases from archaea: the beauty of a molecular motor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:940-52. [PMID: 24650628 DOI: 10.1016/j.bbabio.2014.03.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 11/18/2022]
Abstract
Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot temperatures. How energy is conserved under such harsh environmental conditions is a major question in cellular bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A1AO ATP synthases, a class of ATP synthases distinct from the F1FO ATP synthase ATP synthase found in bacteria, mitochondria and chloroplasts and the V1VO ATPases of eukaryotes. A1AO ATP synthases have distinct structural features such as a collar-like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A1AO ATP synthase during rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this unique class of ATP synthases. An outstanding feature of archaeal A1AO ATP synthases is their diversity in size of rotor subunits and the coupling ion used for ATP synthesis with H(+), Na(+) or even H(+) and Na(+) using enzymes. The evolution of the H(+) binding site to a Na(+) binding site and its implications for the energy metabolism and physiology of the cell are discussed.
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Affiliation(s)
- Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
| | | | - Florian Mayer
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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Zhou M, Politis A, Davies R, Liko I, Wu KJ, Stewart AG, Stock D, Robinson CV. Ion mobility-mass spectrometry of a rotary ATPase reveals ATP-induced reduction in conformational flexibility. Nat Chem 2014; 6:208-215. [PMID: 24557135 PMCID: PMC4067995 DOI: 10.1038/nchem.1868] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/08/2014] [Indexed: 12/20/2022]
Abstract
Rotary ATPases play fundamental roles in energy conversion as their catalytic rotation is associated with interdomain fluctuations and heterogeneity of conformational states. Using ion mobility mass spectrometry we compared the conformational dynamics of the intact ATPase from Thermus thermophilus with those of its membrane and soluble subcomplexes. Our results define regions with enhanced flexibility assigned to distinct subunits within the overall assembly. To provide a structural context for our experimental data we performed molecular dynamics simulations and observed conformational changes of the peripheral stalks that reflect their intrinsic flexibility. By isolating complexes at different phases of cell growth and manipulating nucleotides, metal ions and pH during isolation, we reveal differences that can be related to conformational changes in the Vo complex triggered by ATP binding. Together these results implicate nucleotides in modulating flexibility of the stator components and uncover mechanistic detail that underlies operation and regulation in the context of the holoenzyme.
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Affiliation(s)
- Min Zhou
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Argyris Politis
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Roberta Davies
- The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia
- The University of New South Wales, Sydney NSW 2052, Australia
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Kuan-Jung Wu
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Alastair G Stewart
- The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia
- The University of New South Wales, Sydney NSW 2052, Australia
| | - Daniela Stock
- The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia
- The University of New South Wales, Sydney NSW 2052, Australia
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
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Stewart AG, Laming EM, Sobti M, Stock D. Rotary ATPases--dynamic molecular machines. Curr Opin Struct Biol 2013; 25:40-8. [PMID: 24878343 DOI: 10.1016/j.sbi.2013.11.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/20/2013] [Accepted: 11/26/2013] [Indexed: 01/14/2023]
Abstract
Recent work has provided the detailed overall architecture and subunit composition of three subtypes of rotary ATPases. Composite models of F-type, V-type and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual components into electron microscopy derived envelopes of the intact enzymes. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria. An inherent flexibility in rotary ATPases observed by different techniques suggests greater dynamics during operation than previously envisioned. The concerted movement of subunits within the complex might provide means of regulation and information transfer between distant parts of rotary ATPases thereby fine tuning these molecular machines to their cellular environment, while optimizing their efficiency.
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Affiliation(s)
- Alastair G Stewart
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia.
| | - Elise M Laming
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
| | - Meghna Sobti
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
| | - Daniela Stock
- The Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; The University of New South Wales, Sydney, NSW, Australia
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