1
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Ragunathan P, Sae-Lao P, Hamela C, Alcaraz M, Krah A, Poh WH, Ern Pee CJ, Hou Lim AY, Rice SA, Pethe K, Bond PJ, Dick T, Kremer L, Bates RW, Grüber G. High efficacy of the F-ATP synthase inhibitor TBAJ-5307 against nontuberculous mycobacteria in vitro and in vivo. J Biol Chem 2024; 300:105618. [PMID: 38176652 PMCID: PMC10840338 DOI: 10.1016/j.jbc.2023.105618] [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: 10/26/2023] [Revised: 12/09/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
The F1FO-ATP synthase engine is essential for viability and growth of nontuberculous mycobacteria (NTM) by providing the biological energy ATP and keeping ATP homeostasis under hypoxic stress conditions. Here, we report the discovery of the diarylquinoline TBAJ-5307 as a broad spectrum anti-NTM inhibitor, targeting the FO domain of the engine and preventing rotation and proton translocation. TBAJ-5307 is active at low nanomolar concentrations against fast- and slow-growing NTM as well as clinical isolates by depleting intrabacterial ATP. As demonstrated for the fast grower Mycobacterium abscessus, the compound is potent in vitro and in vivo, without inducing toxicity. Combining TBAJ-5307 with anti-NTM antibiotics or the oral tebipenem-avibactam pair showed attractive potentiation. Furthermore, the TBAJ-5307-tebipenem-avibactam cocktail kills the pathogen, suggesting a novel oral combination for the treatment of NTM lung infections.
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Affiliation(s)
- Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Patcharaporn Sae-Lao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Wee Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Carmen Jia Ern Pee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Albert Yick Hou Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Department for Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Scott A Rice
- School of Biological Sciences, Nanyang Technological University, Singapore; Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore; Microbiomes for One Systems Health and Agriculture and Food, CSIRO, Westmead, New South Wales, Australia
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, Singapore; Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; National Centre for Infectious Diseases (NCID), Singapore
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA; Department of Microbiology and Immunology, Georgetown University, Washington, District of Columbia, USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France; INSERM, IRIM, Montpellier, France.
| | - Roderick W Bates
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore.
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore; Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore.
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2
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Krah A, Ragunathan P, Bond PJ, Grüber G. Variations of the Mycobacterium abscessus F-ATP synthase subunit a-c interface alter binding and potency of the anti-TB drug bedaquiline. Biochem Biophys Res Commun 2024; 690:149249. [PMID: 38000294 DOI: 10.1016/j.bbrc.2023.149249] [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: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
The anti-tuberculosis therapeutic bedaquiline (BDQ) is used against Mycobacterium abscessus. In M. abscessus BDQ is only bacteriostatic and less potent compared to M. tuberculosis or M. smegmatis. Here we demonstrate its reduced ATP synthesis inhibition against M. abscessus inside-out vesicles, including the F1FO-ATP synthase. Molecular dynamics simulations and binding free energy calculations highlight the differences in drug-binding of the M. abscessus and M. smegmatis FO-domain at the lagging site, where the drug deploys its mechanistic action, inhibiting ATP synthesis. These data pave the way for improved anti-M. abscessus BDQ analogs.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.
| | - Priya Ragunathan
- 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 Street, #07-01 Matrix, 138671, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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3
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Yamamoto H, Cheuk A, Shearman J, Nixon PJ, Meier T, Shikanai T. Impact of engineering the ATP synthase rotor ring on photosynthesis in tobacco chloroplasts. PLANT PHYSIOLOGY 2023; 192:1221-1233. [PMID: 36703219 PMCID: PMC10231360 DOI: 10.1093/plphys/kiad043] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 06/01/2023]
Abstract
The chloroplast ATP synthase produces the ATP needed for photosynthesis and plant growth. The trans-membrane flow of protons through the ATP synthase rotates an oligomeric assembly of c subunits, the c-ring. The ion-to-ATP ratio in rotary F1F0-ATP synthases is defined by the number of c-subunits in the rotor c-ring. Engineering the c-ring stoichiometry is, therefore, a possible route to manipulate ATP synthesis by the ATP synthase and hence photosynthetic efficiency in plants. Here, we describe the construction of a tobacco (Nicotiana tabacum) chloroplast atpH (chloroplastic ATP synthase subunit c gene) mutant in which the c-ring stoichiometry was increased from 14 to 15 c-subunits. Although the abundance of the ATP synthase was decreased to 25% of wild-type (WT) levels, the mutant lines grew as well as WT plants and photosynthetic electron transport remained unaffected. To synthesize the necessary ATP for growth, we found that the contribution of the membrane potential to the proton motive force was enhanced to ensure a higher proton flux via the c15-ring without unwanted low pH-induced feedback inhibition of electron transport. Our work opens avenues to manipulate plant ion-to-ATP ratios with potentially beneficial consequences for photosynthesis.
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Affiliation(s)
- Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Anthony Cheuk
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Julia Shearman
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Thomas Meier
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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4
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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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5
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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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6
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Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na + in ion-coupled drug efflux. J Biol Chem 2021; 296:100262. [PMID: 33837745 PMCID: PMC7949106 DOI: 10.1016/j.jbc.2021.100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
In both prokaryotes and eukaryotes, multidrug and toxic-compound extrusion (MATE) transporters catalyze the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are secondary-active antiporters, i.e., their drug-efflux activity is coupled to, and powered by, the uptake of ions down a preexisting transmembrane electrochemical gradient. Key aspects of this mechanism, however, remain to be delineated, such as its ion specificity and stoichiometry. We previously revealed the existence of a Na+-binding site in a MATE transporter from Pyroccocus furiosus (PfMATE) and hypothesized that this site might be broadly conserved among prokaryotic MATEs. Here, we evaluate this hypothesis by analyzing VcmN and ClbM, which along with PfMATE are the only three prokaryotic MATEs whose molecular structures have been determined at atomic resolution, i.e. better than 3 Å. Reinterpretation of existing crystallographic data and molecular dynamics simulations indeed reveal an occupied Na+-binding site in the N-terminal lobe of both structures, analogous to that identified in PfMATE. We likewise find this site to be strongly selective against K+, suggesting it is mechanistically significant. Consistent with these computational results, DEER spectroscopy measurements for multiple doubly-spin-labeled VcmN constructs demonstrate Na+-dependent changes in protein conformation. The existence of this binding site in three MATE orthologs implicates Na+ in the ion-coupled drug-efflux mechanisms of this class of transporters. These results also imply that observations of H+-dependent activity likely stem either from a site elsewhere in the structure, or from H+ displacing Na+ under certain laboratory conditions, as has been noted for other Na+-driven transport systems.
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7
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Krah A, Marzinek JK, Bond PJ. Characterizing the Hydration Properties of Proton Binding Sites in the ATP Synthase c-Rings of Bacillus Species. J Phys Chem B 2020; 124:7176-7183. [PMID: 32687713 DOI: 10.1021/acs.jpcb.0c03896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The membrane-embedded domain of ATP synthases contains the c-ring, which translocates ions across the membrane, and its resultant rotation is coupled to ATP synthesis in the extramembranous domain. During rotation, the c-ring becomes accessible on both sides of the lipid bilayer to solvent via channels connected to the other membrane-embedded component, the a subunit, and thereby allows the ion to be released into the solvent environment. In recent times, many experimental structures of c-rings from different species have been solved. In some of these, a water molecule with a proposed "structural role" has been identified within the c-ring ion binding site, but in general, the requirement for high resolution to resolve specific water densities complicates their interpretation. In the present study, we use molecular dynamics (MD) simulations and rigorous free energy calculations to characterize the dynamics and energetics of a water molecule within the ion binding site of the c-ring from Bacillus pseudofirmus OF4, in its wild type (WT) and P51A mutant forms, along with the c-ring from thermophilic Bacillus PS3. Our data suggest that a water molecule stably binds to the P51A mutant, as well as helping to identify a bound water molecule in Bacillus PS3 whose presence was previously overlooked due to the limited resolution of the structural data. Sequence analysis further identifies a novel conserved sequence motif that is likely required to harbor a water molecule for stable ion coordination in the binding site of such proteins.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jan K Marzinek
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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8
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Novitskaia O, Buslaev P, Gushchin I. Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex. Front Mol Biosci 2019; 6:135. [PMID: 31850368 PMCID: PMC6896225 DOI: 10.3389/fmolb.2019.00135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022] Open
Abstract
Rotor ATPases are large multisubunit membrane protein complexes found in all kingdoms of life. The membrane parts of these ATPases include a ring-like assembly, so-called c-ring, consisting of several subunits c, plugged by a patch of phospholipids. In this report, we use a nature-inspired approach to model the assembly of the spinach (Spinacia oleracea) c14 ring protein-lipid complex, where partially assembled oligomers are pulled toward each other using a biasing potential. The resulting assemblies contain 23 to 26 encapsulated plug lipids, general position of which corresponds well to experimental maps. However, best fit to experimental data is achieved with 15 to 17 lipids inside the c-ring. In all of the simulations, the lipids from one leaflet (loop side of the c subunit) are ordered and static, whereas the lipids from the other leaflet are disordered and dynamic. Spontaneous permeation of water molecules toward Glu61 at the active site is also observed. The presented assembly approach is expected to be generalizable to other protein complexes with encapsulated lipid patches.
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Affiliation(s)
- Olga Novitskaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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9
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Krah A, Marzinek JK, Bond PJ. Insights into water accessible pathways and the inactivation mechanism of proton translocation by the membrane-embedded domain of V-type ATPases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1004-1010. [DOI: 10.1016/j.bbamem.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/29/2019] [Accepted: 02/27/2019] [Indexed: 01/25/2023]
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10
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Zhou W, Faraldo-Gómez JD. Membrane plasticity facilitates recognition of the inhibitor oligomycin by the mitochondrial ATP synthase rotor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:789-796. [PMID: 29630891 DOI: 10.1016/j.bbabio.2018.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/13/2018] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
Enzymes in the respiratory chain are increasingly seen as potential targets against multi-drug resistance of human pathogens and cancerous cells. However, a detailed understanding of the mechanism and specificity determinants of known inhibitors is still lacking. Oligomycin, for example, has been known to be an inhibitor of the membrane motor of the mitochondrial ATP synthase for over five decades, and yet little is known about its mode of action at the molecular level. In a recent breakthrough, a crystal structure of the S. cerevisiae c-subunit ring with bound oligomycin revealed the inhibitor docked on the outer face of the proton-binding sites, deep into the transmembrane region. However, the structure of the complex was obtained in an organic solvent rather than detergent or a lipid bilayer, and therefore it has been unclear whether this mode of recognition is physiologically relevant. Here, we use molecular dynamics simulations to address this question and gain insights into the mechanism of oligomycin inhibition. Our findings lead us to propose that oligomycin naturally partitions into the lipid/water interface, and that in this environment the inhibitor can indeed bind to any of the c-ring proton-carrying sites that are exposed to the membrane, thereby becoming an integral component of the proton-coordinating network. As the c-ring rotates within the membrane, driven either by downhill proton permeation or ATP hydrolysis, one of the protonated, oligomycin-bound sites eventually reaches the subunit-a interface and halts the rotary mechanism of the enzyme.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Room 5N307A, Bethesda, MD 20892, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Room 5N307A, Bethesda, MD 20892, United States.
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11
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Krah A, Zachariae U. Insights into the ion-coupling mechanism in the MATE transporter NorM-VC. Phys Biol 2017; 14:045009. [DOI: 10.1088/1478-3975/aa5ee7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Leone V, Faraldo-Gómez JD. Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling. J Gen Physiol 2016; 148:441-457. [PMID: 27821609 PMCID: PMC5129741 DOI: 10.1085/jgp.201611679] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/13/2016] [Indexed: 01/31/2023] Open
Abstract
The ATP synthase is a molecular rotor that recycles ADP into ATP. Leone and Faraldo-Gómez use structural modeling to reinterpret and reconcile recent cryo-EM data for its membrane domain with other experimental evidence, gaining insights into its mechanism and the mode of inhibition by oligomycin. Two subunits within the transmembrane domain of the ATP synthase—the c-ring and subunit a—energize the production of 90% of cellular ATP by transducing an electrochemical gradient of H+ or Na+ into rotational motion. The nature of this turbine-like energy conversion mechanism has been elusive for decades, owing to the lack of definitive structural information on subunit a or its c-ring interface. In a recent breakthrough, several structures of this complex were resolved by cryo–electron microscopy (cryo-EM), but the modest resolution of the data has led to divergent interpretations. Moreover, the unexpected architecture of the complex has cast doubts on a wealth of earlier biochemical analyses conducted to probe this structure. Here, we use quantitative molecular-modeling methods to derive a structure of the a–c complex that is not only objectively consistent with the cryo-EM data, but also with correlated mutation analyses of both subunits and with prior cross-linking and cysteine accessibility measurements. This systematic, integrative approach reveals unambiguously the topology of subunit a and its relationship with the c-ring. Mapping of known Cd2+ block sites and conserved protonatable residues onto the structure delineates two noncontiguous pathways across the complex, connecting two adjacent proton-binding sites in the c-ring to the space on either side of the membrane. The location of these binding sites and of a strictly conserved arginine on subunit a, which serves to prevent protons from hopping between them, explains the directionality of the rotary mechanism and its strict coupling to the proton-motive force. Additionally, mapping of mutations conferring resistance to oligomycin unexpectedly reveals that this prototypical inhibitor may bind to two distinct sites at the a–c interface, explaining its ability to block the mechanism of the enzyme irrespective of the direction of rotation of the c-ring. In summary, this study is a stepping stone toward establishing the mechanism of the ATP synthase at the atomic level.
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Affiliation(s)
- Vanessa Leone
- Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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13
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Zhou W, Leone V, Krah A, Faraldo-Gómez JD. Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases. J Phys Chem B 2016; 121:3297-3307. [PMID: 27715045 DOI: 10.1021/acs.jpcb.6b08051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent years have witnessed a renewed interest in the ATP synthase as a drug target against human pathogens. Indeed, clinical, biochemical, and structural data indicate that hydrophobic inhibitors targeting the membrane-embedded proton-binding sites of the c-subunit ring could serve as last-resort antibiotics against multidrug resistant strains. However, because inhibition of the mitochondrial ATP synthase in humans is lethal, it is essential that these inhibitors be not only potent but also highly selective for the bacterial enzyme. To this end, a detailed understanding of the structure of this protein target is arguably instrumental. Here, we use computational methods to predict the atomic structures of the proton-binding sites in two prototypical c-rings: that of the ATP synthase from Saccharomyces cerevisiae, which is a model system for mitochondrial enzymes, and that from Escherichia coli, which can be pathogenic for humans. Our study reveals the structure of these binding sites loaded with protons and in the context of the membrane, that is, in the state that would mediate the recognition of a potential inhibitor. Both structures reflect a mode of proton coordination unlike those previously observed in other c-ring structures, whether experimental or modeled.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Vanessa Leone
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Alexander Krah
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.,Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
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14
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Baptista-Hon DT, Krah A, Zachariae U, Hales TG. A role for loop G in the β1 strand in GABAA receptor activation. J Physiol 2016; 594:5555-71. [PMID: 27195487 PMCID: PMC5043033 DOI: 10.1113/jp272463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/09/2016] [Indexed: 01/18/2023] Open
Abstract
KEY POINTS The role of the β1 strand in GABAA receptor function is unclear. It lies anti-parallel to the β2 strand, which is known to participate in receptor activation. Molecular dynamics simulation revealed solvent accessible residues within the β1 strand of the GABAA β3 homopentamer that might be amenable to analysis using the substituted Cys accessibility method. Cys substitutions from Asp43 to Thr47 in the GABAA α1 subunit showed that D43C and T47C reduced the apparent potency of GABA. F45C caused a biphasic GABA concentration-response relationship and increased spontaneous gating. Cys43 and Cys47 were accessible to 2-aminoethyl methanethiosulphonate (MTSEA) modification, whereas Cys45 was not. Both GABA and the allosteric agonist propofol reduced MTSEA modification of Cys43 and Cys47. By contrast, modification of Cys64 in the β2 strand loop D was impeded by GABA but unaffected by propofol. These data reveal movement of β1 strand loop G residues during agonist activation of the GABAA receptor. ABSTRACT The GABAA receptor α subunit β1 strand runs anti-parallel to the β2 strand, which contains loop D, known to participate in receptor activation and agonist binding. However, a role for the β1 strand has yet to be established. We used molecular dynamics simulation to quantify the solvent accessible surface area (SASA) of β1 strand residues in the GABAA β3 homopentamer structure. Residues in the complementary interface equivalent to those between Asp43 and Thr47 in the α1 subunit have an alternating pattern of high and low SASA consistent with a β strand structure. We investigated the functional role of these β1 strand residues in the α1 subunit by individually replacing them with Cys residues. D43C and T47C substitutions reduced the apparent potency of GABA at α1β2γ2 receptors by 50-fold and eight-fold, respectively, whereas the F45C substitution caused a biphasic GABA concentration-response relationship and increased spontaneous gating. Receptors with D43C or T47C substitutions were sensitive to 2-aminoethyl methanethiosulphonate (MTSEA) modification. However, GABA-evoked currents mediated by α1(F45C)β2γ2 receptors were unaffected by MTSEA, suggesting that this residue is inaccessible. Both GABA and the allosteric agonist propofol reduced MTSEA modification of α1(D43C)β2γ2 and α1(T47C)β2γ2 receptors, indicating movement of the β1 strand even during allosteric activation. This is in contrast to α1(F64C)β2γ2 receptors, where only GABA, but not propofol, reduced MTSEA modification. These findings provide the first functional evidence for movement of the β1 strand during gating of the receptor and identify residues that are critical for maintaining GABAA receptor function.
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Affiliation(s)
- Daniel T Baptista-Hon
- The Institute of Academic Anaesthesia, Division of Neuroscience, School of Medicine, Ninewells Hospital, University of Dundee, Dundee, UK
| | - Alexander Krah
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tim G Hales
- The Institute of Academic Anaesthesia, Division of Neuroscience, School of Medicine, Ninewells Hospital, University of Dundee, Dundee, UK.
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15
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Pandini A, Kleinjung J, Taylor WR, Junge W, Khan S. The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance. Biophys J 2016; 109:975-87. [PMID: 26331255 PMCID: PMC4564677 DOI: 10.1016/j.bpj.2015.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/20/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022] Open
Abstract
The proton-driven ATP synthase (FOF1) is comprised of two rotary, stepping motors (FO and F1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other FO subunits (ab2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure. Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge, United Kingdom
| | - Jens Kleinjung
- Mathematical Biology, The Francis Crick Institute (formerly the National Institute for Medical Research), London, United Kingdom
| | - Willie R Taylor
- Mathematical Biology, The Francis Crick Institute (formerly the National Institute for Medical Research), London, United Kingdom
| | - Wolfgang Junge
- Department of Biophysics, University of Osnabrück, Osnabrück, Germany
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, California.
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16
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On the principle of ion selectivity in Na+/H+-coupled membrane proteins: experimental and theoretical studies of an ATP synthase rotor. Proc Natl Acad Sci U S A 2015; 112:E1057-66. [PMID: 25713346 DOI: 10.1073/pnas.1421202112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Numerous membrane transporters and enzymes couple their mechanisms to the permeation of Na(+) or H(+), thereby harnessing the energy stored in the form of transmembrane electrochemical potential gradients to sustain their activities. The molecular and environmental factors that control and modulate the ion specificity of most of these systems are, however, poorly understood. Here, we use isothermal titration calorimetry to determine the Na(+)/H(+) selectivity of the ion-driven membrane rotor of an F-type ATP synthase. Consistent with earlier theoretical predictions, we find that this rotor is significantly H(+) selective, although not sufficiently to be functionally coupled to H(+), owing to the large excess of Na(+) in physiological settings. The functional Na(+) specificity of this ATP synthase thus results from two opposing factors, namely its inherent chemical selectivity and the relative availability of the coupling ion. Further theoretical studies of this membrane rotor, and of two others with a much stronger and a slightly weaker H(+) selectivity, indicate that, although the inherent selectivity of their ion-binding sites is largely set by the balance of polar and hydrophobic groups flanking a conserved carboxylic side chain, subtle variations in their structure and conformational dynamics, for a similar chemical makeup, can also have a significant contribution. We propose that the principle of ion selectivity outlined here may provide a rationale for the differentiation of Na(+)- and H(+)-coupled systems in other families of membrane transporters and enzymes.
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17
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Matthies D, Zhou W, Klyszejko AL, Anselmi C, Yildiz Ö, Brandt K, Müller V, Faraldo-Gómez JD, Meier T. High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase. Nat Commun 2014; 5:5286. [PMID: 25381992 PMCID: PMC4228694 DOI: 10.1038/ncomms6286] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 09/16/2014] [Indexed: 01/03/2023] Open
Abstract
All rotary ATPases catalyse the interconversion of ATP and ADP-Pi through a mechanism that is coupled to the transmembrane flow of H(+) or Na(+). Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps. To begin to rationalize the molecular basis for this functional differentiation, we solved the crystal structure of the Na(+)-driven membrane rotor of the Acetobacterium woodii ATP synthase, at 2.1 Å resolution. Unlike known structures, this rotor ring is a 9:1 heteromer of F- and V-type c-subunits and therefore features a hybrid configuration of ion-binding sites along its circumference. Molecular and kinetic simulations are used to dissect the mechanisms of Na(+) recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit. These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring.
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Affiliation(s)
- Doreen Matthies
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland 20892, USA
| | - Adriana L Klyszejko
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Claudio Anselmi
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland 20892, USA
| | - Özkan Yildiz
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Karsten Brandt
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - José D Faraldo-Gómez
- 1] Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland 20892, USA [2] Cluster of Excellence Macromolecular Complexes, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Thomas Meier
- 1] Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany [2] Cluster of Excellence Macromolecular Complexes, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
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18
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Tikhonov AN. pH-dependent regulation of electron transport and ATP synthesis in chloroplasts. PHOTOSYNTHESIS RESEARCH 2013; 116:511-34. [PMID: 23695653 DOI: 10.1007/s11120-013-9845-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 04/25/2013] [Indexed: 05/02/2023]
Abstract
This review is focused on pH-dependent mechanisms of regulation of photosynthetic electron transport and ATP synthesis in chloroplasts. The light-induced acidification of the thylakoid lumen is known to decelerate the plastoquinol oxidation by the cytochrome b 6 f complex, thus impeding the electron flow between photosystem II and photosystem I. Acidification of the lumen also triggers the dissipation of excess energy in the light-harvesting antenna of photosystem II, thereby protecting the photosynthetic apparatus against a solar stress. After brief description of structural and functional organization of the chloroplast electron transport chain, our attention is focused on the nature of the rate-limiting step of electron transfer between photosystem II and photosystem I. In the context of pH-dependent mechanism of photosynthetic control in chloroplasts, the mechanisms of plastoquinol oxidation by the cytochrome b 6 f complex have been considered. The light-induced alkalization of stroma is another factor of pH-dependent regulation of electron transport in chloroplasts. Alkalization of stroma induces activation of the Bassham-Benson-Calvin cycle reactions, thereby promoting efflux of electrons from photosystem I to NADP(+). The mechanisms of the light-induced activation of ATP synthase are briefly considered.
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Affiliation(s)
- Alexander N Tikhonov
- Department of Biophysics, Faculty of Physics, M. V. Lomonosov, Moscow State University, Moscow, Russia,
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19
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The function of the Na+-driven flagellum of Vibrio cholerae is determined by osmolality and pH. J Bacteriol 2013; 195:4888-99. [PMID: 23974033 DOI: 10.1128/jb.00353-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vibrio cholerae is motile by its polar flagellum, which is driven by a Na(+)-conducting motor. The stators of the motor, composed of four PomA and two PomB subunits, provide access for Na(+) to the torque-generating unit of the motor. To characterize the Na(+) pathway formed by the PomAB complex, we studied the influence of chloride salts (chaotropic, Na(+), and K(+)) and pH on the motility of V. cholerae. Motility decreased at elevated pH but increased if a chaotropic chloride salt was added, which rules out a direct Na(+) and H(+) competition in the process of binding to the conserved PomB D23 residue. Cells expressing the PomB S26A/T or D42N variants lost motility at low Na(+) concentrations but regained motility in the presence of 170 mM chloride. Both PomA and PomB were modified by N,N'-dicyclohexylcarbodiimide (DCCD), indicating the presence of protonated carboxyl groups in the hydrophobic regions of the two proteins. Na(+) did not protect PomA and PomB from this modification. Our study shows that both osmolality and pH have an influence on the function of the flagellum from V. cholerae. We propose that D23, S26, and D42 of PomB are part of an ion-conducting pathway formed by the PomAB stator complex.
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20
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Mussel and mammalian ATP synthase share the same bioenergetic cost of ATP. J Bioenerg Biomembr 2013; 45:289-300. [PMID: 23456170 DOI: 10.1007/s10863-013-9504-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/08/2013] [Indexed: 10/27/2022]
Abstract
The molecular mechanism by which the membrane-embedded FO sector of the mitochondrial ATP synthase translocates protons, thus dissipating the transmembrane protonmotive force and leading to ATP synthesis, involves the neutralization of the carboxylate residues of the c-ring. Carboxylates are thought to constitute the binding sites for ion translocation. In order to cast light on this mechanism, we exploited N,N'-dicyclohexylcarbodiimide, which covalently binds to FO c-ring carboxylates, and ionophores which selectively modulate the transmembrane electric (Δφ) and chemical (ΔpH) gradients such as valinomycin, nigericin and dinitrophenol. ATP hydrolysis was evaluated in mitochondrial preparations and/or inside-out submitochondrial particles from mussel and mammalian tissues under different experimental conditions. The experiments pointed out striking similarities between mussel and mammalian mitochondrial ATP synthase. Our results support the hypothesis that the ATP synthase of Mytilus galloprovincialis induces intersubunit torque generation and translocates H(+) by coordinating the hydronium ion (H3O(+)) in the ion binding site of FO. Our results are consistent with the hypothesis that in mussel mitochondria the main component of the electrochemical gradient driving proton flux and ATP synthesis is Δφ. Therefore, mussel FO probably contains a small c-ring, which implies a low bioenergetic cost of making ATP as in mammals. These features which make mussel mitochondria as efficient in ATP production as mammalian ones may be especially advantageous in facultative aerobic species which intermittently exploit mitochondrial respiration to generate ATP.
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21
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Saroussi S, Schushan M, Ben-Tal N, Junge W, Nelson N. Structure and flexibility of the C-ring in the electromotor of rotary F(0)F(1)-ATPase of pea chloroplasts. PLoS One 2012; 7:e43045. [PMID: 23049735 PMCID: PMC3458034 DOI: 10.1371/journal.pone.0043045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/16/2012] [Indexed: 01/19/2023] Open
Abstract
A ring of 8-15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous F(O)F(1)-ATPase. Here we present the crystal structure at 3.4Å resolution of the c-ring from chloroplasts of a higher plant (Pisum sativum), determined using a native preparation. The crystal structure was found to resemble that of an (ancestral) cyanobacterium. Using elastic network modeling to investigate the ring's eigen-modes, we found five dominant modes of motion that fell into three classes. They revealed the following deformations of the ring: (I) ellipsoidal, (II) opposite twisting of the luminal circular surface of the ring against the stromal surface, and (III) kinking of the hairpin-shaped monomers in the middle, resulting in bending/stretching of the ring. Extension of the elastic network analysis to rings of different c(n)-symmetry revealed the same classes of dominant modes as in P. sativum (c(14)). We suggest the following functional roles for these classes: The first and third classes of modes affect the interaction of the c-ring with its counterparts in F(O), namely subunits a and bb'. These modes are likely to be involved in ion-translocation and torque generation. The second class of deformation, along with deformations of subunits γ and ε might serve to elastically buffer the torque transmission between F(O) and F(1).
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Affiliation(s)
- Shai Saroussi
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Maya Schushan
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Wolfgang Junge
- Division of Biophysics, University of Osnabrück, Osnabrück, Germany
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
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22
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Tikhonov AN. Energetic and regulatory role of proton potential in chloroplasts. BIOCHEMISTRY (MOSCOW) 2012; 77:956-74. [DOI: 10.1134/s0006297912090027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Gohlke H, Schlieper D, Groth G. Resolving the negative potential side (n-side) water-accessible proton pathway of F-type ATP synthase by molecular dynamics simulations. J Biol Chem 2012; 287:36536-43. [PMID: 22942277 DOI: 10.1074/jbc.m112.398396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The rotation of F(1)F(o)-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane F(o) domain, which is coupled to the ATP-producing F(1) domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the "locked" and "open" conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F(1)F(o)-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode.
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Affiliation(s)
- Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, 40204 Düsseldorf, Germany
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24
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Symersky J, Pagadala V, Osowski D, Krah A, Meier T, Faraldo-Gómez JD, Mueller DM. Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation. Nat Struct Mol Biol 2012; 19:485-91, S1. [PMID: 22504883 PMCID: PMC3343227 DOI: 10.1038/nsmb.2284] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/20/2012] [Indexed: 11/09/2022]
Abstract
The proton pore of the F(1)F(o) ATP synthase consists of a ring of c subunits, which rotates, driven by downhill proton diffusion across the membrane. An essential carboxylate side chain in each subunit provides a proton-binding site. In all the structures of c-rings reported to date, these sites are in a closed, ion-locked state. Structures are here presented of the c(10) ring from Saccharomyces cerevisiae determined at pH 8.3, 6.1 and 5.5, at resolutions of 2.0 Å, 2.5 Å and 2.0 Å, respectively. The overall structure of this mitochondrial c-ring is similar to known homologs, except that the essential carboxylate, Glu59, adopts an open extended conformation. Molecular dynamics simulations reveal that opening of the essential carboxylate is a consequence of the amphiphilic nature of the crystallization buffer. We propose that this new structure represents the functionally open form of the c subunit, which facilitates proton loading and release.
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Affiliation(s)
- Jindrich Symersky
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064
| | - Vijayakanth Pagadala
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064
| | - Daniel Osowski
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064
| | - Alexander Krah
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Cluster of Excellence ‘Macromolecular Complexes’, Goethe University of Frankfurt, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Cluster of Excellence ‘Macromolecular Complexes’, Goethe University of Frankfurt, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - David M. Mueller
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064
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25
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New mutations in the mycobacterial ATP synthase: new insights into the binding of the diarylquinoline TMC207 to the ATP synthase C-ring structure. Antimicrob Agents Chemother 2012; 56:2326-34. [PMID: 22354303 DOI: 10.1128/aac.06154-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TMC207 is a new antituberculous drug belonging to the diarylquinoline class which very efficiently inhibits the ATP synthase of mycobacteria such as Mycobacterium tuberculosis, one of the most important pathogens in the world. In order to map the amino acid residues involved in the binding of the drug, we have selected in vitro TMC207-resistant mutants from M. tuberculosis and diverse atypical mycobacteria. Six distinct mutations, Asp28 → Gly, Asp28 → Ala, Leu59 → Val, Glu61 → Asp, Ala63 → Pro, and Ile66 → Met, have been identified in the subunit c forming a C ring in the ATP synthase. They were studied by evaluating the levels of resistance that they confer in the selected clones and by using an isogenic complementation system in Mycobacterium smegmatis. The rates of increase of TMC207 MIC values (8- to 133-fold) were interpreted by constructing by homology modeling a structure of the mycobacterial C ring which was used for docking simulations with TMC207. Our results suggest that the residues found to be mutated in the resistant clones, together with a tyrosine specifically conserved at position 64 in mycobacteria, define a cleft located between two adjacent c subunits in the C ring. This cleft, which encompasses the proton-binding site (Glu61), is well fitted to bind TMC207 at the level of the bromoquinoline moiety, with the drug being anchored by several ionic, hydrogen, and halogen bonds with residues Glu61, Tyr64, and Asp28, respectively. These data shed light on the molecular interactions allowing TMC207 to bind specifically and efficiently at the level of the proton-binding site of the mycobacterial C ring.
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26
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Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation. Proc Natl Acad Sci U S A 2012; 109:947-52. [PMID: 22219361 DOI: 10.1073/pnas.1115796109] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP synthases are the primary source of ATP in all living cells. To catalyze ATP synthesis, these membrane-associated complexes use a rotary mechanism powered by the transmembrane diffusion of ions down a concentration gradient. ATP synthases are assumed to be driven either by H(+) or Na(+), reflecting distinct structural motifs in their membrane domains, and distinct metabolisms of the host organisms. Here, we study the methanogenic archaeon Methanosarcina acetivorans using assays of ATP hydrolysis and ion transport in inverted membrane vesicles, and experimentally demonstrate that the rotary mechanism of its ATP synthase is coupled to the concurrent translocation of both H(+) and Na(+) across the membrane under physiological conditions. Using free-energy molecular simulations, we explain this unprecedented observation in terms of the ion selectivity of the binding sites in the membrane rotor, which appears to have been tuned via amino acid substitutions so that ATP synthesis in M. acetivorans can be driven by the H(+) and Na(+) gradients resulting from methanogenesis. We propose that this promiscuity is a molecular mechanism of adaptation to life at the thermodynamic limit.
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27
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Faraldo-Gómez JD, Forrest LR. Modeling and simulation of ion-coupled and ATP-driven membrane proteins. Curr Opin Struct Biol 2011; 21:173-9. [PMID: 21333528 DOI: 10.1016/j.sbi.2011.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 01/18/2011] [Accepted: 01/27/2011] [Indexed: 01/07/2023]
Abstract
The molecular mechanisms of membrane proteins that are activated either by ions or by ATP are just beginning to come into focus, as long-awaited structural data are revealed. This information is being leveraged and supplemented to great effect by molecular modeling and computer simulation studies. Important examples include the homology modeling of eukaryotic protein structures based on distantly related templates, as well as the use of internal structural symmetry for modeling different states in conformational cycles. Molecular simulation studies have elucidated the location and coordination structure of ion binding sites, and explained their selectivity, while also providing tantalizing insights into the mechanisms that couple conformational change to ion translocation or ATP hydrolysis.
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Affiliation(s)
- José D Faraldo-Gómez
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue-Str 3, 60438 Frankfurt am Main, Germany
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28
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Leone V, Krah A, Faraldo-Gómez JD. On the question of hydronium binding to ATP-synthase membrane rotors. Biophys J 2011; 99:L53-5. [PMID: 20923632 DOI: 10.1016/j.bpj.2010.07.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 07/17/2010] [Accepted: 07/21/2010] [Indexed: 10/19/2022] Open
Abstract
A recently determined atomic structure of an H(+)-coupled ATP-synthase membrane rotor has revived the long-standing question of whether protons may be bound to these structures in the form of a hydronium ion. Using both classical and quantum-mechanical simulations, we show that this notion is implausible. Ab initio molecular dynamics simulations of the binding site demonstrate that the putative H(3)O(+) deprotonates within femtoseconds. The bound proton is thus transferred irreversibly to the carboxylate side chain found in the ion-binding sites of all ATP-synthase rotors. This result is consistent with classical simulations of the rotor in a phospholipid membrane, on the 100-nanosecond timescale. These simulations show that the hydrogen-bond network seen in the crystal structure is incompatible with a bound hydronium. The observed coordination geometry is shown to correspond instead to a protonated carboxylate and a bound water molecule. In conclusion, this study underscores the notion that binding and transient storage of protons in the membrane rotors of ATP synthases occur through a common chemical mechanism, namely carboxylate protonation.
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Pogoryelov D, Krah A, Langer JD, Yildiz Ö, Faraldo-Gómez JD, Meier T. Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases. Nat Chem Biol 2010; 6:891-9. [DOI: 10.1038/nchembio.457] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 09/15/2010] [Indexed: 01/31/2023]
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Dong H, Fillingame RH. Chemical reactivities of cysteine substitutions in subunit a of ATP synthase define residues gating H+ transport from each side of the membrane. J Biol Chem 2010; 285:39811-8. [PMID: 20943664 DOI: 10.1074/jbc.m110.175844] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subunit a plays a key role in coupling H(+) transport to rotations of the subunit c-ring in F(1)F(o) ATP synthase. In Escherichia coli, H(+) binding and release occur at Asp-61 in the middle of the second transmembrane helix (TMH) of F(o) subunit c. Based upon the Ag(+) sensitivity of Cys substituted into subunit a, H(+) are thought to reach Asp-61 via aqueous pathways mapping to surfaces of TMH 2-5. In this study we have extended characterization of the most Ag(+)-sensitive residues in subunit a with cysteine reactive methanethiosulfonate (MTS) reagents and Cd(2+). The effect of these reagents on ATPase-coupled H(+) transport was measured using inside-out membrane vesicles. Cd(2+) inhibited the activity of all Ag(+)-sensitive Cys on the cytoplasmic side of the TMHs, and three of these substitutions were also sensitive to inhibition by MTS reagents. On the other hand, Cd(2+) did not inhibit the activities of substitutions at residues 119 and 120 on the periplasmic side of TMH2, and residues 214 and 215 in TMH4 and 252 in TMH5 at the center of the membrane. When inside-out membrane vesicles from each of these substitutions were sonicated during Cd(2+) treatment to expose the periplasmic surface, the ATPase-coupled H(+) transport activity was strongly inhibited. The periplasmic access to N214C and Q252C, and their positioning in the protein at the a-c interface, is consistent with previous proposals that these residues may be involved in gating H(+) access from the periplasmic half-channel to Asp-61 during the protonation step.
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Affiliation(s)
- Hui Dong
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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Preiss L, Yildiz Ö, Hicks DB, Krulwich TA, Meier T. A new type of proton coordination in an F(1)F(o)-ATP synthase rotor ring. PLoS Biol 2010; 8:e1000443. [PMID: 20689804 PMCID: PMC2914638 DOI: 10.1371/journal.pbio.1000443] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 06/24/2010] [Indexed: 11/26/2022] Open
Abstract
The high-resolution structure of the rotor ring from alkaliphilic Bacillus pseudofirmus OF4 reveals a new type of ion binding in F1Fo-ATP synthases. We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 Å, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle. Like the wind turbines that generate electricity, the F1Fo-ATP synthases are natural “ion turbines” each made up of a stator and a rotor that turns, when driven by a flow of ions, to generate the cell's energy supply of ATP. The Fo motor rotates by reversible binding and release of coupling ions that flow down the electrochemical ion gradient across the cytoplasmic cell membrane (in the case of bacteria) or intracellular organelle membranes (in the case of eukaryotic cells). Here, we present the structure of a rotor (c-)ring from a Bacillus species (B. pseudofirmus OF4) determined at high-resolution by X-ray crystallography. This bacterium prefers alkaline environments where the concentration of protons (H+) is lower outside than inside the cell – the inverse of the situation usually found in organisms that prefer neutral or acidic environments. The amino acid sequence of the protein subunits in this rotor, nevertheless, has features common to an important group of ATP synthases in organisms from bacteria to man. The structure reveals a new type of ion binding in which a protonated glutamate residue in the protein associates with a water molecule. This finding raises the possibility considered by Nobel laureate Paul Boyer several decades ago that a hydronium ion (a protonated water molecule, H3O+), rather than a proton alone, might be the coupling species that energizes ATP synthesis. Also, it demonstrates the finely tuned adaptation of ATP synthase rotor rings and their ion-binding sites to the specific requirements of different organisms.
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Affiliation(s)
- Laura Preiss
- Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt, Germany
| | - Özkan Yildiz
- Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt, Germany
| | - David B. Hicks
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Terry A. Krulwich
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Thomas Meier
- Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt, Germany
- Cluster of Excellence Macromolecular Complexes, Max-Planck Institute of Biophysics, Frankfurt, Germany
- * E-mail:
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Krah A, Pogoryelov D, Langer JD, Bond PJ, Meier T, Faraldo-Gómez JD. Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:763-72. [DOI: 10.1016/j.bbabio.2010.04.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 10/19/2022]
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F1F0-ATP synthases of alkaliphilic bacteria: lessons from their adaptations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1362-77. [PMID: 20193659 DOI: 10.1016/j.bbabio.2010.02.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 12/14/2022]
Abstract
This review focuses on the ATP synthases of alkaliphilic bacteria and, in particular, those that successfully overcome the bioenergetic challenges of achieving robust H+-coupled ATP synthesis at external pH values>10. At such pH values the protonmotive force, which is posited to provide the energetic driving force for ATP synthesis, is too low to account for the ATP synthesis observed. The protonmotive force is lowered at a very high pH by the need to maintain a cytoplasmic pH well below the pH outside, which results in an energetically adverse pH gradient. Several anticipated solutions to this bioenergetic conundrum have been ruled out. Although the transmembrane sodium motive force is high under alkaline conditions, respiratory alkaliphilic bacteria do not use Na+- instead of H+-coupled ATP synthases. Nor do they offset the adverse pH gradient with a compensatory increase in the transmembrane electrical potential component of the protonmotive force. Moreover, studies of ATP synthase rotors indicate that alkaliphiles cannot fully resolve the energetic problem by using an ATP synthase with a large number of c-subunits in the synthase rotor ring. Increased attention now focuses on delocalized gradients near the membrane surface and H+ transfers to ATP synthases via membrane-associated microcircuits between the H+ pumping complexes and synthases. Microcircuits likely depend upon proximity of pumps and synthases, specific membrane properties and specific adaptations of the participating enzyme complexes. ATP synthesis in alkaliphiles depends upon alkaliphile-specific adaptations of the ATP synthase and there is also evidence for alkaliphile-specific adaptations of respiratory chain components.
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