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PMID: 24557135 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Ion mobility-mass spectrometry of a rotary ATPase reveals ATP-induced reduction in conformational flexibility.

Nature chemistry ·Vol. 6 ·No. 3 ·2014-03-00 ·Pages 208-215

Zhou M, Politis A, Davies R, Liko I, Wu KJ, Stewart AG, Stock D, Robinson CV

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.

MeSH Terms
Adenosine Triphosphatases/chemistry,metabolism Ions/chemistry Mass Spectrometry Models, Molecular Molecular Conformation Nucleotides
Chemicals
Ions Nucleotides Adenosine Triphosphatases
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Zhou Min
Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
Politis Argyris
Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
Davies Roberta
The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia. | The University of New South Wales, Sydney NSW 2052, Australia.
Liko Idlir
Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
Wu Kuan-Jung
Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
Stewart Alastair G
The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia. | The University of New South Wales, Sydney NSW 2052, Australia.
Stock Daniela
The Victor Chang Cardiac Research Institute, Darlinghurst NSW 2010, Australia. | The University of New South Wales, Sydney NSW 2052, Australia.
Robinson Carol V
Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
References (46)
46 references, click to expand
  1. GROMACS: fast, flexible, and free.
    J Comput Chem. 2005 Dec;26(16):1701-18 PMID: 16211538
  2. Intrinsically disordered p53 and its complexes populate compact conformations in the gas phase.
    Angew Chem Int Ed Engl. 2013 Jan 2;52(1):361-5 PMID: 22777995
  3. Human islet amyloid polypeptide monomers form ordered beta-hairpins: a possible direct amyloidogenic precursor.
    J Am Chem Soc. 2009 Dec 30;131(51):18283-92 PMID: 19950949
  4. The contents of adenine nucleotides, phosphagens and some glycolytic intermediates in resting muscles from vertebrates and invertebrates.
    Biochem J. 1975 Oct;152(1):23-32 PMID: 1212224
  5. Structural analysis of the stalk subunit Vma5p of the yeast V-ATPase in solution.
    FEBS Lett. 2004 Jul 16;570(1-3):119-25 PMID: 15251451
  6. Conformational stability of Syrian hamster prion protein PrP(90-231).
    J Am Chem Soc. 2010 Jul 7;132(26):8816-8 PMID: 20536231
  7. T-wave ion mobility-mass spectrometry: basic experimental procedures for protein complex analysis.
    J Vis Exp. 2010 Jul 31;(41): PMID: 20729801
  8. Detergent release prolongs the lifetime of native-like membrane protein conformations in the gas-phase.
    J Am Chem Soc. 2013 Apr 24;135(16):6078-83 PMID: 23521660
  9. Regulatory interplay between proton motive force, ADP, phosphate, and subunit epsilon in bacterial ATP synthase.
    J Biol Chem. 2007 Jan 5;282(1):764-72 PMID: 17092944
  10. Ion mobility-mass spectrometry reveals a conformational conversion from random assembly to β-sheet in amyloid fibril formation.
    Nat Chem. 2011 Feb;3(2):172-7 PMID: 21258392
  11. Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.
    Nature. 2011 Dec 18;481(7380):214-8 PMID: 22178924
  12. Unique rotary ATP synthase and its biological diversity.
    Annu Rev Biophys. 2008;37:43-64 PMID: 18573072
  13. Crystal structure of the yeast vacuolar ATPase heterotrimeric EGC(head) peripheral stalk complex.
    Structure. 2012 Nov 7;20(11):1881-92 PMID: 23000382
  14. Origin of asymmetry at the intersubunit interfaces of V1-ATPase from Thermus thermophilus.
    J Mol Biol. 2013 Aug 9;425(15):2699-708 PMID: 23639357
  15. Three-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.
    Structure. 2004 Oct;12(10):1789-98 PMID: 15458628
  16. Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilus.
    Microscopy (Oxf). 2013 Aug;62(4):467-74 PMID: 23572213
  17. Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry.
    Nat Protoc. 2007;2(3):715-26 PMID: 17406634
  18. Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding.
    Science. 2011 Oct 21;334(6054):380-385 PMID: 22021858
  19. Ion mobility mass spectrometry of two tetrameric membrane protein complexes reveals compact structures and differences in stability and packing.
    J Am Chem Soc. 2010 Nov 10;132(44):15468-70 PMID: 20949939
  20. ATP hydrolysis and synthesis of a rotary motor V-ATPase from Thermus thermophilus.
    J Biol Chem. 2008 Jul 25;283(30):20789-96 PMID: 18492667
  21. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W610-4 PMID: 15215461
  22. The role of lipids in defining membrane protein interactions: insights from mass spectrometry.
    Trends Cell Biol. 2013 Jan;23(1):1-8 PMID: 22980035
  23. Micelles protect membrane complexes from solution to vacuum.
    Science. 2008 Jul 11;321(5886):243-6 PMID: 18556516
  24. Rotary ATPases: models, machine elements and technical specifications.
    Bioarchitecture. 2013 Jan-Feb;3(1):2-12 PMID: 23369889
  25. Structural modeling of heteromeric protein complexes from disassembly pathways and ion mobility-mass spectrometry.
    Structure. 2012 Sep 5;20(9):1596-609 PMID: 22841294
  26. Relationship between growth rate and ATP concentration in Escherichia coli: a bioassay for available cellular ATP.
    J Biol Chem. 2004 Feb 27;279(9):8262-8 PMID: 14670952
  27. Mass spectrometry--from peripheral proteins to membrane motors.
    J Mol Biol. 2012 Oct 12;423(1):1-13 PMID: 22750574
  28. Crystal structure of yeast V-ATPase subunit C reveals its stator function.
    EMBO Rep. 2004 Dec;5(12):1148-52 PMID: 15540116
  29. The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase.
    Nat Struct Mol Biol. 2010 Mar;17(3):373-8 PMID: 20173764
  30. A rotary molecular motor that can work at near 100% efficiency.
    Philos Trans R Soc Lond B Biol Sci. 2000 Apr 29;355(1396):473-89 PMID: 10836501
  31. Subunit arrangement in V-ATPase from Thermus thermophilus.
    J Biol Chem. 2003 Oct 24;278(43):42686-91 PMID: 12913005
  32. Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
    Nature. 2013 Jan 31;493(7434):703-7 PMID: 23334411
  33. Charge-state dependent compaction and dissociation of protein complexes: insights from ion mobility and molecular dynamics.
    J Am Chem Soc. 2012 Feb 22;134(7):3429-38 PMID: 22280183
  34. Determining the architectures of macromolecular assemblies.
    Nature. 2007 Nov 29;450(7170):683-94 PMID: 18046405
  35. Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions.
    Nat Methods. 2009 Aug;6(8):585-7 PMID: 19578383
  36. Enhancements in travelling wave ion mobility resolution.
    Rapid Commun Mass Spectrom. 2011 Jun 15;25(11):1559-66 PMID: 21594930
  37. Applications of a travelling wave-based radio-frequency-only stacked ring ion guide.
    Rapid Commun Mass Spectrom. 2004;18(20):2401-14 PMID: 15386629
  38. Characterizing the resolution and accuracy of a second-generation traveling-wave ion mobility separator for biomolecular ions.
    Analyst. 2011 Sep 7;136(17):3534-41 PMID: 21445388
  39. Fundamentals of traveling wave ion mobility spectrometry.
    Anal Chem. 2008 Dec 15;80(24):9689-99 PMID: 18986171
  40. Purification of molecular machines and nanomotors using phage-derived monoclonal antibody fragments.
    Methods Mol Biol. 2013;996:203-17 PMID: 23504426
  41. Structural divergence of the rotary ATPases.
    Q Rev Biophys. 2011 Aug;44(3):311-56 PMID: 21426606
  42. The dynamic stator stalk of rotary ATPases.
    Nat Commun. 2012 Feb 21;3:687 PMID: 22353718
  43. Evidence for major structural changes in subunit C of the vacuolar ATPase due to nucleotide binding.
    FEBS Lett. 2005 Mar 28;579(9):1961-7 PMID: 15792803
  44. Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology.
    Anal Chem. 2010 Nov 15;82(22):9557-65 PMID: 20979392
  45. Biomolecule analysis by ion mobility spectrometry.
    Annu Rev Anal Chem (Palo Alto Calif). 2008;1:293-327 PMID: 20636082
  46. Ion mobility-mass spectrometry analysis of large protein complexes.
    Nat Protoc. 2008;3(7):1139-52 PMID: 18600219
Article Info
Journal
Nature chemistry
Abbr.
Nat Chem
ISSN
1755-4349
DOI
10.1038/nchem.1868
Published
2014-03-00
Epub
2014-00-16
Pages
208-215
Language
English
Region
England
NLM ID
101499734
PMCID
PMC4067995
Subset
IM
Grants
Wellcome Trust · 088150 · United Kingdom
Corrections
CommentIn
PMID: 24557126
External Links
PubMed source DOI: 10.1038/nchem.1868 PMC Full Text View journal details
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