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Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools

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JBIC Journal of Biological Inorganic Chemistry Aims and scope

Abstract

Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3–7.2 range. The structure of the Ni(II) binding site was probed using 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.

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References

  1. Testerman TL, Morris J (2014) World J Gastroenterol 20:12781–12808

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Gobert AP, Wilson KT (2016) Trends Microbiol 24:366–376

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Eusebi LH, Zagari RM, Bazzoli F (2014) Helicobacter 19(Suppl 1):1–5

    PubMed  Google Scholar 

  4. IARC helicobacter pylori Working Group (2014) Helicobacter pylori eradication as a strategy for preventing gastric cancer. International Agency for Research on Cancer (IARC Working Group Reports, No. 8). Lyon, France. Available from: http://www.iarc.fr/en/publications/pdfsonline/wrk/wrk8/index.php

  5. Stathis A, Bertoni F, Zucca E (2010) Expert Opin Pharmacother 11:2141–2152

    CAS  PubMed  Google Scholar 

  6. World health organization (WHO) (2017) Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics

  7. Zambelli B, Ciurli S (2013) Met Ions Life Sci 13:321–357

    PubMed  Google Scholar 

  8. Zambelli B, Musiani F, Benini S, Ciurli S (2011) Acc Chem Res 44:520–530

    CAS  PubMed  Google Scholar 

  9. Kusters JG, van Vliet AH, Kuipers EJ (2006) Clin Microbiol Rev 19:449–490

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Yamaoka Y (2010) Nat Rev Gastro Hepat 7:629–641

    CAS  Google Scholar 

  11. Bauerfeind P, Garner R, Dunn BE, Mobley HLT (1997) Gut 40:25–30

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Maroney MJ, Ciurli S (2014) Chem Rev 114:4206–4228

    CAS  PubMed  Google Scholar 

  13. Eaton KA, Brooks CL, Morgan DR, Krakowka S (1991) Infect Immun 59:2470–2475

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Eaton KA, Krakowka S (1994) Infect Immun 62:3604–3607

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Campanale M, Nucera E, Ojetti V, Cesario V, Di Rienzo TA, D’Angelo G, Pecere S, Barbaro F, Gigante G, De Pasquale T, Rizzi A, Cammarota G, Schiavino D, Franceschi F, Gasbarrini A (2014) Dig Dis Sci 59:1851–1855

    CAS  PubMed  Google Scholar 

  16. Mazzei L, Musiani F, Ciurli S (2017) In: Zamble D, Rowińska-Żyrek M, Kozłowski H (eds) The biological chemistry of nickel. Royal Society of Chemistry, pp 60–97

  17. Pedroso MM, Ely F, Carpenter MC, Mitić NN, Gahan LR, Ollis DL, Wilcox DE, Schenk GG (2017) Biochemistry 56:3328–3336

    CAS  PubMed  Google Scholar 

  18. Fong YH, Wong HC, Yuen MH, Lau PH, Chen YW, Wong KB (2013) PLoS Biol 11:e1001678

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Farrugia MA, Macomber L, Hausinger RP (2013) J Biol Chem 288:13178–13185

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Banaszak K, Martin-Diaconescu V, Bellucci M, Zambelli B, Rypniewski W, Maroney MJ, Ciurli S (2012) Biochem J 441:1017–1026

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Mehta N, Olson JW, Maier RJ (2003) J Bacteriol 185:726–734

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Casalot L, Rousset M (2001) Trends Microbiol 9:228–237

    CAS  PubMed  Google Scholar 

  23. Blum FC, Hu HQ, Servetas SL, Benoit SL, Maier RJ, Maroney MJ, Merrell DS (2017) PLoS One 12:e0183260

    PubMed  PubMed Central  Google Scholar 

  24. Hu HQ, Huang HT, Maroney MJ (2018) Biochemistry 57:2932–2942

    CAS  PubMed  Google Scholar 

  25. Yang X, Li H, Cheng T, Xia W, Lai YT, Sun H (2014) Metallomics 6:1731–1736

    CAS  PubMed  Google Scholar 

  26. Olson JW, Mehta NS, Maier RJ (2001) Mol Microbiol 39:176–182

    CAS  PubMed  Google Scholar 

  27. Hu HQ, Johnson RC, Merrell DS, Maroney MJ (2017) Biochemistry 56:1105–1116

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Johnson RC, Hu HQ, Merrell DS, Maroney MJ (2015) Metallomics 7:674–682

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Kennedy DC, Herbst RW, Iwig JS, Chivers PT, Maroney MJ (2007) J Am Chem Soc 129:16–17

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Herbst RW, Perovic I, Martin-Diaconescu V, O’Brien K, Chivers PT, Pochapsky SS, Pochapsky TC, Maroney MJ (2010) J Am Chem Soc 132:10338–10351

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Xia W, Li H, Sze K-H, Sun H (2009) J Am Chem Soc 131:10031–10040

    CAS  PubMed  Google Scholar 

  32. Watanabe S, Arai T, Matsumi R, Atomi H, Imanaka T, Miki K (2009) J Mol Biol 394:448–459

    CAS  PubMed  Google Scholar 

  33. Watanabe S, Kawashima T, Nishitani Y, Kanai T, Wada T, Inaba K, Atomi H, Imanaka T, Miki K (2015) Proc Natl Acad Sci USA 112:7701–7706

    CAS  PubMed  Google Scholar 

  34. Kwon S, Watanabe S, Nishitani Y, Kawashima T, Kanai T, Atomi H, Miki K (2018) Proc Natl Acad Sci USA 115:7045–7050

    CAS  PubMed  Google Scholar 

  35. Stingl K, De Reuse H (2005) Int J Med Microbiol 295:307–315

    CAS  PubMed  Google Scholar 

  36. Sachs G, Weeks DL, Wen Y, Marcus EA, Scott DR, Melchers K (2005) Physiology 20:429–438

    CAS  PubMed  Google Scholar 

  37. Scott DR, Marcus EA, Weeks DL, Sachs G (2002) Gastroenterology 123:187–195

    CAS  PubMed  Google Scholar 

  38. Wen Y, Marcus EA, Matrubutham U, Gleeson MA, Scott DR, Sachs G (2003) Infect Immun 71:5921–5939

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Jones MD, Li Y, Zamble DB (2018) Proc Nat Acad Sci USA 115(36):8966–8971

    CAS  PubMed  Google Scholar 

  40. Stola M, Musiani F, Mangani S, Turano P, Safarov N, Zambelli B, Ciurli S (2006) Biochemistry 45:6495–6509

    CAS  PubMed  Google Scholar 

  41. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) J Biomol NMR 6:277–293

    CAS  PubMed  Google Scholar 

  42. Keller RLJ (2004) Swiss Federal Institute of Technology, Zurich

  43. Stanek J, Augustyniak R, Kozminski W (2012) J Magn Reson 214:91–102

    CAS  PubMed  Google Scholar 

  44. Goddard TD, Kneller DG (2000) University of California, San Francisco

  45. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) J Biomol NMR 44:213–223

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M (2007) Bioinformatics 23:381–382

    CAS  Google Scholar 

  47. Krieger E, Vriend G (2014) Bioinformatics 30:2981–2982

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Herrmann T, Güntert P, Wüthrich K (2002) J Mol Biol 319:209–227

    CAS  PubMed  Google Scholar 

  49. Nilges M, Bernard A, Bardiaux B, Malliavin TE, Habeck M, Rieping W (2008) Structure 16:1305–1312

    CAS  PubMed  Google Scholar 

  50. Mareuil F, Malliavin TE, Nilges M, Bardiaux B (2015) J Biomol NMR 62:425–438

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K (2009) Proteins 77:114–122

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089–10092

    CAS  Google Scholar 

  53. Vriend G (1990) J Mol Graph 8:52–56

    CAS  PubMed  Google Scholar 

  54. Koradi R, Billeter M, Wuthrich K (1996) J Mol Graph 14:51–55

    CAS  PubMed  Google Scholar 

  55. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) J Comput Chem 25:1605–1612

    CAS  PubMed  Google Scholar 

  56. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A (2005) Nucleic Acids Res 33:W368–W371

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Myers J, Grothaus G, Narayanan S, Onufriev A (2006) Proteins 63:928–938

    CAS  PubMed  Google Scholar 

  58. Anandakrishnan R, Aguilar B, Onufriev AV (2012) Nucleic Acids Res 40:W537–W541

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Proteins 65:712–725

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Jorgensen WL, Chandrasekhar L, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935

    CAS  Google Scholar 

  61. Peters MB, Yang Y, Wang B, Fusti-Molnar L, Weaver MN, Merz KM Jr (2010) J Chem Theory Comput 6:2935–2947

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Berendsen HJC, van der Spoel D, van Drunen R (1995) Comput Phys Commun 91:43–56

    CAS  Google Scholar 

  63. Lindahl E, Hess B, van der Spoel D (2001) J Mol Model 7:306–317

    CAS  Google Scholar 

  64. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) J Comput Chem 26:1701–1718

    Google Scholar 

  65. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) J Chem Phys 81:3684–3690

    CAS  Google Scholar 

  66. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103:8577–8593

    CAS  Google Scholar 

  67. Hoover WG (1985) Phys Rev A 31:1695–1697

    CAS  Google Scholar 

  68. Nosé S (2002) Mol Phys 100:191–198

    Google Scholar 

  69. Nosé S, Klein ML (1983) Mol Phys 50:1055–1076

    Google Scholar 

  70. Parrinello M, Rahman A (1981) J Appl Phys 52:7182–7190

    CAS  Google Scholar 

  71. Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE (1999) Angew Chem 38:236–240

    CAS  Google Scholar 

  72. Horton RM, Ho SN, Pullen JK, Hunt HD, Cai Z, Pease LR (1993) Methods Enzymol 217:270–279

    CAS  PubMed  Google Scholar 

  73. Williamson MP (2013) Prog Nucl Magn Reson Spectrosc 73:1–16

    CAS  PubMed  Google Scholar 

  74. Piccioli M, Turano P (2015) Coord Chem Rev 284:313–328

    CAS  Google Scholar 

  75. Banci L, Bertini I, Luchinat C, Piccioli M, Scozzafava A, Turano P (1989) Inorg Chem 28:4650–4656

    CAS  Google Scholar 

  76. Bertini I, Capozzi F, Ciurli S, Luchinat C, Messori L, Piccioli M (1992) J Am Chem Soc 114:3332–3340

    CAS  Google Scholar 

  77. Neese F (2012) Wiley Interdiscip Rev Comput Mol Sci 2:73–78

    CAS  Google Scholar 

  78. Becke AD (1993) J Chem Phys 98:1372–1377

    CAS  Google Scholar 

  79. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789

    CAS  Google Scholar 

  80. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd J, Brothers EN, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian Inc., Wallingford

  81. Frisch MJ, Pople JA (1984) J Chem Phys 80:3265

    CAS  Google Scholar 

  82. Hay PJ, Wadt WR (1985) J Chem Phys 82:299–310

    CAS  Google Scholar 

  83. Ponzoni L, Polles G, Carnevale V, Micheletti C (2015) Structure 23:1516–1525

    CAS  PubMed  Google Scholar 

  84. Sharma D, Rajarathnam K (2000) J Biomol NMR 18:165–171

    CAS  PubMed  Google Scholar 

  85. Allegrozzi M, Bertini I, Janik MBL, Lee Y-M, Liu G, Luchinat C (2000) J Am Chem Soc 122:4154–4161

    CAS  Google Scholar 

  86. Banci L, Piccioli M (1996) Encyclopedia of magnetic resonance. pp 1365–1378

  87. Ming LJ, Banci L, Luchinat C, Bertini I, Valentine JS (1988) Inorg Chem 27:4458–4463

    CAS  Google Scholar 

  88. Bertini I, Donaire A, Monnanni R, Moratal J-M, Salgado J (1992) J Chem Soc Dalton Trans. https://doi.org/10.1039/DT9920001443:1443-1447

    Article  Google Scholar 

  89. Donaire A, Salgado J, Moratal JM (1998) Biochemistry 37:8659–8673

    CAS  PubMed  Google Scholar 

  90. Rossi P, Swapna GVT, Huang YJ, Aramini JM, Anklin C, Conover K, Hamilton K, Xiao R, Acton T, Ertekin A, Everett JK, Montelione GT (2010) J Biomol NMR 46:11–22

    CAS  PubMed  Google Scholar 

  91. Bertini I, Luchinat C (1986) NMR of paramagnetic molecules in biological systems. Benjamin-Cummings, Menlo Park

    Google Scholar 

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Acknowledgements

This work was supported by a grant from the Polish National Science Centre (MAESTRO—2015/18/A/ST4/00270 to MG, SZ, WK), by a grant from the U.S. National Institutes of Health (NIH—R01-GM069696 to MJM), by the Institut Pasteur, CNRS and the French Institute of Bioinformatics (IFB; ANR-11-INBS-0013, to BB), by the European Cooperation in Science and Technology (COST) Action 15133 (MP), and by the Department of Pharmacy and Biotechnology of the University of Bologna (SC, BZ, FM). The NMR experiments were partially obtained in the frames of access to NMR infrastructure by EuroBioNMR EEIG (http://www.eurobionmr.eu/). The Center for Magnetic Resonance of the University of Florence (CERM) provided access to the high-field NMR spectrometers, and Fabio Calogiuri is acknowledged for spectra data collection.

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Authors and Affiliations

  1. JSC Spronk, Vilnius, Lithuania

    Chris A. E. M. Spronk

  2. Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK

    Chris A. E. M. Spronk

  3. Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland

    Szymon Żerko, Michał Górka & Wiktor Koźmiński

  4. Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland

    Michał Górka

  5. Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France

    Benjamin Bardiaux

  6. Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy

    Barbara Zambelli, Francesco Musiani & Stefano Ciurli

  7. Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy

    Mario Piccioli & Stefano Ciurli

  8. Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA

    Heidi Hu & Michael Maroney

  9. Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA

    Faith C. Blum, Ryan C. Johnson & D. Scott Merrell

  10. Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA

    Priyanka Basak

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  1. Chris A. E. M. Spronk
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Correspondence to Michael Maroney or Stefano Ciurli.

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Chris Spronk passed away on February 28, 2018. This paper is dedicated to his memory.

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Spronk, C.A.E.M., Żerko, S., Górka, M. et al. Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. J Biol Inorg Chem 23, 1309–1330 (2018). https://doi.org/10.1007/s00775-018-1616-y

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