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

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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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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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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Keywords

  • Metallochaperones
  • Metal transport
  • Molecular dynamics
  • Nuclear magnetic resonance
  • Computational chemistry
  • Nickel