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J Biol Inorg Chem. 2018 Dec;23(8):1309-1330. doi: 10.1007/s00775-018-1616-y. Epub 2018 Sep 27.

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

Author information

1
JSC Spronk, Vilnius, Lithuania.
2
Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.
3
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
4
Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
5
Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
6
Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
7
Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.
8
Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.
9
Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
10
Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA. mmaroney@chem.umass.edu.
11
Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. stefano.ciurli@unibo.it.
12
Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy. stefano.ciurli@unibo.it.

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.

KEYWORDS:

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

PMID:
30264175
PMCID:
PMC6733409
DOI:
10.1007/s00775-018-1616-y
[Indexed for MEDLINE]
Free PMC Article

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