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On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies

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Abstract

Helicobacter pylori (Hp) is a carcinogen that relies on Ni(II) to survive in the extreme pH conditions of the human guts. The regulation of genes coding for Ni(II) enzymes and proteins is effected by the nickel-responsive transcription factor NikR, composed of a DNA-binding domain (DBD) and a metal-binding domain (MBD). The scope of this study is to obtain the molecular details of the HpNikR interaction with the urease operator OP ureA , in solution. The size of the full-length protein prevents the characterization of the HpNikR–OP ureA interaction using NMR. We thus investigated the two separate domains of HpNikR. The conservation of their oligomeric state was established by multiple-angle light scattering. Isothermal calorimetric titrations indicated that the thermodynamics of Ni(II) binding to the isolated MBD is independent of the presence of the adjacent DBDs. The NMR spectra of the isolated DBD support considerable conservation of its structural properties. The spectral perturbations induced on the DBD by OP ureA provided information useful to calculate a structural model of the HpNikR–OP ureA complex using a docking computational protocol. The NMR assignment of the residues involved in the protein–DNA interaction represents a starting point for the development of drugs potentially able to eradicate H. pylori infections. All evidences so far collected, in this and previous studies, consistently indicate that binding of Ni(II) to the MBD increases the HpNikR–DNA affinity by modulating the dynamic, and not the structural, properties of the protein, suggesting that the formation of a stable complex relies upon an induced fit mechanism.

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Abbreviations

AIC:

Akaike’s Information Criteria

CSP:

Chemical shift perturbations

DBD:

DNA-binding domain

Ec :

Escherichia coli

Hp :

Helicobacter pylori

MALS:

Multiple-angle light scattering

MDB:

Metal-binding domain

NMR:

Nuclear magnetic resonance

Ph :

Pyrococcus horikoshii

SAXS:

Small-angle X-ray scattering

SEC:

Size-exclusion chromatography

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Acknowledgments

CERM (Center for Magnetic Resonance, University of Florence) is acknowledged for granting access to the NMR facility. Massimo Lucci and Fabio Calogiuri from CERM are acknowledged for data collection and useful discussions. Research supported by the University of Bologna through the FARB Program (Finanziamenti dell’Alma Mater Studiorum alla Ricerca di Base) “Modulation of protein-DNA interactions with small molecules: novel opportunities for drug design”. L. M., O. D. and F. M. were supported by fellowships from CIRMMP (Consorzio Interuniversitario di Risonanze Magnetiche di Metallo-Proteine).

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  1. Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40127, Italy

    Luca Mazzei, Olena Dobrovolska, Francesco Musiani, Barbara Zambelli & Stefano Ciurli

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  1. Luca Mazzei
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Correspondence to Stefano Ciurli.

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Mazzei, L., Dobrovolska, O., Musiani, F. et al. On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies. J Biol Inorg Chem 20, 1021–1037 (2015). https://doi.org/10.1007/s00775-015-1284-0

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