期刊
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
卷 20, 期 6, 页码 1021-1037出版社
SPRINGER
DOI: 10.1007/s00775-015-1284-0
关键词
Binding affinity; Calorimetry; Computational chemistry; Ligand binding; Nuclear magnetic resonance
资金
- University of Bologna through the FARB Program (Finanziamenti dell'Alma Mater Studiorum alla Ricerca di Base)
- CIRMMP (Consorzio Interuniversitario di Risonanze Magnetiche di Metallo-Proteine)
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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