Probing the Nickel Coordination Environment in Helicobacter Pylori NikR

Abstract

Nickel homeostasis in gram-negative bacteria is often regulated at the transcriptional level by the nickel-dependent protein NikR, which belongs to the ribbon-helix-helix DNA-binding protein family. Generally, NikR is found as a homotetramer, with four nickel ions bound of the tetrameric interface at a metal binding domain (MBD). In Helicobacter pylori, NikR (HpNikR), unlike homologous NikR proteins, sits at a regulatory hub and has been found to have a variety of regulatory roles. HpNikR has been implicated in the regulation of proteins that function in acid acclimation, nickel uptake, virulence, and stress response. There are a number of questions about the nickel coordination environment in HpNikR due to a series of puzzling and sometimes contradictory structural and experimental results. Here we present results from complimentary computational and experimental techniques to help further resolve these questions. Specifically, we use molecular dynamics simulations and spectroscopic experiments to investigate the nickel coordination environment. We use circular dichroism to observe differences in the thermal stability of HpNikR depending on the nickel:protein stoichiometry, with stabilization increasing as nickel concentration increases. Stability of HpNikR is found to be pH dependent. Elucidation of details about nickel coordination in HpNikR will improve our understanding of the functional role of genetic regulatory pathways in H. pylori pathogenicity.