Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations.

ABSTRACT: NikR is a homotetrameric nickel regulatory protein whose binding to free Ni(2+) increases its binding affinity for a gene that codes for a nickel transporter protein. It is comprised of a tetrameric nickel-binding domain, flanked by two dimeric DNA-binding domains. Though X-ray crystallography data for various species (Escherichia coli, Heliobacter pylori, and Pyrococcus horikoshii) of NikR reveal large conformational differences between nickel-bound, DNA-bound, and unbound forms, transitions between them have never been observed. We have run all-atom molecular dynamics simulations of three forms of the Pyrococcus horikoshii species of NikR including two apo-forms and one nickel-bound form. Though all 552 residues of this species occur naturally, quantum-mechanics-based force-field paramet

SUBMITTER: Sindhikara DJ 

PROVIDER: S-EPMC2795120 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature