F. Musiani, B. Bertosa, A. Magistrato, B. Zambelli, P. Turano, V. Losasso, C. Micheletti, S. Ciurli and P. Carloni
Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+
J. Chem. Theory Comput., 2010 6 3503-3515
Link to online article
ABSTRACT
An integrated approach, combining atomistic molecular dynamics simulations, coarsegrained
models, and solution NMR, was used to characterize the internal dynamics of HpNikR,
a Ni-dependent transcription factor. Specifically, these methods were used to ascertain how
the presence of bound Ni2+ ions affects the stability of the known open, cis, and trans forms
observed in the crystal structures of this protein as well as their interconversion capability. The
consensus picture emerging from all the collected data hint at the interconversion of NikR among
the three types of conformations, regardless of content of bound Ni2+. On the basis of atomistic
and coarse-grained simulations, we suggest that the interconversion capability is particularly
effective between the cis and the open forms and appreciably less so between the trans
conformer and the other two forms. The presence of the bound Ni2+ ions does, however, affect
significantly the degree of the correlations on the two DNA-binding domains of NikR, which is
significantly suppressed as compared to the apo form. Overall, the findings suggest that the
binding of HpNikR to DNA occurs through a sophisticated multistep process that might involve
both a conformational selection and an induced fit.