TY  - JOUR
AU  - Musiani, Francesco
AU  - Bertoša, Branimir
AU  - Magistrato, Alessandra
AU  - Zambelli, Barbara
AU  - Turano, Paola
AU  - Losasso, Valeria
AU  - Micheletti, Cristian
AU  - Ciurli, Stefano
AU  - Carloni, Paolo
TI  - Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni $^{2+}$
JO  - Journal of chemical theory and computation
VL  - 6
IS  - 11
SN  - 1549-9626
CY  - Washington, DC
PB  - American Chemical Society (ACS)
M1  - FZJ-2015-03574
SP  - 3503 - 3515
PY  - 2010
AB  - An integrated approach, combining atomistic molecular dynamics simulations, coarse-grained 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 hints at the interconversion of NikR among the three types of conformations, regardless of the content of bound Ni2+. On the basis of atomistic and coarse-grained simulations, we deduce 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 involving both a conformational selection and an induced fit.
LB  - PUB:(DE-HGF)16
UR  - <Go to ISI:>//WOS:000283884300021
DO  - DOI:10.1021/ct900635z
UR  - https://juser.fz-juelich.de/record/201269
ER  -