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000201269 1001_ $$0P:(DE-HGF)0$$aMusiani, Francesco$$b0
000201269 245__ $$aComputational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni $^{2+}$
000201269 260__ $$aWashington, DC$$bAmerican Chemical Society (ACS)$$c2010
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000201269 520__ $$aAn 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.
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000201269 7001_ $$0P:(DE-HGF)0$$aBertoša, Branimir$$b1
000201269 7001_ $$0P:(DE-HGF)0$$aMagistrato, Alessandra$$b2
000201269 7001_ $$0P:(DE-HGF)0$$aZambelli, Barbara$$b3
000201269 7001_ $$0P:(DE-HGF)0$$aTurano, Paola$$b4
000201269 7001_ $$0P:(DE-HGF)0$$aLosasso, Valeria$$b5
000201269 7001_ $$0P:(DE-HGF)0$$aMicheletti, Cristian$$b6
000201269 7001_ $$0P:(DE-HGF)0$$aCiurli, Stefano$$b7$$eCorresponding Author
000201269 7001_ $$0P:(DE-Juel1)145614$$aCarloni, Paolo$$b8$$ufzj
000201269 773__ $$0PERI:(DE-600)2166976-4$$a10.1021/ct900635z$$gVol. 6, no. 11, p. 3503 - 3515$$n11$$p3503 - 3515$$tJournal of chemical theory and computation$$v6$$x1549-9626$$y2010
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