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@ARTICLE{Musiani:201269,
      author       = {Musiani, Francesco and Bertoša, Branimir and Magistrato,
                      Alessandra and Zambelli, Barbara and Turano, Paola and
                      Losasso, Valeria and Micheletti, Cristian and Ciurli,
                      Stefano and Carloni, Paolo},
      title        = {{C}omputational {S}tudy of the {DNA}-{B}inding {P}rotein
                      {H}elicobacter pylori {N}ik{R}: {T}he {R}ole of {N}i
                      $^{2+}$},
      journal      = {Journal of chemical theory and computation},
      volume       = {6},
      number       = {11},
      issn         = {1549-9626},
      address      = {Washington, DC},
      publisher    = {American Chemical Society (ACS)},
      reportid     = {FZJ-2015-03574},
      pages        = {3503 - 3515},
      year         = {2010},
      abstract     = {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.},
      cin          = {GRS / IAS-5},
      ddc          = {540},
      cid          = {I:(DE-Juel1)GRS-20100316 / I:(DE-Juel1)IAS-5-20120330},
      pnm          = {899 - ohne Topic (POF2-899)},
      pid          = {G:(DE-HGF)POF2-899},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000283884300021},
      doi          = {10.1021/ct900635z},
      url          = {https://juser.fz-juelich.de/record/201269},
}