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@ARTICLE{FenollarFerrer:201298,
      author       = {Fenollar-Ferrer, Cristina and Anselmi, Claudio and
                      Carnevale, Vincenzo and Raugei, Simone and Carloni, Paolo},
      title        = {{I}nsights on the acetylated {NF}-κ{B} transcription
                      factor complex with {DNA} from molecular dynamics
                      simulations},
      journal      = {Proteins},
      volume       = {80},
      number       = {6},
      issn         = {0887-3585},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {FZJ-2015-03603},
      pages        = {1560 - 1568},
      year         = {2012},
      abstract     = {The nuclear factor-κB (NF-κB) is a DNA sequence-specific
                      regulator of many important biological processes, whose
                      activity is modulated by enzymatic acetylation. In one of
                      the best functionally characterized NF-κB complexes, the
                      p50/p65 heterodimer, acetylation of K221 at p65 causes a
                      decrease of DNA dissociation rate, whilst the acetylation of
                      K122 and K123, also at p65, markedly decreases the binding
                      affinity for DNA. By means of molecular dynamics simulations
                      based on the X-ray structure of the p50/p65 complex with
                      DNA, we provide insights on the structural determinants of
                      the acetylated complexes in aqueous solution. Lysine
                      acetylation involves the loss of favorable electrostatic
                      interactions between DNA and NF-κB, which is partially
                      compensated by the reduction of the desolvation free-energy
                      of the two binding partners. Acetylation at both positions
                      K122 and K123 is associated with a decrease of the
                      electrostatic potential at the p65/DNA interface, which is
                      only partially counterbalanced by an increase of the local
                      Na+ concentration. It induces the disruption of
                      base-specific and nonspecific interactions between DNA and
                      NF-κB and it is consistent with the observed decrease of
                      binding affinity. In contrast, acetylation at position K221
                      results in the loss of nonspecific protein–DNA
                      interactions, but the DNA recognition sites are not
                      affected. In addition, the loss of protein–DNA
                      interactions is likely to be counterbalanced by an increase
                      of the configurational entropy of the complex, which
                      provides, at a speculative level, a justification for the
                      observed decrease of NF-κB/DNA dissociation rate},
      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:000303759000004},
      doi          = {10.1002/prot.24047},
      url          = {https://juser.fz-juelich.de/record/201298},
}