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@ARTICLE{Musiani:186049,
      author       = {Musiani, Francesco and Rossetti, Giulia and Capece, Luciana
                      and Gerger, Thomas Martin and Micheletti, Cristian and
                      Varani, Gabriele and Carloni, Paolo},
      title        = {{M}olecular {D}ynamics {S}imulations {I}dentify {T}ime
                      {S}cale of {C}onformational {C}hanges {R}esponsible for
                      {C}onformational {S}election in {M}olecular {R}ecognition of
                      {HIV}-1 {T}ransactivation {R}esponsive {RNA}},
      journal      = {Journal of the American Chemical Society},
      volume       = {136},
      number       = {44},
      issn         = {1520-5126},
      address      = {Washington, DC},
      publisher    = {American Chemical Society},
      reportid     = {FZJ-2015-00150},
      pages        = {15631 - 15637},
      year         = {2014},
      abstract     = {The HIV-1 Tat protein and several small molecules bind to
                      HIV-1 transactivation responsive RNA (TAR) by selecting
                      sparsely populated but pre-existing conformations. Thus, a
                      complete characterization of TAR conformational ensemble and
                      dynamics is crucial to understand this paradigmatic system
                      and could facilitate the discovery of new antivirals
                      targeting this essential regulatory element. We show here
                      that molecular dynamics simulations can be effectively used
                      toward this goal by bridging the gap between functionally
                      relevant time scales that are inaccessible to current
                      experimental techniques. Specifically, we have performed
                      several independent microsecond long molecular simulations
                      of TAR based on one of the most advanced force fields
                      available for RNA, the parmbsc0 AMBER. Our simulations are
                      first validated against available experimental data,
                      yielding an excellent agreement with measured residual
                      dipolar couplings and order parameter S2. This contrast with
                      previous molecular dynamics simulations (Salmon et al., J.
                      Am. Chem. Soc. 2013 135, 5457–5466) based on the CHARMM36
                      force field, which could achieve only modest accord with the
                      experimental RDC values. Next, we direct the computation
                      toward characterizing the internal dynamics of TAR over the
                      microsecond time scale. We show that the conformational
                      fluctuations observed over this previously elusive time
                      scale have a strong functionally oriented character in that
                      they are primed to sustain and assist ligand binding.},
      cin          = {JSC / IAS-5 / INM-9},
      ddc          = {540},
      cid          = {I:(DE-Juel1)JSC-20090406 / I:(DE-Juel1)IAS-5-20120330 /
                      I:(DE-Juel1)INM-9-20140121},
      pnm          = {411 - Computational Science and Mathematical Methods
                      (POF2-411)},
      pid          = {G:(DE-HGF)POF2-411},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000344516600033},
      pubmed       = {pmid:25313638},
      doi          = {10.1021/ja507812v},
      url          = {https://juser.fz-juelich.de/record/186049},
}