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@ARTICLE{Dibenedetto:201097,
      author       = {Dibenedetto, Domenica and Rossetti, Giulia and Caliandro,
                      Rocco and Carloni, Paolo},
      title        = {{A} {M}olecular {D}ynamics {S}imulation-{B}ased
                      {I}nterpretation of {N}uclear {M}agnetic {R}esonance
                      {M}ultidimensional {H}eteronuclear {S}pectra of
                      α-{S}ynuclein·{D}opamine {A}dducts},
      journal      = {Biochemistry},
      volume       = {52},
      number       = {38},
      issn         = {1520-4995},
      address      = {Columbus, Ohio},
      publisher    = {American Chemical Society},
      reportid     = {FZJ-2015-03402},
      pages        = {6672 - 6683},
      year         = {2013},
      abstract     = {Multidimensional heteronuclear nuclear magnetic resonance
                      (NMR) spectroscopy provides valuable structural information
                      about adducts between naturally unfolded proteins and their
                      ligands. These are often highly pharmacologically relevant.
                      Unfortunately, the determination of the contributions to
                      observed chemical shifts changes upon ligand binding is
                      complicated. Here we present a tool that uses molecular
                      dynamics (MD) trajectories to help interpret two-dimensional
                      (2D) NMR data. We apply this tool to the naturally unfolded
                      protein human α-synuclein interacting with dopamine, an
                      inhibitor of fibril formation, and with its oxidation
                      products in water solutions. By coupling 2D NMR experiments
                      with MD simulations of the adducts in explicit water, the
                      tool confirms with experimental data that the ligands bind
                      preferentially to 125YEMPS129 residues in the C-terminal
                      region and to a few residues of the so-called NAC region
                      consistently. It also suggests that the ligands might cause
                      conformational rearrangements of distal residues located at
                      the N-terminus. Hence, the performed analysis provides a
                      rationale for the observed changes in chemical shifts in
                      terms of direct contacts with the ligand and conformational
                      changes in the protein.},
      cin          = {IAS-5 / JSC / GRS},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)JSC-20090406 /
                      I:(DE-Juel1)GRS-20100316},
      pnm          = {411 - Computational Science and Mathematical Methods
                      (POF2-411)},
      pid          = {G:(DE-HGF)POF2-411},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000330099300011},
      pubmed       = {pmid:23964651},
      doi          = {10.1021/bi400367r},
      url          = {https://juser.fz-juelich.de/record/201097},
}