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@ARTICLE{Nguyen:186051,
      author       = {Nguyen, Trung Hai and Rossetti, Giulia and Arnesano, Fabio
                      and Ippoliti, Emiliano and Natile, Giovanni and Carloni,
                      Paolo},
      title        = {{M}olecular {R}ecognition of {P}latinated {DNA} from
                      {C}hromosomal {HMGB}1},
      journal      = {Journal of chemical theory and computation},
      volume       = {10},
      number       = {8},
      issn         = {1549-9626},
      address      = {Washington, DC},
      publisher    = {American Chemical Society (ACS)},
      reportid     = {FZJ-2015-00152},
      pages        = {3578 - 3584},
      year         = {2014},
      abstract     = {Cisplatin cures testicular and ovarian cancers with
                      unprecedented potency. It induces its beneficial activity by
                      covalently binding to DNA. Repair enzymes, which remove the
                      platinated lesions from DNA, cause drug resistance.
                      Chromosomal High Mobility Group Box proteins (HMGB) may
                      interfere with this process by binding to platinated DNA.
                      Using 8 μs multiple-walker well-tempered metadynamics
                      simulations, here, we investigated the structural and the
                      energetic determinants of one of the HMGB proteins (HMGB1A)
                      in complex with the platinated oligonucleotide
                      [Pt(NH3)2]2+-d(CCUCTCTG*G*ACCTTCC)-d(GGAGAGACCTGGAAGG) (*G
                      are platinated guanines), for which experimental structural
                      information is available. The calculated affinity is in good
                      agreement with experiment. The process is predicted to be
                      enthalpy-driven, as found for other protein/DNA complexes.
                      The Lys7 residue, whose side-chain was not resolved in the
                      X-ray structure, is found to interact with the C4
                      5′-phosphate and this interaction emerges as a key facet
                      for the molecular recognition process. In addition, our
                      calculations provide a molecular basis for the
                      experimentally measured decreased affinity of HMGB1A for
                      platinated DNA, as a consequence of Cys22-Cys44 S–S bridge
                      formation (such an oxidation cannot take place in some
                      members of this protein family present in the testis, where
                      the drug is particularly effective). This decrease is likely
                      to be caused by a small yet significant rearrangement of
                      helices H1 and H2 with consequent alteration of the Phe37
                      juxtaposition.},
      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:000340351200068},
      pubmed       = {pmid:26588321},
      doi          = {10.1021/ct500402e},
      url          = {https://juser.fz-juelich.de/record/186051},
}