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@ARTICLE{Bochicchio:858888,
      author       = {Bochicchio, Anna and Krepl, Miroslav and Yang, Fan and
                      Varani, Gabriele and Sponer, Jiri and Carloni, Paolo},
      title        = {{M}olecular basis for the increased affinity of an {RNA}
                      recognition motif with re-engineered specificity: {A}
                      molecular dynamics and enhanced sampling simulations study},
      journal      = {PLoS Computational Biology},
      volume       = {14},
      number       = {12},
      issn         = {1553-7358},
      address      = {San Francisco, Calif.},
      publisher    = {Public Library of Science},
      reportid     = {FZJ-2018-07724},
      pages        = {e1006642 -},
      year         = {2018},
      abstract     = {The RNA recognition motif (RRM) is the most common RNA
                      binding domain across eukaryotic proteins. It is therefore
                      of great value to engineer its specificity to target RNAs of
                      arbitrary sequence. This was recently achieved for the RRM
                      in Rbfox protein, where four mutations R118D, E147R, N151S,
                      and E152T were designed to target the precursor to the
                      oncogenic miRNA 21. Here, we used a variety of molecular
                      dynamics-based approaches to predict specific interactions
                      at the binding interface. Overall, we have run approximately
                      50 microseconds of enhanced sampling and plain molecular
                      dynamics simulations on the engineered complex as well as on
                      the wild-type Rbfox·pre-miRNA 20b from which the mutated
                      systems were designed. Comparison with the available NMR
                      data on the wild type molecules (protein, RNA, and their
                      complex) served to establish the accuracy of the
                      calculations.Free energy calculations suggest that further
                      improvements in affinity and selectivity are achieved by the
                      S151T replacement.},
      cin          = {IAS-5 / INM-11 / INM-9},
      ddc          = {610},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-11-20170113 /
                      I:(DE-Juel1)INM-9-20140121},
      pnm          = {574 - Theory, modelling and simulation (POF3-574)},
      pid          = {G:(DE-HGF)POF3-574},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:30521520},
      UT           = {WOS:000454835100039},
      doi          = {10.1371/journal.pcbi.1006642},
      url          = {https://juser.fz-juelich.de/record/858888},
}