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      Molecular Determinants of Snurportin 1 Ligand Affinity and Structural Response upon Binding

      , , ,
      Biophysical Journal
      Elsevier BV

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          Abstract

          The transport of large biomolecules such as proteins and RNA across nuclear pore complexes is a field of strong interest and research. Although the basic mechanisms are fairly well understood, the details of the underlying intermolecular interaction within these transport complexes are still unclear. The recognition dynamics and energetics of cargo binding to the transport receptor are not yet resolved. Here, the binding of dimethylated RNA-caps to snurportin 1 is studied by molecular-dynamics simulations. The simulations reveal a strong structural response of the protein upon RNA-cap release. In particular, major rearrangements occur in regions already intrinsically flexible in the holo structure. Additionally, the difference in free energy of binding to snurportin 1 between the two methylation states of the RNA-cap, responsible for the directionality of the transport is quantified. In particular, desolvation of the ligand is revealed as the key-step in binding to snurportin 1. These findings suggest that the binding of m(3)G-capped RNA is mainly driven by the enhanced water entropy gain of the solvation shell.

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          Author and article information

          Journal
          Biophysical Journal
          Biophysical Journal
          Elsevier BV
          00063495
          July 2009
          July 2009
          : 97
          : 2
          : 581-589
          Article
          10.1016/j.bpj.2009.04.049
          2711343
          19619473
          7ef46abc-1372-4c7b-acb9-1410f15bd9ee
          © 2009

          https://www.elsevier.com/tdm/userlicense/1.0/

          http://creativecommons.org/licenses/by-nc-nd/3.0/

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