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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.