Probing the disordered domain of the nuclear pore complex through coarse-grained molecular dynamics simulations.

ABSTRACT: The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed differe

SUBMITTER: Ghavami A 

PROVIDER: S-EPMC4167297 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature