Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Barak Raveh*, Jerome M. Karp, Samuel Sparks, Kaushik Dutta, Michael P. Rout, Andrej Sali, David Cowburn

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

74 Scopus citations


Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport.

Original languageAmerican English
Pages (from-to)E2489-E2497
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number18
StatePublished - 3 May 2016
Externally publishedYes

Bibliographical note

Funding Information:
Simulations used the Anton special-purpose supercomputer provided by the National Resource for Biomedical Supercomputing (NRBSC), the Pittsburgh Supercomputing Center (PSC), and the Biomedical Technology Research Center for Multiscale Modeling of Biological Systems (MMBioS) through Grant P41GM103712-S1 from the National Institutes of Health. D. E. Shaw Research generously made the Anton machine at NRBSC/ PSC available. Additional simulations used XSEDE resources supported by National Science Foundation Grant ACI-1053575. J.M.K. was supported by NIH Grant T32 GM007288-39. We were also funded by Grants R01 GM112108, P41 GM109824, U01 GM098256 (to M.P.R. and A.S.), and R01 GM117212 and S10 OD016305 (to D.C.).


  • Molecular dynamics
  • NMR
  • Nuclear pore
  • Nucleoporins
  • Transport factors


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