title: Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating.
abstract: Nuclear pore complexes (NPCs) form gateways for material transfer across the nuclear envelope of eukaryotic cells. Disordered proteins, rich in phenylalanine-glycine repeat motifs (FG-nups), form the central transport channel. Understanding how nups are arranged in the interior of the NPC may explain how NPC functions as a selectivity filter for transport of large molecules and a sieve-like filter for diffusion of small molecules (<9 nm or 40 kDa). We employed molecular dynamics to model the structures formed by various assemblies of one kind of nup, namely the 609-aa-long FG domain of Nsp1 (Nsp1-FG). The simulations started from different initial conformations and geometrical arrangements of Nsp1-FGs. In all cases Nsp1-FGs collectively formed brush-like structures with bristles made of bundles of 2-27 nups, however, the bundles being cross-linked through single nups leaving one bundle and joining a nearby one. The degree of cross-linking varies with different initial nup conformations and arrangements. Structural analysis reveals that FG-repeats of the nups not only involve formation of bundle structures, but are abundantly present in cross-linking regions where the epitopes of FG-repeats are highly accessible. Large molecules that are assisted by transport factors (TFs) are selectively transported through NPC apparently by binding to FG-nups through populated FG-binding pockets on the TF surface. Therefore, our finding suggests that TFs bind concertedly to multiple FGs in cross-linking regions and break-up the bundles to create wide pores for themselves and their cargoes to pass. In addition, the cross-linking between Nsp1-FG bundles, arising from simulations, is found to set a molecular size limit of <9 nm (40 kDa) for passive diffusion of molecules. Our simulations suggest that the NPC central channel, near the periphery where tethering of nups is dominant, features brush-like moderately cross-linked bundles, but in the central region, where tethering loses its effect, features a sieve-like structure of bundles and frequent cross-links.
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.
authors.forename: Ramya
authors.initials: R
authors.lastname: Gamini
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.
authors.forename: Wei
authors.initials: W
authors.lastname: Han
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America; Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D003432:Cross-Linking Reagents / Q000737:chemistry; D004058:Diffusion; D000939:Epitopes; D056004:Molecular Dynamics Simulation; D022022:Nuclear Pore / Q000502:physiology*; D028861:Nuclear Pore Complex Proteins / Q000235:genetics* / Q000502:physiology*; D009687:Nuclear Proteins / Q000235:genetics* / Q000502:physiology*; D011487:Protein Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000502:physiology*; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D000939:Epitopes; C062748:NSP1 protein, S cerevisiae; D028861:Nuclear Pore Complex Proteins; D009687:Nuclear Proteins; D029701:Saccharomyces cerevisiae Proteins