Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating

• Published in: PLoS computational biology Vol. 10; no. 3; p. e1003488
• Main Authors: Gamini, Ramya, Han, Wei, Stone, John E, Schulten, Klaus
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.03.2014; Public Library of Science (PLoS)
• Subjects: Aquaporins; Biology; Carrier proteins; Computational Biology; Computer Simulation; Cross-Linking Reagents - chemistry; Diffusion; Epitopes; Molecular Dynamics Simulation; Nuclear Pore - physiology; Nuclear Pore Complex Proteins - genetics; Nuclear Pore Complex Proteins - physiology; Nuclear Proteins - genetics; Nuclear Proteins - physiology; Physiological aspects; Protein Conformation; Protein research; Protein-protein interactions; Proteins; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - physiology; Simulation; Software; United States; Cross-Linking Reagents; Nuclear Pore Complex Proteins; Computational Biology; Epitopes; Molecular Dynamics Simulation; Nuclear Proteins; Computer Simulation; Saccharomyces cerevisiae Proteins; Protein Conformation; Software; Diffusion; Nuclear Pore; Saccharomyces cerevisiae
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1003488

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.