title: Simple rules for passive diffusion through the nuclear pore complex.
abstract: Passive macromolecular diffusion through nuclear pore complexes (NPCs) is thought to decrease dramatically beyond a 30-60-kD size threshold. Using thousands of independent time-resolved fluorescence microscopy measurements in vivo, we show that the NPC lacks such a firm size threshold; instead, it forms a soft barrier to passive diffusion that intensifies gradually with increasing molecular mass in both the wild-type and mutant strains with various subsets of phenylalanine-glycine (FG) domains and different levels of baseline passive permeability. Brownian dynamics simulations replicate these findings and indicate that the soft barrier results from the highly dynamic FG repeat domains and the diffusing macromolecules mutually constraining and competing for available volume in the interior of the NPC, setting up entropic repulsion forces. We found that FG domains with exceptionally high net charge and low hydropathy near the cytoplasmic end of the central channel contribute more strongly to obstruction of passive diffusion than to facilitated transport, revealing a compartmentalized functional arrangement within the NPC.
authors.affiliation: Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065.
authors.forename: Benjamin L
authors.identifier: http://orcid.org/0000-0002-4525-0455
authors.initials: BL
authors.lastname: Timney
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158.
authors.forename: Barak
authors.identifier: http://orcid.org/0000-0002-2073-3936
authors.initials: B
authors.lastname: Raveh
authors.affiliation: Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065.
authors.forename: Roxana
authors.initials: R
authors.lastname: Mironska
authors.affiliation: Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065.
authors.forename: Jill M
authors.identifier: http://orcid.org/0000-0001-7007-2278
authors.initials: JM
authors.lastname: Trivedi
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158.
authors.forename: Seung Joong
authors.initials: SJ
authors.lastname: Kim
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158.
authors.forename: Daniel
authors.identifier: http://orcid.org/0000-0002-0225-6654
authors.initials: D
authors.lastname: Russel
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232.
authors.forename: Susan R
authors.identifier: http://orcid.org/0000-0002-6240-548X
authors.initials: SR
authors.lastname: Wente
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158 sali@salilab.org rout@rockefeller.edu.
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
authors.affiliation: Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 sali@salilab.org rout@rockefeller.edu.
authors.forename: Michael P
authors.identifier: http://orcid.org/0000-0003-2010-706X
authors.initials: MP
authors.lastname: Rout
mesh_terms: D001692:Biological Transport; D003198:Computer Simulation; D004058:Diffusion; D036681:Fluorescence Recovery After Photobleaching; D007700:Kinetics; D046911:Macromolecular Substances / Q000378:metabolism; D008970:Molecular Weight; D009154:Mutation / Q000235:genetics; D022022:Nuclear Pore / Q000378:metabolism; D028861:Nuclear Pore Complex Proteins / Q000378:metabolism*; D010539:Permeability; D000072417:Protein Domains; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D013379:Substrate Specificity; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D046911:Macromolecular Substances; D028861:Nuclear Pore Complex Proteins