Evidence map›Paper›PMID 27697925›Full record

ArticleThe Journal of cell biology2016

Simple rules for passive diffusion through the nuclear pore complex.

Benjamin L Timney, Barak Raveh, Roxana Mironska, Jill M Trivedi, Seung Joong Kim, Daniel Russel, Susan R Wente, Andrej Sali, Michael P Rout

Open access · bronzeAbstract read
In one paragraph

Article in The Journal of cell biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 275 papers.

0numbers the graph read from it
0cells of the map it votes in
275citing papers in PubMed
20.7field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

275 citing papers in PubMed, 462 citations in OpenAlex.

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  19. Programmable artificial RNA condensates in mammalian cells.bioRxiv : the preprint server for biology · 2026
    Article
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215 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 3 institutions in 1 country.

Benjamin L TimneyLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065.ORCID http://orcid.org/0000-0002-4525-0455
Barak RavehDepartment 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.ORCID http://orcid.org/0000-0002-2073-3936
Roxana MironskaLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065.
Jill M TrivediLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065.ORCID http://orcid.org/0000-0001-7007-2278
Seung Joong KimDepartment 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.
Daniel RusselDepartment 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.ORCID http://orcid.org/0000-0002-0225-6654
Susan R WenteDepartment of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232.ORCID http://orcid.org/0000-0002-6240-548X
Andrej SaliDepartment 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.
Michael P RoutLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 sali@salilab.org rout@rockefeller.edu.ORCID http://orcid.org/0000-0003-2010-706X
QB3 · USRockefeller University · USVanderbilt University · US

Funding

TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
Structure-Function Mapping of the Nuclear Pore Complex-RenewalR01GM112108 · NIGMS · ROCKEFELLER UNIVERSITY · PI JOHN D. AITCHISON, MICHAEL P ROUT · 2015 to 2026
$9.1M
Molecular Analysis of Nuclear Pore Complex FunctionR37GM051219 · NIGMS · VANDERBILT UNIVERSITY · PI WENTE, SUSAN R. · 2010 to 2019
$5.6M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Virtual Gating Machines for Protein PurificationR01GM071329 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2004 to 2013
$4.6M
Nucleocytoplasmic transport: a target for cellular controlU01GM098256 · NIGMS · ROCKEFELLER UNIVERSITY · PI AITCHISON, JOHN D., ROUT, MICHAEL P · 2011 to 2014
$3.0M
NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM071329NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM112108NIGMS NIH HHS R37 GM051219NIGMS NIH HHS U01 GM098256
6 · The paper itself

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.

Indexed as

Biological TransportComputer SimulationDiffusionFluorescence Recovery After PhotobleachingKineticsMacromolecular SubstancesMolecular WeightMutationNuclear PoreNuclear Pore Complex ProteinsPermeabilityProtein DomainsSaccharomyces cerevisiaeSubstrate SpecificityThermodynamicsTime FactorsMacromolecular SubstancesNuclear Pore Complex Proteins

Identifiers

PMID27697925
PMCPMC5057280
OpenAlexW2529120786

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-SA
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.