ArticlePLoS computational biology2011
Brownian dynamics simulation of nucleocytoplasmic transport: a coarse-grained model for the functional state of the nuclear pore complex.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Kap-centric Nsp1-mediated nuclear transport at full amino acid resolution.Nature communications · 2025Article
- Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Targeting colorectal cancer at the level of nuclear pore complex.Journal of advanced research · 2025Review
- Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory.PLoS computational biology · 2025Article
- The TEMPO integrator: accelerating molecular simulations by temporally multiscale force prediction.Bioinformatics advances · 2025Article
- Regulating transport efficiency through the nuclear pore complex: The role of binding affinity with FG-Nups.Molecular biology of the cell · 2024Article
- Kinetic cooperativity resolves bidirectional clogging within the nuclear pore complex.Biophysical journal · 2024Article
- Spatial resolution enhancement in photon-starved STED imaging using deep learning-based fluorescence lifetime analysis.Nanoscale · 2023Article
- Self-regulation of the nuclear pore complex enables clogging-free crowded transport.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Unveiling the complexity: assessing models describing the structure and function of the nuclear pore complex.Frontiers in cell and developmental biology · 2023Review
- Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex.Nature communications · 2022Article
- On the nuclear pore complex and its emerging role in cellular mechanotransduction.APL bioengineering · 2022Review
- Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies.eLife · 2022Article
- Structure and dynamics of nanoconfined water and aqueous solutions.The European physical journal. E, Soft matter · 2021Review
- Free energy calculations shed light on the nuclear pore complex's selective barrier nature.Biophysical journal · 2021Article
- Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment.Physics reports · 2021Article
- Theoretical Modeling of Chemical Equilibrium in Weak Polyelectrolyte Layers on Curved Nanosystems.Polymers · 2020Review
- The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes.The Journal of cell biology · 2020Article
- Design principles of selective transport through biopolymer barriers.Physical review. E · 2019Article
- Polymer translocation through a hairy channel mimicking the inner plug of a nuclear pore complex.European biophysics journal : EBJ · 2019Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the length scale of tens of nanometers; however, the transport mechanism remains elusive. Central to the transport process is the hydrophobic interactions between karyopherins (kaps) and Phe-Gly (FG) repeat domains. Taking into account the polymeric nature of FG-repeats grafted on the elastic structure of the NPC, and the kap-FG hydrophobic affinity, we have established a coarse-grained model of the NPC structure that mimics nucleocytoplasmic transport. To establish a foundation for future works, the methodology and biophysical rationale behind the model is explained in details. The model predicts that the first-passage time of a 15 nm cargo-complex is about 2.6±0.13 ms with an inverse Gaussian distribution for statistically adequate number of independent Brownian dynamics simulations. Moreover, the cargo-complex is primarily attached to the channel wall where it interacts with the FG-layer as it passes through the central channel. The kap-FG hydrophobic interaction is highly dynamic and fast, which ensures an efficient translocation through the NPC. Further, almost all eight hydrophobic binding spots on kap-β are occupied simultaneously during transport. Finally, as opposed to intact NPCs, cytoplasmic filaments-deficient NPCs show a high degree of permeability to inert cargos, implying the defining role of cytoplasmic filaments in the selectivity barrier.
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