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Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex

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  • Mohaddeseh Peyro
  • Mohammad Soheilypour
  • Ali Ghavami
  • Mohammad R K Mofrad

Abstract

Nucleocytoplasmic transport has been the subject of a large body of research in the past few decades. Recently, the focus of investigations in this field has shifted from studies of the overall function of the nuclear pore complex (NPC) to the examination of the role of different domains of phenylalanine-glycine nucleoporin (FG Nup) sequences on the NPC function. In our recent bioinformatics study, we showed that FG Nups have some evolutionarily conserved sequence-based features that might govern their physical behavior inside the NPC. We proposed the ‘like charge regions’ (LCRs), sequences of charged residues with only one type of charge, as one of the features that play a significant role in the formation of FG network inside the central channel. In this study, we further explore the role of LCRs in the distribution of FG Nups, using a recently developed coarse-grained molecular dynamics model. Our results demonstrate how LCRs affect the formation of two transport pathways. While some FG Nups locate their FG network at the center of the NPC forming a homogeneous meshwork of FG repeats, other FG Nups cover the space adjacent to the NPC wall. LCRs in the former group, i.e. FG Nups that form an FG domain at the center, tend to regulate the size of the highly dense, doughnut-shaped FG meshwork and leave a small low FG density area at the center of the pore for passive diffusion. On the other hand, LCRs in the latter group of FG Nups enable them to maximize their interactions and cover a larger space inside the NPC to increase its capability to transport numerous cargos at the same time. Finally, a new viewpoint is proposed that reconciles different models for the nuclear pore selective barrier function.

Suggested Citation

  • Mohaddeseh Peyro & Mohammad Soheilypour & Ali Ghavami & Mohammad R K Mofrad, 2015. "Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-17, December.
  • Handle: RePEc:plo:pone00:0143745
    DOI: 10.1371/journal.pone.0143745
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    References listed on IDEAS

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    1. Frank Alber & Svetlana Dokudovskaya & Liesbeth M. Veenhoff & Wenzhu Zhang & Julia Kipper & Damien Devos & Adisetyantari Suprapto & Orit Karni-Schmidt & Rosemary Williams & Brian T. Chait & Andrej Sali, 2007. "The molecular architecture of the nuclear pore complex," Nature, Nature, vol. 450(7170), pages 695-701, November.
    2. Ruhollah Moussavi-Baygi & Yousef Jamali & Reza Karimi & Mohammad R K Mofrad, 2011. "Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex," PLOS Computational Biology, Public Library of Science, vol. 7(6), pages 1-16, June.
    3. Frank Alber & Svetlana Dokudovskaya & Liesbeth M. Veenhoff & Wenzhu Zhang & Julia Kipper & Damien Devos & Adisetyantari Suprapto & Orit Karni-Schmidt & Rosemary Williams & Brian T. Chait & Michael P. , 2007. "Determining the architectures of macromolecular assemblies," Nature, Nature, vol. 450(7170), pages 683-694, November.
    4. Martin Beck & Vladan Lučić & Friedrich Förster & Wolfgang Baumeister & Ohad Medalia, 2007. "Snapshots of nuclear pore complexes in action captured by cryo-electron tomography," Nature, Nature, vol. 449(7162), pages 611-615, October.
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