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Title: A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics

Abstract

The phenylalanine-glycine–repeat nucleoporins (FG-Nups), which occupy the lumen of the nuclear pore complex (NPC), are critical for transport between the nucleus and cytosol. Although NPCs differ in composition across species, they are largely conserved in organization and function. Transport through the pore is on the millisecond timescale. Here, to explore the dynamics of nucleoporins on this timescale, we use coarse-grained computational simulations. These simulations generate predictions that can be experimentally tested to distinguish between proposed mechanisms of transport. Our model reflects the conserved structure of the NPC, in which FG-Nup filaments extend into the lumen and anchor along the interior of the channel. The lengths of the filaments in our model are based on the known characteristics of yeast FG-Nups. The FG-repeat sites also bind to each other, and we vary this association over several orders of magnitude and run 100-ms simulations for each value. The autocorrelation functions of the orientation of the simulated FG-Nups are compared with in vivo anisotropy data. We observe that FG-Nups reptate back and forth through the NPC at timescales commensurate with experimental measurements of the speed of cargo transport through the NPC. Our results are consistent with models of transport where FG-Nup filaments aremore » free to move across the central channel of the NPC, possibly informing how cargo might transverse the NPC.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [1]
  1. Rockefeller Univ., New York, NY (United States)
  2. Courant Institute of Mathematical Sciences, New Orleans, LA (United States)
  3. Rockefeller Univ., New York, NY (United States); Icahn School of Medicine at Mount Sinai, New York, NY (United States)
Publication Date:
Research Org.:
New York Univ. (NYU), NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
OSTI Identifier:
1380055
Alternate Identifier(s):
OSTI ID: 1499126
Grant/Contract Number:  
FG02-88ER25053; DEFG0288ER25053
Resource Type:
Published Article
Journal Name:
Journal of General Physiology
Additional Journal Information:
Journal Volume: 149; Journal Issue: 10; Journal ID: ISSN 0022-1295
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Pulupa, Joan, Rachh, Manas, Tomasini, Michael D., Mincer, Joshua S., and Simon, Sanford M. A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics. United States: N. p., 2017. Web. doi:10.1085/jgp.201711769.
Pulupa, Joan, Rachh, Manas, Tomasini, Michael D., Mincer, Joshua S., & Simon, Sanford M. A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics. United States. doi:10.1085/jgp.201711769.
Pulupa, Joan, Rachh, Manas, Tomasini, Michael D., Mincer, Joshua S., and Simon, Sanford M. Fri . "A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics". United States. doi:10.1085/jgp.201711769.
@article{osti_1380055,
title = {A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics},
author = {Pulupa, Joan and Rachh, Manas and Tomasini, Michael D. and Mincer, Joshua S. and Simon, Sanford M.},
abstractNote = {The phenylalanine-glycine–repeat nucleoporins (FG-Nups), which occupy the lumen of the nuclear pore complex (NPC), are critical for transport between the nucleus and cytosol. Although NPCs differ in composition across species, they are largely conserved in organization and function. Transport through the pore is on the millisecond timescale. Here, to explore the dynamics of nucleoporins on this timescale, we use coarse-grained computational simulations. These simulations generate predictions that can be experimentally tested to distinguish between proposed mechanisms of transport. Our model reflects the conserved structure of the NPC, in which FG-Nup filaments extend into the lumen and anchor along the interior of the channel. The lengths of the filaments in our model are based on the known characteristics of yeast FG-Nups. The FG-repeat sites also bind to each other, and we vary this association over several orders of magnitude and run 100-ms simulations for each value. The autocorrelation functions of the orientation of the simulated FG-Nups are compared with in vivo anisotropy data. We observe that FG-Nups reptate back and forth through the NPC at timescales commensurate with experimental measurements of the speed of cargo transport through the NPC. Our results are consistent with models of transport where FG-Nup filaments are free to move across the central channel of the NPC, possibly informing how cargo might transverse the NPC.},
doi = {10.1085/jgp.201711769},
journal = {Journal of General Physiology},
number = 10,
volume = 149,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1085/jgp.201711769

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