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Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex

Lucy J. Colwell, Michael P. Brenner, Katharina Ribbeck, Michael Gilson
2010 PLoS Computational Biology  
Citation: Colwell LJ, Brenner MP, Ribbeck K (2010) Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex. PLoS Comput Biol 6(4): e1000747.  ...  We suggest that negative charge is an essential criterion for selective passage through the NPC.  ...  Acknowledgments We thank Jacob Israelachvili, Andrew Murray, Carey Nadell, Erin O'Shea, Michael Rexach, Thomas Schwartz and Boris Shraiman, for important conversations. Author Contributions  ... 
doi:10.1371/journal.pcbi.1000747 pmid:20421988 pmcid:PMC2858669 fatcat:nk4l4ndmpjbffequghz3vyd2uq

Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex

Mario Tagliazucchi, Orit Peleg, Martin Kröger, Yitzhak Rabin, Igal Szleifer
2013 Proceedings of the National Academy of Sciences of the United States of America  
for selective transport through the pore (10-14) .  ...  The molecular structure of the yeast nuclear pore complex (NPC) and the translocation of model particles have been studied with a molecular theory that accounts for the geometry of the pore and the sequence  ...  for selective transport through the pore (10) (11) (12) (13) (14) .  ... 
doi:10.1073/pnas.1212909110 pmid:23404701 pmcid:PMC3587244 fatcat:d3kjnie6lnf3jn2vg55jhccpou

Role of Molecular Charge in Nucleocytoplasmic Transport

Alexander Goryaynov, Weidong Yang, Maria Gasset
2014 PLoS ONE  
Recently, negative surface charge was postulated to be another essential criterion for selective passage through the NPC.  ...  Transport of genetic materials and proteins between the nucleus and cytoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs).  ...  Cronican for providing the plasmids and purification protocols for charged GFPs, and thank S. Wunder and J. Drazenovic for their help in the measurement of dynamic light scattering.  ... 
doi:10.1371/journal.pone.0088792 pmid:24558427 pmcid:PMC3928296 fatcat:xf2ibnch5vfh5cdn76d45yt4sm

Viruses Challenge Selectivity Barrier of Nuclear Pores

Aksana Labokha, Ariberto Fassati
2013 Viruses  
Exchange between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs) embedded in the double membrane of the nuclear envelope.  ...  In this review, we will discuss the functional principles of NPC barrier and nuclear transport machinery, as well as the various strategies viruses use to cross the selective barrier of NPCs.  ...  Thus, the main sorting criterion of NPCs' barrier is partitioning into a selective phase that is a good "solvent" for NTRs, but not for polar inert macromolecules.  ... 
doi:10.3390/v5102410 pmid:24084236 pmcid:PMC3814595 fatcat:yktp3x6v4bd4fcgmnsyplwbyiy

The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion

K. Ribbeck
2002 EMBO Journal  
Nuclear pore complexes (NPCs) restrict the nucleo-cytoplasmic¯ux of most macromolecules, but permit facilitated passage of nuclear transport receptors and their cargo complexes.  ...  We found that a simple hydrophobic interaction column can mimic the selectivity of NPCs surprisingly well and that nuclear transport receptors appear to be the most hydrophobic soluble proteins.  ...  the MBP±Ran constructs, and the DFG for ®nancial support.  ... 
doi:10.1093/emboj/21.11.2664 pmid:12032079 pmcid:PMC126029 fatcat:442666afqbawrb4iuj3eg66ldm

Translocation, Rejection and Trapping of Polyampholytes

Yeong-Beom Kim, Min-Kyung Chae, Jeong-Man Park, Albert Johner, Nam-Kyung Lee
2022 Polymers  
We investigated the translocation behavior of random polyampholyte chains through a pore under the action of an electric field by means of Monte Carlo simulations.  ...  We also provided operational criteria for the translocation behavior of a sequence, explaining the selection by the translocation process.  ...  In nature, charged polymers (proteins, RNA) are imported in or exported from the cell nucleus by translocation through a nuclear pore [12] .  ... 
doi:10.3390/polym14040797 pmid:35215709 pmcid:PMC8877523 fatcat:vvojv7blancavhcz42b5xni2wu

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

Joan Pulupa, Manas Rachh, Michael D. Tomasini, Joshua S. Mincer, Sanford M. Simon
2017 The Journal of General Physiology  
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.  ...  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.  ...  I n t R o d u c t I o n In all eukaryotes, nuclear pore complexes (NPCs) facilitate the transport of biomolecular cargo across the barrier of the nuclear envelope.  ... 
doi:10.1085/jgp.201711769 pmid:28887410 pmcid:PMC5694938 fatcat:5jwpplwzf5elnhtjqyp2cgiqpu

Kinetic analysis of translocation through nuclear pore complexes

Katharina Ribbeck, Dirk Görlich
2001 EMBO Journal  
The mechanism of facilitated translocation through nuclear pore complexes (NPCs) is only poorly understood. Here, we present a kinetic analysis of the process using various model substrates.  ...  We propose a'selective phase model' that could explain how NPCs function as a permeability barrier for inert molecules and yet become selectively permeable for nuclear transport receptors and receptor±  ...  Acknowledgements We thank Drs M.Pool, T.A.Rapoport, I.Vetter and D.Oesterhelt, the members of our laboratory, I.W.Mattaj and the anonymous reviewers for stimulating discussions/constructive comments on  ... 
doi:10.1093/emboj/20.6.1320 pmid:11250898 pmcid:PMC145537 fatcat:wxplbptitvccxbpr6hohlkyhbq

Transport receptor occupancy in Nuclear Pore Complex mimics [article]

Alessio Fragasso, Hendrik W. de Vries, John Andersson, Eli O. van der Sluis, Erik van der Giessen, Patrick Onck, Cees Dekker
2021 bioRxiv   pre-print
Nuclear Pore Complexes (NPCs) regulate all molecular transport between the nucleus and the cytoplasm in eukaryotic cells.  ...  : one population that is transported across the pore in milliseconds, and a second population that is stably assembled within the FG mesh of the pore.  ...  Acknowledgements We would like to thank the Görlich Lab for sharing purified Nsp1, Meng-yue Wu for technical assistance on the TEM, and Marc op den Kamp, Sjoerd Meesters and Koen Wortelboer for their assistance  ... 
doi:10.1101/2021.12.22.473839 fatcat:tvpz7zcai5dqhahtw6hebj7zqy

The particle in the spider's web: transport through biological hydrogels

Jacob Witten, Katharina Ribbeck
2017 Nanoscale  
Abstract Biological hydrogels such as mucus, extracellular matrix, biofilms, and the nuclear pore have diverse functions and compositions, but all act as selectively permeable barriers to the diffusion  ...  Graphical abstract Transport through biological hydrogels is an important biological process and of fundamental importance for drug delivery.  ...  Alan Grodzinsky at MIT for his valuable feedback and helpful discussions, and Erica Shapiro, Wes Chen, Tahoura Samad, Caroline Wagner, Kathryn Smith-Dupont, and Lisa Walker for careful reading of the manuscript  ... 
doi:10.1039/c6nr09736g pmid:28580973 pmcid:PMC5841163 fatcat:2bdhnej6tjat5bmtnxrgfq3lxy

Nucleocytoplasmic transport of intrinsically disordered proteins studied by high-speed super-resolution microscopy

Samuel L. Junod, Joseph M. Kelich, Jiong Ma, Weidong Yang
2020 Protein Science  
Both natively folded and intrinsically disordered proteins (IDPs) destined for the nucleus need to transport through the nuclear pore complexes (NPCs) in eukaryotic cells.  ...  Our data revealed that the rules executed for folded proteins are not well followed by the IDPs. Instead, both large and small IDPs can passively diffuse through the NPCs.  ...  ACKNOWLEDGMENTS We greatly thank Vladimir Uversky (University of South Florida, Tampa, USA) for providing helpful information on IDP characteristics to aid in our protein selections. We thank M.  ... 
doi:10.1002/pro.3845 pmid:32096308 fatcat:baqzdwfahvddtless7zp5da2im

Mechanism of Tc toxin action revealed in molecular detail

Dominic Meusch, Christos Gatsogiannis, Rouslan G. Efremov, Alexander E. Lang, Oliver Hofnagel, Ingrid R. Vetter, Klaus Aktories, Stefan Raunser
2014 Nature  
TcA forms a large bell-shaped pentameric structure 5,10,11 and enters the membrane like a syringe, forming a translocation channel through which the cytotoxic domain is probably transported into the cytoplasm  ...  This unique mechanism differs from that of typical pore-forming toxins 12 or other toxins that form translocation pores, for example, diphtheria 13 and anthrax toxin 14 .  ...  Bergbrede for technical support and the Raunser laboratory for selecting particles.  ... 
doi:10.1038/nature13015 pmid:24572368 fatcat:ik4vew5gyndfzm27leokq4ebzm

Transmembrane protein rotaxanes reveal kinetic traps in the refolding of translocated substrates

Jianfei Feng, Pablo Martin-Baniandres, Michael J. Booth, Gianluca Veggiani, Mark Howarth, Hagan Bayley, David Rodriguez-Larrea
2020 Communications Biology  
Here, we describe a single-molecule method to characterize the folded state of individual proteins after membrane translocation, by monitoring the ionic current passing through the pore.  ...  We trap the protein in the nanopore as a rotaxane-like complex using streptavidin stoppers. The protein is subjected to cycles of unfolding-translocation-refolding switching the voltage polarity.  ...  Jonathan Hopper and Professor Carol Robinson for the MS of the construct oligo(dC) 30 -V5-oligo(dA) 30  ... 
doi:10.1038/s42003-020-0840-5 pmid:32246060 fatcat:ro2n5a4msbf5vl4x5tq3y4szvy

Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes

Aksana A Labokha, Sabine Gradmann, Steffen Frey, Bastian B Hülsmann, Henning Urlaub, Marc Baldus, Dirk Görlich
2012 EMBO Journal  
Nuclear pore complexes (NPCs) control the traffic between cell nucleus and cytoplasm.  ...  While facilitating translocation of nuclear transport receptors (NTRs) and NTR . cargo complexes, they suppress passive passage of macromolecules X30 kDa.  ...  Acknowledgements We wish to thank Jü rgen Schü nemann and Uwe Plemann for excellent technical support; Koray Kirli for the pKK vectors; Maarten Fornerod for a xlNup214 clone; Irene Böttcher-Gajewski for  ... 
doi:10.1038/emboj.2012.302 pmid:23202855 pmcid:PMC3553378 fatcat:njjqbdljujeijc6gjj5xeh2hsu

Clustering by common friends finds locally significant proteins mediating modules

B. Andreopoulos, A. An, X. Wang, M. Faloutsos, M. Schroeder
2007 Bioinformatics  
We apply the algorithm to a yeast network. Results: Clusters and mediators are organized in hierarchies, where clusters are mediated by and act as mediators for other clusters.  ...  We illustrate the above findings with an example of membrane protein translocation from the cytoplasm to the inner nuclear membrane. Availability: All software is freely available under Supplementary  ...  ACKNOWLEDGEMENTS The authors are grateful for the comments of Christof Winter, the financial support of the Natural Sciences and Engineering Research Council (NSERC), the Ontario Graduate Scholarship Program  ... 
doi:10.1093/bioinformatics/btm064 pmid:17314122 fatcat:e2qs6bp34rhojhr26qumabalbe
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