Literature DB >> 23931304

A simple kinetic model with explicit predictions for nuclear transport.

Sanghyun Kim1, M Elbaum.   

Abstract

Molecular exchange between the cell nucleus and cytoplasm is one of the most fundamental features of eukaryotic cell biology. The nuclear pores act as a conduit of this transport, both for cargo that crosses the pore autonomously as well as that whose translocation requires an intermediary receptor. The major class of such receptors is regulated by the small GTPase Ran, via whose interaction the nucleo-cytoplasmic transport system functions as a selective molecular pump. We propose a simple analytical model for transport that includes both translocation and receptor binding kinetics. The model is suitable for steady-state kinetics such as fluorescence recovery after photobleaching. Time constants appear as a combination of parameters whose effects on measured kinetics are not separable. Competitive cargo binding to receptors and large cytoplasmic volume buffer the transport properties of any particular cargo. Specific limits to the solutions provide a qualitative insight and interpretation of nuclear transport in the cellular context. Most significantly, we find that under realistic conditions receptor binding, rather than permeability of the nuclear pores, may be rate-limiting for nucleo-cytoplasmic exchange.
Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23931304      PMCID: PMC3736664          DOI: 10.1016/j.bpj.2013.04.025

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  22 in total

1.  Kinetic analysis of translocation through nuclear pore complexes.

Authors:  K Ribbeck; D Görlich
Journal:  EMBO J       Date:  2001-03-15       Impact factor: 11.598

2.  Quantitative analysis of nuclear localization signal (NLS)-importin alpha interaction through fluorescence depolarization. Evidence for auto-inhibitory regulation of NLS binding.

Authors:  P Fanara; M R Hodel; A H Corbett; A E Hodel
Journal:  J Biol Chem       Date:  2000-07-14       Impact factor: 5.157

3.  Systems analysis of Ran transport.

Authors:  Alicia E Smith; Boris M Slepchenko; James C Schaff; Leslie M Loew; Ian G Macara
Journal:  Science       Date:  2002-01-18       Impact factor: 47.728

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

Authors:  Katharina Ribbeck; Dirk Görlich
Journal:  EMBO J       Date:  2002-06-03       Impact factor: 11.598

5.  A spatial model of cellular molecular trafficking including active transport along microtubules.

Authors:  A Cangiani; R Natalini
Journal:  J Theor Biol       Date:  2010-09-08       Impact factor: 2.691

6.  Nucleocytoplasmic transport: a thermodynamic mechanism.

Authors:  Ronen Benjamine Kopito; Michael Elbaum
Journal:  HFSP J       Date:  2009-03-18

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

Authors:  Mario Tagliazucchi; Orit Peleg; Martin Kröger; Yitzhak Rabin; Igal Szleifer
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-12       Impact factor: 11.205

8.  Accelerating the rate of disassembly of karyopherin.cargo complexes.

Authors:  Daniel Gilchrist; Brook Mykytka; Michael Rexach
Journal:  J Biol Chem       Date:  2002-02-26       Impact factor: 5.157

9.  Charge as a selection criterion for translocation through the nuclear pore complex.

Authors:  Lucy J Colwell; Michael P Brenner; Katharina Ribbeck
Journal:  PLoS Comput Biol       Date:  2010-04-22       Impact factor: 4.475

10.  Simple kinetic relationships and nonspecific competition govern nuclear import rates in vivo.

Authors:  Benjamin L Timney; Jaclyn Tetenbaum-Novatt; Diana S Agate; Rosemary Williams; Wenzhu Zhang; Brian T Chait; Michael P Rout
Journal:  J Cell Biol       Date:  2006-11-20       Impact factor: 10.539

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  13 in total

1.  Enzymatically driven transport: a kinetic theory for nuclear export.

Authors:  Sanghyun Kim; M Elbaum
Journal:  Biophys J       Date:  2013-11-05       Impact factor: 4.033

2.  Enhanced Nucleocytoplasmic Transport due to Competition for Elastic Binding Sites.

Authors:  Ben Fogelson; James P Keener
Journal:  Biophys J       Date:  2018-07-03       Impact factor: 4.033

3.  Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos.

Authors:  Shai R Joseph; Máté Pálfy; Lennart Hilbert; Mukesh Kumar; Jens Karschau; Vasily Zaburdaev; Andrej Shevchenko; Nadine L Vastenhouw
Journal:  Elife       Date:  2017-04-20       Impact factor: 8.140

4.  Thermodynamic Paradigm for Solution Demixing Inspired by Nuclear Transport in Living Cells.

Authors:  Ching-Hao Wang; Pankaj Mehta; Michael Elbaum
Journal:  Phys Rev Lett       Date:  2017-04-10       Impact factor: 9.161

5.  Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment.

Authors:  Bart W Hoogenboom; Loren E Hough; Edward A Lemke; Roderick Y H Lim; Patrick R Onck; Anton Zilman
Journal:  Phys Rep       Date:  2021-03-24       Impact factor: 30.510

6.  Mechanical force application to the nucleus regulates nucleocytoplasmic transport.

Authors:  Ion Andreu; Ignasi Granero-Moya; Nimesh R Chahare; Kessem Clein; Marc Molina-Jordán; Amy E M Beedle; Alberto Elosegui-Artola; Juan F Abenza; Leone Rossetti; Xavier Trepat; Barak Raveh; Pere Roca-Cusachs
Journal:  Nat Cell Biol       Date:  2022-06-09       Impact factor: 28.213

7.  Balance of osmotic pressures determines the nuclear-to-cytoplasmic volume ratio of the cell.

Authors:  Dan Deviri; Samuel A Safran
Journal:  Proc Natl Acad Sci U S A       Date:  2022-05-17       Impact factor: 12.779

8.  Molecular determinants of large cargo transport into the nucleus.

Authors:  Giulia Paci; Tiantian Zheng; Joana Caria; Anton Zilman; Edward A Lemke
Journal:  Elife       Date:  2020-07-21       Impact factor: 8.140

9.  Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex.

Authors:  Petra Popken; Ali Ghavami; Patrick R Onck; Bert Poolman; Liesbeth M Veenhoff
Journal:  Mol Biol Cell       Date:  2015-01-28       Impact factor: 4.138

10.  Dissecting in vivo steady-state dynamics of karyopherin-dependent nuclear transport.

Authors:  Ogheneochukome Lolodi; Hiroya Yamazaki; Shotaro Otsuka; Masahiro Kumeta; Shige H Yoshimura
Journal:  Mol Biol Cell       Date:  2015-11-04       Impact factor: 4.138

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