Simulations of nuclear pore transport yield mechanistic insights and quantitative predictions

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 31, 2011, Pages

  Mincer, Joshua S ^a,b   Simon, Sanford M ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Filament dynamics; Mathematical modeling; Molecular motor; Nuclear cytoplasmic transport; Nucleoporins

Indexed keywords

GLYCINE; PHENYLALANINE;

ARTICLE; CONTROLLED STUDY; CROSS LINKING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NUCLEAR PORE COMPLEX; PARTICLE SIZE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ACTIVE TRANSPORT, CELL NUCLEUS; CELL NUCLEUS; GLYCINE; KARYOPHERINS; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; NUCLEAR LOCALIZATION SIGNALS; NUCLEAR PORE; NUCLEAR PORE COMPLEX PROTEINS; PHENYLALANINE; PROTEIN BINDING; RAN GTP-BINDING PROTEIN;

EID: 79961241643     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1104521108     Document Type: Article

References (26)

1. Lim RY, Ullman KS, Fahrenkrog B (2008) Biology and biophysics of the nuclear pore complex and its components. Int Rev Cell Mol Biol 267:299-342.
2. Peters R (2009) Translocation through the nuclear pore: Kaps pave the way. BioEssays 31:466-477.
3. Strawn LA, Shen T, Shulga N, Goldfarb DS, Wente SR (2004) Minimal nuclear pore complexes define FG repeat domains essential for transport. Nat Cell Biol 6:197-206. (Pubitemid 38344357)
4. Frey S, Richter RP, Gorlich D (2006) FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties. Science 314:815-817. (Pubitemid 44706647)
5. Ribbeck K, Gorlich D (2002) The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion. EMBO J 21:2664-2671. (Pubitemid 34619382)
6. Rout MP, Aitchison JD, Magnasco MO, Chait BT (2003) Virtual gating and nuclear transport: The hole picture. Trends Cell Biol 13:622-628. (Pubitemid 37415027)
7. Jovanovic-Talisman T, et al. (2009) Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature 457:1023-1027.
8. Peters R (2005) Translocation through the nuclear pore complex: Selectivity and speed by reduction-of-dimensionality. Traffic 6:421-427.
9. Lim RY, et al. (2007) Nanomechanical basis of selective gating by the nuclear pore complex. Science 318:640-643. (Pubitemid 350014836)
10. Melcak I, Hoelz A, Blobel G (2007) Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding. Science 315:1729-1732. (Pubitemid 46515630)
11. Simon SM, Peskin CS, Oster GF (1992) What drives the translocation of proteins? Proc Natl Acad Sci USA 89:3770-3774.
12. Miao L, Schulten K (2009) Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. Structure 17:449-459.
13. Zilman A, Di Talia S, Chait BT, Rout MP, Magnasco MO (2007) Efficiency, selectivity, and robustness of nucleocytoplasmic transport. PLoS Comput Biol 3:e125.
14. Kustanovich T, Rabin Y (2004) Metastable network model of protein transport through nuclear pores. Biophys J 86:2008-2016. (Pubitemid 38524393)
15. Alberts JB (2009) Biophysically realistic filament bending dynamics in agent-based biological simulation. PLoS ONE 4:e4748.
16. Grunwald D, Singer RH (2010) In vivo imaging of labelled endogenous beta-actin mRNA during nucleocytoplasmic transport. Nature 467:604-607.
17. Delphin C, Guan T, Melchior F, Gerace L (1997) RanGTP targets p97 to RanBP2, a filamentous protein localized at the cytoplasmic periphery of the nuclear pore complex. Mol Biol Cell 8:2379-2390. (Pubitemid 27528208)
18. Walther TC, et al. (2001) The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins. EMBO J 20:5703-5714. (Pubitemid 33010047)
19. Tu LC, Musser SM (2010) Single molecule studies of nucleocytoplasmic transport. Biochim Biophys Acta, 10.1016/j.bbamcr.2010.12.011.
20. Sun C, Yang W, Tu LC, Musser SM (2008) Single-molecule measurements of importin alpha/cargo complex dissociation at the nuclear pore. Proc Natl Acad Sci USA 105:8613-8618.
21. Dange T, Grunwald D, Grunwald A, Peters R, Kubitscheck U (2008) Autonomy and robustness of translocation through the nuclear pore complex: A single-molecule study. J Cell Biol 183:77-86.
22. Mattheyses AL, Kampmann M, Atkinson CT, Simon SM (2010) Fluorescence anisotropy reveals order and disorder of protein domains in the nuclear pore complex. Biophys J 99:1706-1717.
23. Kampmann M, Atkinson CE, Mattheyses AL, Simon SM (2011) Nat Struct Mol Biol, 18 pp:643-649.
24. Feynman R, Leighton R, Sands M (1963) The Feynman Lectures on Physics (Addison- Wesley, Reading, MA).
25. Stewart M (2007) Ratcheting mRNA out of the nucleus. Mol Cell 25:327-330.
26. Yamada J, et al. (2010) A bimodal distribution of two distinct categories of intrinsically-disordered structures with separate functions in FG nucleoporins. Mol Cell Proteomics 9(10):2205-2224.