Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics

Structure

Volumn 17, Issue 3, 2009, Pages 449-459

  Miao, Lingling ^a   Schulten, Klaus ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

PROTEINS; RNA

Indexed keywords

GLYCINE; PHENYLALANINE; PROTEIN; PROTEIN NSP 1; PROTEIN NTF2; TRANSPORT RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR PORE COMPLEX; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; STRUCTURE ANALYSIS;

CELL NUCLEUS; COMPUTER SIMULATION; CYTOPLASM; MODELS, MOLECULAR; NUCLEAR PORE; NUCLEOCYTOPLASMIC TRANSPORT PROTEINS;

EID: 61449201281     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.12.021     Document Type: Article

References (49)

1. Alber F., Dokudovskaya S., Veenhoff L.M., Zhang W., Kipper J., Devos D., Suprapto A., Karni-Schmidt O., Williams R., Chait B.T., et al. Determining the architectures of macromolecular assemblies. Nature 450 (2007) 683-694
2. Alber F., Dokudovskaya S., Veenhoff L.M., Zhang W., Kipper J., Devos D., Suprapto A., Karni-Schmidt O., Williams R., Chait B.T., et al. The molecular architecture of the nuclear pore complex. Nature 450 (2007) 695-701
3. Alexander S. Polymer adsorption on small spheres. A scaling approach. Le Journal de Physique 38 (1977) 977-981
4. Bayliss R., Leung S.W., Baker R.P., Quimby B.B., Corbett A.H., and Stewart M. Structural basis for the interaction between NTF2 and nucleoporin FxFG repeats. EMBO J. 21 (2002) 2843-2853
5. Bayliss R., Littlewood T., Strawn L.A., Wente S.R., and Stewart M. GLFG and FxFG nucleoporins bind to overlapping sites on importin-β. J. Biol. Chem. 277 (2002) 50597-50606
6. Beck M., Förster F., Ecke M., Plitzko J.M., Melchior F., Gerisch G., Baumeister W., and Medalia O. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306 (2004) 1387-1390
7. Bednenko J., Cingolani G., and Gerace L. Importin-β contains a COOH-terminal nucleoporin binding region important for nuclear transport. J. Cell Biol. 162 (2003) 391-401
8. Cronshaw J.M., Krutchinsky A., Zhang W., Chait B., and Matunis M. Proteomic analysis of the mammalian nuclear pore complex. J. Cell Biol. 158 (2002) 915-927
9. Darden T., York D., and Pedersen L. Particle mesh Ewald. An N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
10. de Gennes P.G. Conformations of polymers attached to an interface. Macromolecules 13 (1980) 1069-1075
11. Denning D.P., and Rexach M. Rapid evolution exposes the boundaries of domain structure and function in natively unfolded FG nucleoporins. Mol. Cell. Proteomics 6 (2007) 272-282
12. Denning D.P., Patel S.S., Uversky V., Fink A.L., and Rexach M. Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc. Natl. Acad. Sci. USA 100 (2003) 2450-2455
13. Feller S.E., Zhang Y.H., Pastor R.W., and Brooks B.R. Constant pressure molecular dynamics simulation - the Langevin piston method. J. Chem. Phys. 103 (1995) 4613-4621
14. Freddolino P.L., Arkhipov A., Shih A.Y., Yin Y., Chen Z., and Schulten K. Application of residue-based and shape-based coarse graining to biomolecular simulations. In: Voth G.A. (Ed). Coarse-Graining of Condensed Phase and Biomolecular Systems (2008), Chapman and Hall/CRC Press, Taylor and Francis Group, Boca Raton, FL 299-315 Chapter 20
15. Frey S., and Görlich D. A saturated FG-repeat hydrogel can reproduce the permeability properties of nuclear pore complexes. Cell 130 (2007) 512-523
16. Frey S., Richter R., and Görlich D. FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties. Science 314 (2006) 815-817
17. Gerace L., and Burke B. Functional organization of the nuclear envelope. Annu. Rev. Cell Biol. 4 (1988) 335-374
18. Görlich D., and Kutay U. Transport between the cell nucleus and the cytoplasm. Annu. Rev. Cell Dev. Biol. 15 (1999) 607-660
19. Grubmüller H., Heller H., Windemuth A., and Schulten K. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul. 6 (1991) 121-142
20. Gumbart J., Wang Y., Aksimentiev A., Tajkhorshid E., and Schulten K. Molecular dynamics simulations of proteins in lipid bilayers. Curr. Opin. Struct. Biol. 15 (2005) 423-431
21. Heller H., Schaefer M., and Schulten K. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases. J. Phys. Chem. 97 (1993) 8343-8360
22. Humphrey W., Dalke A., and Schulten K. VMD - Visual Molecular Dynamics. J. Mol. Graph. 14 (1996) 33-38
23. Isgro T.A., and Schulten K. Binding dynamics of isolated nucleoporin repeat regions to importin-β. Structure 13 (2005) 1869-1879
24. Isgro T.A., and Schulten K. Association of nuclear pore FG-repeat domains to NTF2 import and export complexes. J. Mol. Biol. 366 (2007) 330-345
25. Isgro T.A., and Schulten K. Cse1p binding dynamics reveal a novel binding pattern for FG-repeat nucleoporins on transport receptors. Structure 15 (2007) 977-991
26. Lim R.Y., Huang N., Köser J., Deng J., Lau K., Schwarz-Herion K., Fahrenkrog B., and Aebi U. Flexible phenylalanine-glycine nucleoporins as entropic barriers to nucleocytoplasmic transport. Proc. Natl. Acad. Sci. USA 103 (2006) 9512-9517
27. Lim R.Y.H., Fahrenkrog B., Koser J., Schwarz-Herion K., Deng J., and Aebi U. Nanomechanical basis of selective gating by the nuclear pore complex. Science 318 (2007) 640-643
28. Lim R.Y.H., Aebi U., and Fahrenkrog B. Towards reconciling structure and function in the nuclear pore complex. Histochem. Cell Biol. 129 (2008) 105-116
29. Liu S.M., and Stewart M. Structural basis for the high-affinity binding of nucleoporin Nup1p to the Saccharomyces cerevisiae importin-β homologue, Kap95p. J. Mol. Biol. 349 (2005) 515-525
30. Macara I.G. Transport into and out of the nucleus. Microbiol. Mol. Biol. Rev. 65 (2001) 570-594
31. Marrink S.J., de Vries A.H., and Mark A.E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 108 (2004) 750-760
32. Marrink S.J., Risselada J., and Mark A.E. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem. Phys. Lipids 135 (2005) 223-244
33. Martyna G.J., Tobias D.J., and Klein M.L. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101 (1994) 4177-4189
34. Milner S.T. Polymer brushes. Science 251 (1991) 905-914
35. Morrison J., Yang J., Stewart M., and Neuhaus D. Solution NMR study of the interaction between NTF2 and nucleoporin FxFG repeats. J. Mol. Biol. 333 (2003) 587-603
36. Pemberton L.F., and Paschal B. Mechanisms of receptor-mediated nuclear import and nuclear export. Traffic 6 (2005) 187-198
37. Peters R. Translocation through the nuclear pore complex: selectivity and speed by reduction-of-dimensionality. Traffic 6 (2005) 421-427
38. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., and Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 1781-1802
39. Rexach M., and Blobel G. Protein import into nuclei: association and dissociation reactions involving transport substrate, transport factors, and nucleoporins. Cell 83 (1995) 683-692
40. Ribbeck K., and Görlich D. The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion. EMBO J. 21 (2002) 2664-2671
41. Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., and Chait B.T. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148 (2000) 635-651
42. Schlick T., Skeel R., Brünger A., Kalé L., Board Jr. J.A., Hermans J., and Schulten K. Algorithmic challenges in computational molecular biophysics. J. Comp. Physiol. 151 (1999) 9-48
43. Shih A.Y., Arkhipov A., Freddolino P.L., and Schulten K. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B 110 (2006) 3674-3684
44. Shih A.Y., Arkhipov A., Freddolino P.L., Sligar S.G., and Schulten K. Assembly of lipids and proteins into lipoprotein particles. J. Phys. Chem. B 111 (2007) 11095-11104
45. Shih A.Y., Freddolino P.L., Arkhipov A., and Schulten K. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. J. Struct. Biol. 157 (2007) 579-592
46. Shih A.Y., Freddolino P.L., Sligar S.G., and Schulten K. Disassembly of nanodiscs with cholate. Nano Lett. 7 (2007) 1692-1696
47. Shih A.Y., Freddolino P.L., Arkhipov A., Sligar S.G., and Schulten K. Molecular modeling of the structural properties and formation of high-density lipoprotein particles. In: Feller S. (Ed). Current Topics in Membranes: Computational Modeling of Membrane Bilayers, Chapter 11 (2008), Elsevier, San Diego 313-342
48. Stewart M., Kent H.M., and McCoy A.J. Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. J. Mol. Biol. 277 (1998) 635-646
49. Strawn L.A., Shen T., Shulga N., Goldfarb D.S., and Wente S.R. Minimal nuclear pore complexes define FG repeat domains essential for transport. Nat. Cell Biol. 6 (2004) 197-206