The interaction of CRM1 and the nuclear pore protein Tpr

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Zhao, Charles L ^a   Mahboobi, Seyed Hanif ^a   Moussavi Baygi, Ruhollah ^a   Mofrad, Mohammad R K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; EXPORTIN 1; NUCLEAR PROTEIN; RAN PROTEIN; SNURPORTIN; TRANSLOCATED PROMOTER REGION PROTEIN; UNCLASSIFIED DRUG; CAP BINDING PROTEIN; CELL RECEPTOR; EXPORTIN 1 PROTEIN; KARYOPHERIN; LIGAND; MESSENGER RNA; NUCLEOPORIN; ONCOPROTEIN; PROTEIN BINDING; SNUPN PROTEIN, HUMAN; TPR PROTEIN, HUMAN;

ARTICLE; BINDING AFFINITY; BINDING SITE; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; HUMAN; METABOLISM; NUCLEAR PORE; PHYSIOLOGY;

BINDING SITES; HUMANS; KARYOPHERINS; LIGANDS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; NUCLEAR PORE; NUCLEAR PORE COMPLEX PROTEINS; PROTEIN BINDING; PROTO-ONCOGENE PROTEINS; RAN GTP-BINDING PROTEIN; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RNA CAP-BINDING PROTEINS; RNA, MESSENGER; SOFTWARE;

EID: 84899585317     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093709     Document Type: Article

References (57)

1. Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, et al. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol 148: 635-651.
2. Monecke T, Guttler T, Neumann P, Dickmanns A, Gorlich D, et al. (2009) Crystal structure of the nuclear export receptor CRM1 in complex with Snurportin1 and RanGTP. Science 324: 1087-1091.
3. Sorokin AV, Kim ER, Ovchinnikov LP (2007) Nucleocytoplasmic transport of proteins. Biochemistry (Mosc) 72: 1439-1457.
4. Pemberton LF, Paschal BM (2005) Mechanisms of receptor-mediated nuclear import and nuclear export. Traffic 6: 187-198. (Pubitemid 40298153)
5. Cingolani G, Lashuel HA, Gerace L, Muller CW (2000) Nuclear import factors importin alpha and importin beta undergo mutually induced conformational changes upon association. FEBS Lett 484: 291-298.
6. Lusk CP, Waller DD, Makhnevych T, Dienemann A, Whiteway M, et al. (2007) Nup53p is a target of two mitotic kinases, Cdk1p and Hrr25p. Traffic 8: 647-660. (Pubitemid 46785148)
7. Fornerod M, Ohno M, Yoshida M, Mattaj IW (1997) CRM1 is an export receptor for leucine-rich nuclear export signals. Cell 90: 1051-1060. (Pubitemid 27408519)
8. Wente SR, Rout MP (2010) The Nuclear Pore Complex and Nuclear Transport. Cold Spring Harb Perspect Biol.
9. Jamali T, Jamali Y, Mehrbod M, Mofrad MRK (2011) Nuclear Pore Complex: Biochemistry and Biophysics of Nucleocytoplasmic Transport in Health and Disease. nternational Reviews of Cell and Molecular Biology 28706 233.
10. Lapalombella R, Sun Q, Williams K, Tangeman L, Jha S, et al. (2012) Selective inhibitors of nuclear export (SINE) show that CRM1/XPO1 is a target in chronic lymphocytic leukemia. Blood.
11. Guttler T, Madl T, Neumann P, Deichsel D, Corsini L, et al. (2010) NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Nat Struct Mol Biol 17: 1367-1376.
12. Williams P, Verhagen J, Elliott G (2008) Characterization of a CRM1- dependent nuclear export signal in the C terminus of herpes simplex virus type 1 tegument protein UL47. J Virol 82: 10946-10952. (Pubitemid 352691185)
13. Forgues M, Difilippantonio MJ, Linke SP, Ried T, Nagashima K, et al. (2003) Involvement of Crm1 in hepatitis B virus X protein-induced aberrant centriole replication and abnormal mitotic spindles. Mol Cell Biol 23: 5282-5292. (Pubitemid 36950883)
14. Wolff B, Sanglier JJ, Wang Y (1997) Leptomycin B is an inhibitor of nuclear export: inhibition of nucleo-cytoplasmic translocation of the human immunodeficiency virus type 1 (HIV-1) Rev protein and Rev-dependent mRNA. Chem Biol 4: 139-147. (Pubitemid 27161752)
15. Fukuda M, Asano S, Nakamura T, Adachi M, Yoshida M, et al. (1997) CRM1 is responsible for intracellular transport mediated by the nuclear export signal. Nature 390: 308-311. (Pubitemid 27513316)
16. Zhang K, Wang M, Tamayo AT, Shacham S, Kauffman M, et al. (2012) Novel selective inhibitors of nuclear export CRM1 antagonists for therapy in mantle cell lymphoma. Exp Hematol.
17. Ben-Efraim I, Frosst PD, Gerace L (2009) Karyopherin binding interactions and nuclear import mechanism of nuclear pore complex protein Tpr. BMC Cell Biol 10: 74.
18. Hase ME, Kuznetsov NV, Cordes VC (2001) Amino acid substitutions of coiled-coil protein Tpr abrogate anchorage to the nuclear pore complex but not parallel, in-register homodimerization. Mol Biol Cell 12: 2433-2452. (Pubitemid 33051967)
19. Krull S, Thyberg J, Bjorkroth B, Rackwitz HR, Cordes VC (2004) Nucleoporins as components of the nuclear pore complex core structure and Tpr as the architectural element of the nuclear basket. Mol Biol Cell 15: 4261-4277. (Pubitemid 39122028)
20. Frosst P, Guan T, Subauste C, Hahn K, Gerace L (2002) Tpr is localized within the nuclear basket of the pore complex and has a role in nuclear protein export. J Cell Biol 156: 617-630. (Pubitemid 34839878)
21. Shibata S, Matsuoka Y, Yoneda Y (2002) Nucleocytoplasmic transport of proteins and poly(A) + RNA in reconstituted Tpr-less nuclei in living mammalian cells. Genes to cells : devoted to molecular & cellular mechanisms 7: 421-434.
22. Ben-Efraim I, Frosst PD, Gerace L (2009) Karyopherin binding interactions and nuclear import mechanism of nuclear pore complex protein Tpr. BMC cell biology 10: 74.
23. Frosst P, Guan T, Subauste C, Hahn K, Gerace L (2002) Tpr is localized within the nuclear basket of the pore complex and has a role in nuclear protein export. The Journal of cell biology 156: 617-630. (Pubitemid 34839878)
24. Coyle JH, Bor YC, Rekosh D, Hammarskjold ML (2011) The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway. RNA 17: 1344-1356.
25. Rajanala K, Nandicoori VK (2012) Localization of nucleoporin Tpr to the nuclear pore complex is essential for Tpr mediated regulation of the export of unspliced RNA. PloS one 7: e29921.
26. Park M, Dean M, Cooper CS, Schmidt M, O'Brien SJ, et al. (1986) Mechanism of met oncogene activation. Cell 45: 895-904. (Pubitemid 16083694)
27. Zimowska G, Aris JP, Paddy MR (1997) A Drosophila Tpr protein homolog is localized both in the extrachromosomal channel network and to nuclear pore complexes. Journal of cell science 110 (Pt 8): 927-944. (Pubitemid 27216113)
28. Bangs P, Burke B, Powers C, Craig R, Purohit A, et al. (1998) Functional analysis of Tpr: identification of nuclear pore complex association and nuclear localization domains and a role in mRNA export. The Journal of cell biology 143: 1801-1812. (Pubitemid 29022605)
29. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802. (Pubitemid 43078511)
30. Klauda JB, Brooks BR, MacKerell AD Jr., Venable RM, Pastor RW (2005) An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J Phys Chem B 109: 5300-5311. (Pubitemid 40407752)
31. Feller SE, MacKerell AD Jr. (2000) An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids. J Phys Chem B 104: 7510-7515.
32. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38, 27-38.
33. Dong X, Biswas A, Suel KE, Jackson LK, Martinez R, et al. (2009) Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 458: 1136-1141.
34. Singh B (2004) PepBuild: a web server for building structure data of peptides/proteins. Nucleic Acids Res 32: W559-561.
35. Isgro TA, Schulten K (2005) Binding dynamics of isolated nucleoporin repeat regions to importin-beta. Structure 13: 1869-1879. (Pubitemid 41772955)
36. Isgro TA, Schulten K (2007) Cse1p-binding dynamics reveal a binding pattern for FG-repeat nucleoporins on transport receptors. Structure 15: 977-991. (Pubitemid 47212749)
37. Isgro TA, Schulten K (2007) Association of nuclear pore FG-repeat domains to NTF2 import and export complexes. J Mol Biol 366: 330-345. (Pubitemid 46123344)
38. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723. (Pubitemid 28059943)
39. Darden T, York D, Pedersen L (1993) Particle Mesh Ewald - an N.Log(N) Method for Ewald Sums in Large Systems. Journal of Chemical Physics 98: 10089-10092.
40. Schlick T, Skeel RD, Brunger AT, Kale LV, Board JA, et al. (1999) Algorithmic challenges in computational molecular biophysics. Journal of Computational Physics 151: 9-48.
41. Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method. Journal of Chemical Physics 103: 4613-4621.
42. Magrane M, Consortium U (2011) UniProt Knowledgebase: a hub of integrated protein data. Database-the Journal of Biological Databases and Curation.
43. Bairoch A (2009) UniProtKB/Swiss-Prot: from sequences to functions. Febs Journal 276: 9-9.
44. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
45. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research 31: 3497-3500. (Pubitemid 37442184)
46. Marsh JA, Teichmann SA (2011) Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding. Structure 19: 859-867. 47. de Vries SJ, Bonvin AMJJ (2008) How proteins get in touch: Interface prediction in the study of biomolecular complexes. Current Protein & Peptide Science 9: 394-406.
47. Chen H, Zhou HX (2005) Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins-Structure Function and Bioinformatics 61: 21-35. (Pubitemid 41262914)
48. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R (2007) PIER: protein interface recognition for structural proteomics. Proteins-Structure Function and Bioinformatics 67: 400-417. (Pubitemid 46449416)
49. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, et al. (2003) ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. Bioinformatics 19: 163-164. (Pubitemid 36150199)
50. Neuvirth H, Raz R, Schreiber G (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338: 181-199. (Pubitemid 38429796)
51. Tuncbag N, Gursoy A, Nussinov R, Keskin O (2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nature Protocols 6: 1341-1354.
52. Porollo A, Meller J (2007) Prediction-based fingerprints of protein-protein interactions. Proteins-Structure Function and Bioinformatics 66: 630-645.
53. de Vries SJ, van Dijk AD, Bonvin AM (2006) WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins-Structure Function and Bioinformatics 63: 479-489.
54. Meller J, Porollo A (2012) Computational Methods for Prediction of Protein-Protein Interaction Sites. In: Cai W, Hong H, editors. Protein-Protein Interactions - Computational and Experimental Tools: InTech.
55. Güttler T, Madl T, Neumann P, Deichsel D, Corsini L, et al. (2010) NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Nature Structural & Molecular Biology 17: 1367-1376.
56. Chook YM, Blobel G (2001) Karyopherins and nuclear import. Curr Opin Struct Biol 11: 703-715.
57. Terry LJ, Wente SR (2009) Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport. Eukaryotic Cell 8: 1814-1827.