RRM Proteins Interacting with the Cap Region of Topoisomerase I

Journal of Molecular Biology

Volumn 369, Issue 4, 2007, Pages 1098-1112

  Trzcińska Daneluti, Agata M ^a   Górecki, Adam ^a   Czubaty, Alicja ^a   Kowalska Loth, Barbara ^a   Girstun, Agnieszka ^a   Murawska, Magdalena ^a   Lesyng, Bogdan ^a   Staroń, Krzysztof ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

proteins interaction; RRM proteins; topoisomerase I

Indexed keywords

ALTERNATIVE SPLICING FACTOR; DNA TOPOISOMERASE; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; PROTEIN DERIVATIVE; PROTEIN MAGO; PROTEIN P54; PROTEIN Y14; SPLICING FACTOR 2; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CATALYSIS; DNA CLEAVAGE; ENZYME ACTIVITY; ENZYME MECHANISM; HYBRID; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN MOTIF; RNA RECOGNITION MOTIF; TRANSCRIPTION INITIATION SITE; YEAST;

MAGO;

EID: 34248589272     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.04.017     Document Type: Article

References (51)

1. Maris Ch., Dominguez C., and Allain F.H.-T. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J. 272 (2005) 2118-2131
2. Fiset S., and Chabot B. hnRNP A1 may interact simultaneously with telomeric DNA and the human telomerase RNA in vitro. Nucl. Acids Res. 29 (2001) 2268-2275
3. Samuels M., Deshpande G., and Schedl P. Activities of the Sex-lethal protein in RNA binding and protein:protein interactions. Nucl. Acids Res. 26 (1998) 2625-2637
4. Shi H., and Xu R.-M. Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes Dev. 17 (2003) 971-976
5. Lau C.-K., Diem M.D., Dreyfuss G., and Van Duyne G.D. Structure of the Y14-Magoh core of the exon junction complex. Curr. Biol. 13 (2003) 933-941
6. Fribourg S., Gatfield D., Izaurralde E., and Conti E. A novel mode of RBD-protein recognition in the Y14-Mago complex. Nature Struct. Biol. 10 (2003) 433-439
7. Khaleghpour K., Kahvejian A., De Crescenzo G., Roy G., Svitkin Y.V., Imataka H., et al. Dual interactions of the translational repressor Paip2 with poly(A) binding protein. Mol. Cell. Biol. 21 (2001) 5200-5213
8. Petersen-Mahrt S.K., Estmer C., Ohrmalm C., Matthews D.A., Russell W.C., and Akusjarvi G. The splicing factor-associated protein, p32, regulates RNA splicing by inhibiting ASF/SF2 RNA binding and phosphorylation. EMBO J. 18 (1999) 1014-1024
9. Estmer Nilsson C., Petersen-Mahrt S., Durot C., Shtrichman R., Krainer A.R., Kleinberger T., et al. The adenovirus E4-ORF4 splicing enhancer protein interacts with a subset of phosphorylated SR proteins. EMBO J. 20 (2001) 864-871
10. Kielkopf C.L., Lücke S., and Green M.R. U2AF homology motifs: protein recognition in the RRM world. Genes Dev. 18 (2004) 1513-1526
11. Kowalska-Loth B., Girstun A., Trzcińska A.M., Piekiełko-Witkowska A., and Staroń K. SF2/ASF protein binds to the cap region of human topoisomerase I through two RRM domains. Biochem. Biophys. Res. Commun. 331 (2005) 398-403
12. Leppard J.B., and Champoux J.J. Human DNA topoisomerase I: relaxation, roles, and damage control. Chromosoma 114 (2005) 75-85
13. Corbett K.D., and Berger J.M. Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct. 33 (2004) 95-118
14. Rossi F., Labourier E., Forné T., Divita G., Derancourt J., Riou J.F., et al. Specific phosphorylation of SR proteins by mammalian DNA topoisomerase I. Nature 381 (1996) 80-82
15. Kowalska-Loth B., Girstun A., Piekiełko A., and Staroń K. SF2/ASF protein inhibits camptothecin-induced DNA cleavage by human topoisomerase I. Eur. J. Biochem. 269 (2002) 3504-3510
16. Andersen F.F., Tange T.Ø., Sinnathamby T., Olsen J.R., Andersen K.E., Westergaard O., et al. The RNA splicing factor ASF/SF2 inhibits human topoisomerase I mediated DNA relaxation. J. Mol. Biol. 322 (2002) 677-686
17. Yang Z., and Champoux J.J. Reconstitution of enzymatic activity by the association of the cap and catalytic domains of human topoisomerase I. J. Biol. Chem. 277 (2002) 30815-30823
18. Czubaty A., Girstun A., Kowalska-Loth B., Trzcińska A.M., Purta E., Winczura A., et al. Proteomic analysis of complexes formed by human topoisomerase I. Biochim. Biophys. Acta 1749 (2005) 133-141
19. Ma A.S., Moran-Jones K., Shan J., Trent P., Munro T.P., Snee M.J., et al. Heterogeneous nuclear ribonucleoprotein A3, a novel RNA trafficking response element-binding protein. J. Biol. Chem. 277 (2002) 18010-18020
20. Shav-Tal Y., and Zipori D. PSF and p54(nrb)/NonO-multi-functional nuclear proteins. FEBS Lett. 531 (2002) 109-114
21. Ding J., Hayashi M.K., Zhang Y., Manche L., Krainer A.R., and Xu R.M. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 13 (1999) 1102-1115
22. Myers J.C., and Shamoo Y. Human UP1 as a model for understanding purine recognition in the family of proteins containing the RNA recognition motif (RRM). J. Mol. Biol. 342 (2004) 743-756
23. Laurie A.T., and Jackson R.M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21 (2005) 1908-1916
24. Binkowski T.A., Naghibzadeh S., and Liang J. CASTp: computed atlas of surface topography of proteins. Nucl. Acids Res. 31 (2003) 3352-3355
25. Kortemme T., Kim D.E., and Baker D. Computational alanine scanning of protein-protein interfaces. Sci. STKE 2004 (2004) pl2
26. Humphrey W., Dalke A., and Schulten K. VMD - Visual Molecular Dynamics. J. Molec. Graphics 14 (1996) 33-38
27. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 1781-1802
28. McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
29. Stapley B.J., and Doig A.J. Hydrogen bonding interactions between glutamine and asparagine in α-helical peptides. J. Mol. Biol. 272 (1997) 465-473
30. Shimoni L., and Glusker J.P. Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups. Protein Sci. 4 (1995) 67-74
31. Froloff N., Windemuth A., and Honig B. On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions. Protein Sci. 6 (1997) 1293-1301
32. Antosiewicz J., Błachut-Okrasinska E., Grycuk T., and Lesyng B. A correlation between protonation equilibria in biomolecular systems and their shapes: studies using a Poisson-Boltzmann model. In: Kenmochi N. (Ed). Free Boundary Problems. Theory and Applications. Mathematical Sciences and Applications vol. 14 (2000), Gakuto International Series, Tokyo 11-17
33. Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98 (2001) 10037-10041
34. Gruziel M., Kmiec P., Trylska J., and Lesyng B. Selected microscopic and mezoscopic modelling tools and models - an overview. In: Sokalski A. (Ed). Molecular Materials with Specific Interactions: Modeling and Design (2007), Springer, London 203-224
35. Ding J., Mariko K., Hayashi M.K., Zhang Y., Manche L., Krainer A.R., et al. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 13 (1999) 1102-1115
36. Dallaire F., Dupuis S., Fiset S., and Chabot B. Heterogeneous nuclear ribonucleoprotein A1 and UP1 protect mammalian telomeric repeats and modulate telomere replication in vitro. J. Biol. Chem. 275 (2000) 14509-14516
37. Fox A.H., Bond C.S., and Lamond A.I. P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Mol. Biol. Cell. 16 (2005) 5304-5315
38. Soret J., Gabut M., Dupon C., Kohlhagen G., Stévenin J., Pommier Y., et al. Altered serine/arginine-rich protein phosphorylation and exonic enhancer-dependent splicing in mammalian cells lacking topoisomerase I. Cancer Res. 63 (2003) 8203-8211
39. Pilch B., Allemand E., Facompré M., Bailly C., Riou J.F., Soret J., et al. Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-5061. Cancer Res. 61 (2001) 6876-6884
40. Straub T., Grue P., Uhse A., Lisby M., Knudsen B.R., Tange T.Ø., et al. The RNA-splicing factor PSF/p54nrb controls DNA-topoisomerase I activity by a direct interaction. J. Biol. Chem. 273 (1998) 26261-26264
41. Dallaire F., Dupuis S., Fiset S., and Chabot B. Heterogeneous nuclear ribonucleoprotein A1 and UP1 protect mammalian telomeric repeats and modulate telomere replication in vitro. J. Biol. Chem. 275 (2000) 14509-14516
42. Kang M.R., Muller M.T., and Chung I.K. Telomeric DNA damage by topoisomerase I. A possible mechanism for cell killing by camptothecin. J. Biol. Chem. 279 (2004) 12535-12541
43. Ghigna C., Moroni M., Porta G., Riva S., and Biamonti G. Altered expression of heterogeneous nuclear ribonucleoproteins and SR factors in human colon adenocarcinomas. Cancer Res. 58 (1998) 5818-5824
44. Maeda T., and Furukawa S. Transformation-associated changes in gene expression of alternative splicing regulatory factors in mouse fibroblast cells. Oncol. Rep. 8 (2001) 563-566
45. Zerbe L.K., Pino I., Pio R., Cosper P.F., Dwyer-Nield L.D., Meyer A.M., et al. Relative amounts of antagonistic splicing factors, hnRNP A1 and ASF/SF2, change during neoplastic lung growth: implications for pre-mRNA processing. Mol. Carcinogen. 41 (2004) 187-196
46. James P., Halladay J., and Craig E.A. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144 (1996) 1425-1436
47. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25 (1997) 4876-4882
48. Leach A.R. Molecular Modelling. Principles and Applications (2001), Pearson Education Limited, Essex, UK
49. Horton N., and Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci. 1 (1992) 169-181
50. Yang Ch., Jas G.S., and Kuczera K. Structure and dynamics of calcium-activated calmodulin in solution. J. Biomol. Struct. Dynam. 19 (2001) 247-271
51. Trylska J., McCammon J.A., and Brookes III Ch.L. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J. Am. Chem. Soc. 127 (2005) 11125-11133