Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: The p53 example

Molecular BioSystems

Volumn 5, Issue 12, 2009, Pages 1770-1778

  Tuncbag, Nurcan ^a   Kar, Gozde ^a   Gursoy, Attila ^a   Keskin, Ozlem ^a   Nussinov, Ruth ^b,c  

^a KOÇ UNIVERSITY   (Turkey)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN MDM2; PROTEIN P53; RETINOBLASTOMA PROTEIN; TP53 PROTEIN, HUMAN;

ALGORITHM; ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN BINDING; SIGNAL TRANSDUCTION; TIME;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; PROTO-ONCOGENE PROTEINS C-MDM2; RETINOBLASTOMA PROTEIN; SIGNAL TRANSDUCTION; TIME FACTORS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 72949088633     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/b905661k     Document Type: Article

References (57)

1. P. Aloy M. Pichaud R. B. Russell Protein complexes: structure prediction challenges for the 21st century Curr. Opin. Struct. Biol. 2005 15 1 15 22
2. P. Aloy R. B. Russell Interrogating protein interaction networks through structural biology Proc. Natl. Acad. Sci. U. S. A. 2002 99 9 5896 5901
3. P. Aloy R. B. Russell The third dimension for protein interactions and complexes Trends Biochem. Sci. 2002 27 12 633 638
4. P. Aloy R. B. Russell Structural systems biology: modelling protein interactions Nat. Rev. Mol. Cell Biol. 2006 7 3 188 197
5. P. Bork L. Serrano Towards cellular systems in 4D Cell (Cambridge, Mass.) 2005 121 4 507 509
6. G. Dawelbait C. Winter Y. Zhang C. Pilarsky R. Grutzmann J. C. Heinrich M. Schroeder Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data Bioinformatics 2007 23 13 i115 i124
7. A. Gursoy O. Keskin R. Nussinov Topological properties of protein interaction networks from a structural perspective Biochem. Soc. Trans. 2008 36 Pt 6 1398 1403
8. O. Keskin A. Gursoy B. Ma R. Nussinov Towards drugs targeting multiple proteins in a systems biology approach Curr. Top. Med. Chem. 2007 7 10 943 951
9. C. Kiel P. Beltrao L. Serrano Analyzing protein interaction networks using structural information Annu. Rev. Biochem. 2008 77 415 441
10. P. M. Kim L. J. Lu Y. Xia M. B. Gerstein Relating three-dimensional structures to protein networks provides evolutionary insights Science 2006 314 5807 1938 1941
11. A. S. Aytuna A. Gursoy O. Keskin Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces Bioinformatics 2005 21 12 2850 2855
12. O. Keskin R. Nussinov Similar binding sites and different partners: implications to shared proteins in cellular pathways Structure (London) 2007 15 3 341 354
13. O. Keskin R. Nussinov A. Gursoy PRISM: protein-protein interaction prediction by structural matching Methods Mol. Biol. (Totowa, N. J.) 2008 484 505 521
14. O. Keskin N. Tuncbag A. Gursoy Characterization and prediction of protein interfaces to infer protein-protein interaction networks Curr. Pharm. Biotechnol. 2008 9 2 67 76
15. U. Ogmen O. Keskin A. S. Aytuna R. Nussinov A. Gursoy PRISM: protein interactions by structural matching Nucleic Acids Res. 2005 33 W331 W336
16. C. Kiel S. Wohlgemuth F. Rousseau J. Schymkowitz J. Ferkinghoff-Borg F. Wittinghofer L. Serrano Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations J. Mol. Biol. 2005 348 3 759 775
17. T. Kortemme L. A. Joachimiak A. N. Bullock A. D. Schuler B. L. Stoddard D. Baker Computational redesign of protein-protein interaction specificity Nat. Struct. Mol. Biol. 2004 11 4 371 379
18. T. Selzer S. Albeck G. Schreiber Rational design of faster associating and tighter binding protein complexes Nat. Struct. Biol. 2000 7 7 537 541
19. T. Z. Sen A. Kloczkowski R. L. Jernigan Functional clustering of yeast proteins from the protein-protein interaction network BMC Bioinformatics 2006 7 355
20. J. D. Han N. Bertin T. Hao D. S. Goldberg G. F. Berriz L. V. Zhang D. Dupuy A. J. Walhout M. E. Cusick F. P. Roth M. Vidal Evidence for dynamically organized modularity in the yeast protein-protein interaction network Nature 2004 430 6995 88 93
21. K. Komurov M. White Revealing static and dynamic modular architecture of the eukaryotic protein interaction network Mol. Syst. Biol. 2007 3 110
22. U. de Lichtenberg L. J. Jensen S. Brunak P. Bork Dynamic complex formation during the yeast cell cycle Science 2005 307 5710 724 727
23. N. Tuncbag A. Gursoy E. Guney R. Nussinov O. Keskin Architectures and functional coverage of protein-protein interfaces J. Mol. Biol. 2008 381 3 785 802
24. J. D. Thompson D. G. Higgins T. J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 1994 22 22 4673 4680
25. O. Keskin C. J. Tsai H. Wolfson R. Nussinov A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications Protein Sci. 2004 13 4 1043 1055
26. H. Zhu F. S. Domingues I. Sommer T. Lengauer NOXclass: prediction of protein-protein interaction types BMC Bioinformatics 2006 7 27
27. E. Guney N. Tuncbag O. Keskin A. Gursoy HotSprint: database of computational hot spots in protein interfaces Nucleic Acids Res. 2008 36 D662 D666
28. K. W. Kohn Molecular interaction map of the mammalian cell cycle control and DNA repair systems Mol. Biol. Cell 1999 10 8 2703 2734
29. NACCESS [http://www.bioinf.manchester.ac.uk/naccess/]
30. M. Shatsky O. Dror D. Schneidman-Duhovny R. Nussinov H. J. Wolfson BioInfo3D: a suite of tools for structural bioinformatics Nucleic Acids Res. 2004 32 W503 W507
31. M. Shatsky R. Nussinov H. J. Wolfson A method for simultaneous alignment of multiple protein structures Proteins: Struct., Funct., Genet. 2004 56 1 143 156
32. L. Dartnell E. Simeonidis M. Hubank S. Tsoka I. D. Bogle L. G. Papageorgiou Robustness of the p53 network and biological hackers FEBS Lett. 2005 579 14 3037 3042
33. L. Salwinski C. S. Miller A. J. Smith F. K. Pettit J. U. Bowie D. Eisenberg The Database of Interacting Proteins 2004 Update Nucleic Acids Res. 2004 32 D449 D451
34. G. D. Bader D. Betel C. W. Hogue BIND: The Biomolecular Interaction Network Database Nucleic Acids Res. 2003 31 1 248 250
35. A. Chatr-aryamontri A. Ceol L. M. Palazzi G. Nardelli M. V. Schneider L. Castagnoli G. Cesareni MINT: The Molecular INTeraction Database Nucleic Acids Res. 2007 35 D572 D574
36. P. H. Kussie S. Gorina V. Marechal B. Elenbaas J. Moreau A. J. Levine N. P. Pavletich Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain Science 1996 274 5289 948 953 (Pubitemid 26398409)
37. R. Rosal M. R. Pincus P. W. Brandt-Rauf R. L. Fine J. Michl H. Wang NMR solution structure of a peptide from the mdm-2 binding domain of the p53 protein that is selectively cytotoxic to cancer cells Biochemistry 2004 43 7 1854 1861
38. D. W. Meek W. Eckhart Phosphorylation of p53 in normal and simian virus 40-transformed NIH 3T3 cells Mol. Cell. Biol. 1988 8 1 461 465
39. A. Samad C. W. Anderson R. B. Carroll Mapping of phosphomonoester and apparent phosphodiester bonds of the oncogene product p53 from simian virus 40-transformed 3T3 cells Proc. Natl. Acad. Sci. U. S. A. 1986 83 4 897 901
40. Y. Wang W. Eckhart Phosphorylation sites in the amino-terminal region of mouse p53 Proc. Natl. Acad. Sci. U. S. A. 1992 89 10 4231 4235
41. J. Ni V. Sakanyan D. Charlier N. Glansdorff G. D. Van Duyne Structure of the arginine repressor from Bacillus stearothermophilus Nat. Struct. Biol. 1999 6 5 427 432
42. A. Shulman-Peleg M. Shatsky R. Nussinov H. J. Wolfson MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions Nucleic Acids Res. 2008 36 W260 W264
43. M. D. McDowall M. S. Scott G. J. Barton PIPs human protein-protein interaction prediction database Nucleic Acids Res. 2009 37 D651 D656
44. Y. Jing M. Wang W. Tang T. Qi C. Gu S. Hao X. Zeng c-Abl tyrosine kinase activates p21 transcription via interaction with p53 J. Biochem. 2007 141 5 621 626
45. J. R. Walker R. A. Corpina J. Goldberg Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair Nature 2001 412 6847 607 614
46. M. Koike T. Ikuta T. Miyasaka T. Shiomi Ku80 can translocate to the nucleus independent of the translocation of Ku70 using its own nuclear localization signal Oncogene 1999 18 52 7495 7505
47. V. B. Holcomb F. Rodier Y. Choi R. A. Busuttil H. Vogel J. Vijg J. Campisi P. Hasty Ku80 deletion suppresses spontaneous tumors and induces a p53-mediated DNA damage response Cancer Res. 2008 68 22 9497 9502
48. S. N. Savvides T. Boone P. Andrew Karplus Flt3 ligand structure and unexpected commonalities of helical bundles and cystine knots Nat. Struct. Biol. 2000 7 6 486 491
49. S. Daujat H. Neel J. Piette MDM2: life without p53 Trends Genet. 2001 17 8 459 464
50. K. Martin D. Trouche C. Hagemeier T. S. Sorensen N. B. La Thangue T. Kouzarides Stimulation of E2F1/DP1 transcriptional activity by MDM2 oncoprotein Nature 1995 375 6533 691 694
51. Z. X. Xiao J. Chen A. J. Levine N. Modjtahedi J. Xing W. R. Sellers D. M. Livingston Interaction between the retinoblastoma protein and the oncoprotein MDM2 Nature 1995 375 6533 694 698
52. C. Lee J. H. Chang H. S. Lee Y. Cho Structural basis for the recognition of the E2F transactivation domain by the retinoblastoma tumor suppressor Genes Dev. 2002 16 24 3199 3212
53. Z. Goldberg R. Vogt Sionov M. Berger Y. Zwang R. Perets R. A. Van Etten M. Oren Y. Taya Y. Haupt Tyrosine phosphorylation of Mdm2 by c-Abl: implications for p53 regulation EMBO J. 2002 21 14 3715 3727 (Pubitemid 34787045)
54. S. Kerrien Y. Alam-Faruque B. Aranda I. Bancarz A. Bridge C. Derow E. Dimmer M. Feuermann A. Friedrichsen R. Huntley C. Kohler J. Khadake C. Leroy A. Liban C. Lieftink,et al. IntAct-open source resource for molecular interaction data Nucleic Acids Res. 2007 35 D561 D565
55. Y. Jin S. X. Zeng M. S. Dai X. J. Yang H. Lu MDM2 inhibits PCAF (p300/CREB-binding protein-associated factor)-mediated p53 acetylation J. Biol. Chem. 2002 277 34 30838 30843
56. K. Garber Missing the target: ubiquitin ligase drugs stall J. Natl. Cancer Inst. 2005 97 3 166 167
57. Z. Zhang H. Wang M. Li E. R. Rayburn S. Agrawal R. Zhang Stabilization of E2F1 protein by MDM2 through the E2F1 ubiquitination pathway Oncogene 2005 24 48 7238 7247