A model for the interaction between NF-kappa-B and ASPP2 suggests an I-kappa-B-like binding mechanism

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 3, 2009, Pages 602-611

  Benyamini, Hadar ^a   Leonov, Hadas ^a   Rotem, Shahar ^a   Katz, Chen ^a   Arkin, Isaiah T ^a   Friedler, Assaf ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Apoptosis; ASPP2; Docking; Molecular dynamics; NFkB; p53; Peptides

Indexed keywords

ANKYRIN; APOPTOSIS STIMULATING PROTEIN OF P53; I KAPPA B; PROTEIN SH3; SYNAPTOTAGMIN I; TRANSCRIPTION FACTOR RELA; UNCLASSIFIED DRUG;

ARTICLE; BINDING KINETICS; BINDING SITE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NUCLEAR LOCALIZATION SIGNAL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM;

ALGORITHMS; APOPTOSIS; APOPTOSIS REGULATORY PROTEINS; BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CYTOPLASM; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; I-KAPPA B KINASE; NF-KAPPA B; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; STATIC ELECTRICITY; TUMOR SUPPRESSOR PROTEIN P53;

EID: 70349326457     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22473     Document Type: Article

References (38)

1. Iwabuchi K, Bartel PL, Li B, Marraccino R, Fields S. Two cellular proteins that bind to wild-type but not mutant p53. Proc Natl Acad Sci USA 1994;91:6098-6102. (Pubitemid 24188290)
2. Naumovski L, Cleary ML. The p53-binding protein 53BP2 also interacts with Bcl2 and impedes cell cycle progression at G2/M. Mol Cell Biol 1996;16:3884-3892. (Pubitemid 26199908)
3. Samuels-Lev Y, O'Connor DJ, Bergamaschi D, Trigiante G, Hsieh JK, Zhong S, Campargue I, Naumovski L, Crook T, Lu X. ASPP proteins specifically stimulate the apoptotic function of p53. Mol Cell 2001;8:781-794. (Pubitemid 33030212)
4. Tidow H, Andreeva A, Rutherford TJ, Fersht AR. Solution structure of ASPP2 N-terminal domain (N-ASPP2) reveals a ubiquitin-like fold. J Mol Biol 2007;371:948-958.
5. Rotem S, Katz C, Benyamini H, Lebendiker M, Veprintsev D, Rudiger S, Danieli T, Friedler A. The structure and interactions of the proline-rich domain of ASPP2. J Biol Chem 2008;283:18990-18999.
6. Gorina S, Pavletich NP. Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. Science 1996;274:1001-1005. (Pubitemid 26398426)
7. Robinson RA, Lu X, Jones EY, Siebold C. Biochemical and structural studies of ASPP proteins reveal differential binding to p53, p63, and p73. Structure 2008;16:259-268. (Pubitemid 351215211)
8. Katz C, Benyamini H, Rotem S, Lebendiker M, Danieli T, Iosub A, Refaely H, Dines M, Bronner V, Bravman T, Shalev DE, Rudiger S, Friedler A. Molecular basis of the interaction between the antiapoptotic Bcl-2 family proteins and the proapoptotic protein ASPP2. Proc Natl Acad Sci USA 2008;105:12277-12282.
9. Helps NR, Barker HM, Elledge SJ, Cohen PT. Protein phosphatase 1 interacts with p53BP2, a protein which binds to the tumour suppressor p53. FEBS Lett 1995;377:295-300.
10. Espanel X, Sudol M. Yes-associated protein and p53-binding protein- 2 interact through their WW and SH3 domains. J Biol Chem 2001;276:14514-14523. (Pubitemid 37391846)
11. Cao Y, Hamada T, Matsui T, Date T, Iwabuchi K. Hepatitis C virus core protein interacts with p53-binding protein, 53BP2/Bbp/ASPP2, and inhibits p53-mediated apoptosis. Biochem Biophys Res Commun 2004;315:788-795. (Pubitemid 38249372)
12. Yang JP, Hori M, Takahashi N, Kawabe T, Kato H, Okamoto T. NF-kappaB subunit p65 binds to 53BP2 and inhibits cell death induced by 53BP2. Oncogene 1999;18:5177-5186. (Pubitemid 29460653)
13. Gilmore TD. Introduction to NF-kappaB: players, pathways, perspectives. Oncogene 2006;25:6680-6684.
14. Hacker H, Karin M. Regulation and function of IKK and IKKrelated kinases. Sci STKE 2006;2006(357):re13.
15. Jacobs MD, Harrison SC. Structure of an IkappaBalpha/NF-kappaB complex. Cell 1998;95:749-758.
16. Basseres DS, Baldwin AS. Nuclear factor-kappaB and inhibitor of kappaB kinase pathways in oncogenic initiation and progression. Oncogene 2006;25:6817-6830.
17. Dutta J, Fan Y, Gupta N, Fan G, Gelinas C. Current insights into the regulation of programmed cell death by NF-kappaB. Oncogene 2006;25:6800-6816. (Pubitemid 44657853)
18. Takahashi N, Kobayashi S, Kajino S, Imai K, Tomoda K, Shimizu S, Okamoto T. Inhibition of the 53BP2S-mediated apoptosis by nuclear factor kappaB and Bcl-2 family proteins. Genes Cells 2005;10:803-811. (Pubitemid 41158739)
19. Yang JP, Hori M, Sanda T, Okamoto T. Identification of a novel inhibitor of nuclear factor-kappaB. Rel A-associated inhibitor J Biol Chem 1999;274:15662-15670.
20. Delano WL. The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific LLC; 2002. Available at: http://www.pymol. org.
21. Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T. HingeProt: automated prediction of hinges in protein structures. Proteins 2008;70:1219-1227. Available at: http://bioinfo3d. cs.tau.ac.il/HingeProt/index. html. (Pubitemid 351304082)
22. Suhre K, Sanejouand YH. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 2004;32(Web Server issue): W610-614. http://www.igs.cnrs-mrs. fr/elnemo/. (Pubitemid 38997408)
23. Duhovny D, Nussinov R, Wolfson HJ. Efficient unbound docking of rigid molecules. In: Guigo R, Gusfield D, editors. Rome, Italy: LNCS; 2002. pp 185-200.
24. Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007;69:139-159. (Pubitemid 47339146)
25. Kingsford CL, Chazelle B, Singh M. Solving and analyzing sidechain positioning problems using linear and integer programming. Bioinformatics 2005;21:1028-1036. (Pubitemid 40467925)
26. Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726. (Pubitemid 27170692)
27. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. Gromacs: fast, flexible, and free. J Comput Chem 2005;26:1701-1718.
28. Lindahl E, Hess B, Van Der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 2001; 7:306-317. (Pubitemid 36153547)
29. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 2004;25:1656-1676.
30. Berendsen HJC, Postma JPM, Van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. Nature 1969;224:175-177.
31. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: a linear constraint solver for molecular simulations. J Comp Chem 1997; 18:1463-1472. (Pubitemid 127637344)
32. Ivanov I, Tainer JA, McCammon JA. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci USA 2007;104:1465-1470. (Pubitemid 46214613)
33. Berendsen HJC, Postma JPM, Gunsteren WFV, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
34. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995; 103:8577-8593.
35. Chen FE, Huang DB, Chen YQ, Ghosh G. Crystal structure of p50/ p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature 1998;391:410-413. (Pubitemid 28093519)
36. Alva V, Devi DP, Sowdhamini R. Coilcheck: an interactive server for the analysis of interface regions in coiled coils. Protein Pept Lett 2008;15:33-38. (Pubitemid 351206473)
37. Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 2005;21:2534-2536. (Pubitemid 40731617)
38. Latzer J, Papoian GA, Prentiss MC, Komives EA, Wolynes PG. Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. J Mol Biol 2007;367:262-274. (Pubitemid 46290653)