Resilience of death: Intrinsic disorder in proteins involved in the programmed cell death

Cell Death and Differentiation

Volumn 20, Issue 9, 2013, Pages 1257-1267

  Peng, Z ^a   Xue, B ^b   Kurgan, L ^a   Uversky, V N ^b,c  

^a UNIVERSITY OF ALBERTA   (Canada)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

^c INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

interaction network; intrinsically disordered proteins; molecular recognition; programmed cell death; protein function; protein structure; protein protein interaction

Indexed keywords

DNA; HEME; LIGAND; NUCLEIC ACID; PROTEIN; PROTEIN INHIBITOR; PROTEIN P53; RNA;

AEDES; ANIMAL CELL; ANOPHELES; APOPTOSIS; ARTICLE; AUTOPHAGY; AUTOREGULATION; CHICKEN; CHIMPANZEE; CIONA INTESTINALIS; CONTROLLED STUDY; COW; DIPTERA; DOG; ELECTRON TRANSPORT; ENTROPY; ENZYME BINDING; FINCH; GASTEROSTEUS; GENETIC CONSERVATION; GORILLA; HORSE; HUMAN; HUMAN CELL; IMMUNE RESPONSE; INTRACELLULAR SIGNALING; LIZARD; MACACA; METAL BINDING; MOUSE; NECROPTOSIS; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; OPOSSUM; ORANG UTAN; ORYZIAS; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN INTRINSIC DISORDER; PROTEIN LIPID INTERACTION; PROTEIN POLYMERIZATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE, FUNCTION AND VARIABILITY; PUFFER FISH; RABBIT; RAT; REGULATORY MECHANISM; SPECIES DIFFERENTIATION; TETRAODONTIFORMES; TRANSACTIVATION; WORM; XENOPUS; YEAST; ZEBRA FISH;

ANIMALIA; METAZOA;

APOPTOSIS; APOPTOSIS REGULATORY PROTEINS; AUTOPHAGY; HUMANS; INTRINSICALLY DISORDERED PROTEINS; NECROSIS; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84882279043     PISSN: 13509047     EISSN: 14765403     Source Type: Journal    
DOI: 10.1038/cdd.2013.65     Document Type: Article

References (57)

1. Bialik S, Zalckvar E, Ber Y, Rubinstein AD, Kimchi A. Systems biology analysis of programmed cell death. Trends Biochem Sci 2010; 35: 556-564.
2. Galluzzi L, Vanden Berghe T, Vanlangenakker N, Buettner S, Eisenberg T, Vandenabeele P et al. Programmed necrosis from molecules to health and disease. Int Rev Cell Mol Biol 2011; 289: 1-35.
3. Ouyang L, Shi Z, Zhao S, Wang FT, Zhou TT, Liu B et al. Programmed cell death pathways in cancer: a review of apoptosis, autophagy and programmed necrosis. Cell Prolif 2012; 45: 487-498.
4. Tan ML, Ooi JP, Ismail N, Moad AI, Muhammad TS. Programmed cell death pathways and current antitumor targets. Pharm Res 2009; 26: 1547-1560.
5. Xie Z, Klionsky DJ. Autophagosome formation: core machinery and adaptations. Nat Cell Biol 2007; 9: 1102-1109.
6. Huett A, Goel G, Xavier RJ. A systems biology viewpoint on autophagy in health and disease. Curr Opin Gastroenterol 2010; 26: 302-309.
7. Chen S, Rehman SK, Zhang W, Wen A, Yao L, Zhang J. Autophagy is a therapeutic target in anticancer drug resistance. Biochim Biophys Acta 2010; 1806: 220-229.
8. Li ZY, Yang Y, Ming M, Liu B, Mitochondrial ROS. generation for regulation of autophagic pathways in cancer. Biochem Biophys Res Commun 2011; 414: 5-8.
9. Liu JJ, Lin M, Yu JY, Liu B, Bao JK. Targeting apoptotic and autophagic pathways for cancer therapeutics. Cancer Lett 2011; 300: 105-114.
10. Henriquez M, Armisen R, Stutzin A, Quest AF. Cell death by necrosis, a regulated way to go. Curr Mol Med 2008; 8: 187-206.
11. Cohen GM. Caspases: the executioners of apoptosis. Biochem J 1997; 326(Pt 1): 1-16.
12. Eisenberg-Lerner A, Bialik S, Simon HU, Kimchi A. Life and death partners: apoptosis, autophagy and the cross-talk between them. Cell Death Differ 2009; 16: 966-975.
13. He C, Klionsky DJ. Regulation mechanisms and signaling pathways of autophagy. Annu Rev Genet 2009; 43: 67-93.
14. Liu B, Cheng Y, Liu Q, Bao JK, Yang JM. Autophagic pathways as new targets for cancer drug development. Acta Pharmacol Sin 2010; 31: 1154-1164.
15. Festjens N, Vanden Berghe T, Vandenabeele P. Necrosis, a well-orchestrated form of cell demise: signalling cascades, important mediators and concomitant immune response. Biochim Biophys Acta 2006; 1757: 1371-1387.
16. Boujrad H, Gubkina O, Robert N, Krantic S, Susin SA. AIF-mediated programmed necrosis: a highly regulated way to die. Cell Cycle 2007; 6: 2612-2619.
17. Eisenberg-Lerner A, Kimchi A. DAP kinase regulates JNK signaling by binding and activating protein kinase D under oxidative stress. Cell Death Differ 2007; 14: 1908-1915.
18. Morgan MJ, Kim YS, Liu ZG. TNFalpha and reactive oxygen species in necrotic cell death. Cell Res 2008; 18: 343-349.
19. Degterev A, Huang Z, Boyce M, Li Y, Jagtap P, Mizushima N et al. Chemical inhibitor of nonapoptotic cell death with therapeutic potential for ischemic brain injury. Nat Chem Biol 2005; 1: 112-119.
20. Cohen JJ, Duke RC, Fadok VA, Sellins KS. Apoptosis and programmed cell death in immunity. Annu Rev Immunol 1992; 10: 267-293.
21. Hedrick SM, Ch'en IL, Alves BN. Intertwined pathways of programmed cell death in immunity. Immunol Rev 2010; 236: 41-53.
22. Lu JV, Walsh CM. Programmed necrosis and autophagy in immune function. Immunol Rev 2012; 249: 205-217.
23. Gatzka M, Walsh CM. Apoptotic signal transduction and T cell tolerance. Autoimmunity 2007; 40: 442-452.
24. Uversky VN, Dunker AK. Understanding protein non-folding. BBA Proteins Proteom 2010; 1804: 1231-1264.
25. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004; 337: 635-645.
26. Xue B, Dunker AK, Uversky VN. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J Biomol Struct Dyn 2012; 30: 137-149.
27. Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, Oldfield CJ et al. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci USA 2006; 103: 8390-8395.
28. Hsu WL, Oldfield C, Meng J, Huang F, Xue B, Uversky VN et al. Intrinsic protein disorder and protein-protein interactions. Pac Symp Biocomput 2012; 116-127.
29. Uversky VN, Oldfield CJ, Dunker AK. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 2008; 37: 215-246.
30. Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN. Flexible nets: the roles of intrinsic disorder in protein interaction networks. FEBS J 2005; 272: 5129-5148.
31. Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Intrinsic disorder and functional proteomics. Biophys J 2007; 92: 1439-1456.
32. Iakoucheva LM, Brown CJ, Lawson JD, Obradovic Z, Dunker AK. Intrinsic disorder in cellsignaling and cancer-associated proteins. J Mol Biol 2002; 323: 573-584.
33. Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK. Comparing and combining predictors of mostly disordered proteins. Biochemistry 2005; 44: 1989-2000.
34. Uversky VN, Gillespie JR, Fink AL. Why are 'natively unfolded' proteins unstructured under physiologic conditions? Proteins 2000; 41: 415-427.
35. Huang F, Oldfield C, Meng J, Hsu WL, Xue B, Uversky VN et al. Subclassifying disordered proteins by the CH-CDF plot method. Pac Symp Biocomput 2012; 128-139.
36. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A et al. DisProt: the Database of Disordered Proteins. Nucleic Acids Res 2007; 35(Database issue): D786-D793.
37. Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 2005; 44: 12454-12470.
38. Rajagopalan K, Mooney SM, Parekh N, Getzenberg RH, Kulkarni P. A majority of the cancer/testis antigens are intrinsically disordered proteins. J Cell Biochem 2011; 112: 3256-3267.
39. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011; 39(Database issue): D561-D568.
40. Dawson R, Muller L, Dehner A, Klein C, Kessler H, Buchner J. The N-terminal domain of p53 is natively unfolded. J Mol Biol 2003; 332: 1131-1141.
41. Lee H, Mok KH, Muhandiram R, Park KH, Suk JE, Kim DH et al. Local structural elements in the mostly unstructured transcriptional activation domain of human p53. J Biol Chem 2000; 275: 29426-29432.
42. Oldfield CJ, Meng J, Yang JY, Yang MQ, Uversky VN, Dunker AK. Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 2008; 9(Suppl 1): S1.
43. Muchmore SW, Sattler M, Liang H, Meadows RP, Harlan JE, Yoon HS et al. X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death. Nature 1996; 381: 335-341.
44. Hinds MG, Smits C, Fredericks-Short R, Risk JM, Bailey M, Huang DC et al. Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets. Cell Death Differ 2007; 14: 128-136.
45. Sattler M, Liang H, Nettesheim D, Meadows RP, Harlan JE, Eberstadt M et al. Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis. Science 1997; 275: 983-986.
46. Rautureau GJ, Day CL, Hinds MG. Intrinsically disordered proteins in bcl-2 regulated apoptosis. Int J Mol Sci 2010; 11: 1808-1824.
47. Hinds MG, Day CL. Regulation of apoptosis: uncovering the binding determinants. Curr Opin Struct Biol 2005; 15: 690-699.
48. Mark WY, Liao JC, Lu Y, Ayed A, Laister R, Szymczyna B et al. Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions? J Mol Biol 2005; 345: 275-287.
49. Demarest SJ, Martinez-Yamout M, Chung J, Chen H, Xu W, Dyson HJ et al. Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. Nature 2002; 415: 549-553.
50. Li M, Song J. The N-and C-termini of the human Nogo molecules are intrinsically unstructured: bioinformatics, CD, NMR characterization, and functional implications. Proteins 2007; 68: 100-108.
51. Reingewertz TH, Shalev DE, Sukenik S, Blatt O, Rotem-Bamberger S, Lebendiker M et al. Mechanism of the interaction between the intrinsically disordered C-terminus of the proapoptotic ARTS protein and the Bir3 domain of XIAP. PLoS ONE 2011; 6: e24655.
52. Libich DS, Schwalbe M, Kate S, Venugopal H, Claridge JK, Edwards PJ et al. Intrinsic disorder and coiled-coil formation in prostate apoptosis response factor 4. FEBS J 2009; 276: 3710-3728.
53. Zeng Y, He Y, Yang F, Mooney SM, Getzenberg RH, Orban J et al. The cancer/testis antigen prostate-associated gene 4 (PAGE4) is a highly intrinsically disordered protein. J Biol Chem 2011; 286: 13985-13994.
54. Andresen C, Helander S, Lemak A, Fares C, Csizmok V, Carlsson J et al. Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Res 2012; 40: 6353-6366.
55. Diez J, Walter D, Munoz-Pinedo C, Gabaldon T. DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death. Cell Death Differ 2010; 17: 735-736.
56. Van Herreweghe F, Festjens N, Declercq W, Vandenabeele P. Tumor necrosis factormediated cell death: to break or to burst, that's the question. Cell Mol Life Sci 2010; 67: 1567-1579.
57. Meulmeester E, Jochemsen AG. p53: a guide to apoptosis. Curr Cancer Drug Targets 2008; 8: 87-97.