1,319
Views
41
CrossRef citations to date
0
Altmetric
Perspective

Intrinsically disordered proteins and conformational noise

Implications in cancer

, , , , &
Pages 26-31 | Published online: 19 Dec 2012

References

  • Uversky VN, Dunker AK. Understanding protein non-folding. Biochim Biophys Acta 2010; 1804:1231 - 64; http://dx.doi.org/10.1016/j.bbapap.2010.01.017; PMID: 20117254
  • Uversky VN, Oldfield CJ, Dunker AK. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 2008; 37:215 - 46; http://dx.doi.org/10.1146/annurev.biophys.37.032807.125924; PMID: 18573080
  • Patil A, Kinoshita K, Nakamura H. Hub promiscuity in protein-protein interaction networks. Int J Mol Sci 2010; 11:1930 - 43; http://dx.doi.org/10.3390/ijms11041930; PMID: 20480050
  • Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, et al. Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2006; 2:e100; http://dx.doi.org/10.1371/journal.pcbi.0020100; PMID: 16884331
  • Gsponer J, Babu MM. The rules of disorder or why disorder rules. Prog Biophys Mol Biol 2009; 99:94 - 103; http://dx.doi.org/10.1016/j.pbiomolbio.2009.03.001; PMID: 19344736
  • Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010; 329:533 - 8; http://dx.doi.org/10.1126/science.1188308; PMID: 20671182
  • Munsky B, Neuert G, van Oudenaarden A. Using gene expression noise to understand gene regulation. Science 2012; 336:183 - 7; http://dx.doi.org/10.1126/science.1216379; PMID: 22499939
  • Ladbury JE, Arold ST. Noise in cellular signaling pathways: causes and effects. Trends Biochem Sci 2012; 37:173 - 8; http://dx.doi.org/10.1016/j.tibs.2012.01.001; PMID: 22341496
  • Tompa P, Csermely P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004; 18:1169 - 75; http://dx.doi.org/10.1096/fj.04-1584rev; PMID: 15284216
  • Turoverov KK, Kuznetsova IM, Uversky VN. The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation. Prog Biophys Mol Biol 2010; 102:73 - 84; http://dx.doi.org/10.1016/j.pbiomolbio.2010.01.003; PMID: 20097220
  • Huang Y, Liu Z. Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the “fly-casting” mechanism. J Mol Biol 2009; 393:1143 - 59; http://dx.doi.org/10.1016/j.jmb.2009.09.010; PMID: 19747922
  • Eldar A, Elowitz MB. Functional roles for noise in genetic circuits. Nature 2010; 467:167 - 73; http://dx.doi.org/10.1038/nature09326; PMID: 20829787
  • Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 2010; 141:69 - 80; http://dx.doi.org/10.1016/j.cell.2010.02.027; PMID: 20371346
  • Babu MM, van der Lee R, de Groot NS, Gsponer J. Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 2011; 21:432 - 40; http://dx.doi.org/10.1016/j.sbi.2011.03.011; PMID: 21514144
  • Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet 2002; 31:69 - 73; http://dx.doi.org/10.1038/ng869; PMID: 11967532
  • Yamada T, Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 2009; 10:791 - 803; http://dx.doi.org/10.1038/nrm2787; PMID: 19851337
  • Kar G. Gursoy, Keskin, O. Human cancer protein-protein interaction network: a structural perspective. PloS Comp Biol 2009; 5:e1000601; http://dx.doi.org/10.1371/journal.pcbi.1000601
  • Liu J, Perumal NB, Oldfield CJ, Su EW, Uversky VN, Dunker AK. Intrinsic disorder in transcription factors. Biochemistry 2006; 45:6873 - 88; http://dx.doi.org/10.1021/bi0602718; PMID: 16734424
  • Martinez SR, Miranda JL. CTCF terminal segments are unstructured. Protein Sci 2010; 19:1110 - 6; http://dx.doi.org/10.1002/pro.367; PMID: 20196073
  • Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res 2012; 22:1680 - 8; http://dx.doi.org/10.1101/gr.136101.111; PMID: 22955980
  • Sandhu KS. Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. J Mol Recognit 2009; 22:1 - 8; http://dx.doi.org/10.1002/jmr.915; PMID: 18802931
  • Beh LY, Colwell LJ, Francis NJ. A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence. Proc Natl Acad Sci USA 2012; 109:E1063 - 71; http://dx.doi.org/10.1073/pnas.1118678109; PMID: 22517748
  • Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 2009; 138:198 - 208; http://dx.doi.org/10.1016/j.cell.2009.04.029; PMID: 19596244
  • Marcotte EM, Tsechansky M. Disorder, promiscuity, and toxic partnerships. Cell 2009; 138:16 - 8; http://dx.doi.org/10.1016/j.cell.2009.06.024; PMID: 19596229
  • Gsponer J, Futschik ME, Teichmann SA, Babu MM. Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 2008; 322:1365 - 8; http://dx.doi.org/10.1126/science.1163581; PMID: 19039133
  • Edwards YJ, Lobley AE, Pentony MM, Jones DT. Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol 2009; 10:R50; http://dx.doi.org/10.1186/gb-2009-10-5-r50; PMID: 19432952
  • Iakoucheva LM, Brown CJ, Lawson JD, Obradović Z, Dunker AK. Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 2002; 323:573 - 84; http://dx.doi.org/10.1016/S0022-2836(02)00969-5; PMID: 12381310
  • 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 - 67; http://dx.doi.org/10.1002/jcb.23252; PMID: 21748782
  • Erdős P, Rényi A. On random graphs. Publ Math 1959; 6:290 - 7
  • Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999; 286:509 - 12; http://dx.doi.org/10.1126/science.286.5439.509; PMID: 10521342
  • Jonsson PF, Bates PA. Global topological features of cancer proteins in the human interactome. Bioinformatics 2006; 22:2291 - 7; http://dx.doi.org/10.1093/bioinformatics/btl390; PMID: 16844706
  • Di Domenico T, Walsh I, Martin AJM, Tosatto SCE. MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics 2012; 28:2080 - 1; http://dx.doi.org/10.1093/bioinformatics/bts327; PMID: 22661649
  • Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, et al. Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2006; 2:e100; http://dx.doi.org/10.1371/journal.pcbi.0020100; PMID: 16884331
  • Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010; 11:R53; http://dx.doi.org/10.1186/gb-2010-11-5-r53; PMID: 20482850
  • Xia J, Sun J, Jia P, Zhao Z. Do cancer proteins really interact strongly in the human protein-protein interaction network?. Comput Biol Chem 2011; 35:121 - 5; http://dx.doi.org/10.1016/j.compbiolchem.2011.04.005; PMID: 21666777
  • Barrat A, Barthelemy M, Vespignani A. In Dynamical Processes on Complex Networks. Cambridge University Press (2008).
  • Rodrigues FA, Costa LdaF, Barbieri AL. Resilience of protein-protein interaction networks as determined by their large-scale topological features. Mol Biosyst 2011; 7:1263 - 9; http://dx.doi.org/10.1039/c0mb00256a; PMID: 21298132
  • Newman MEJ. Assortative mixing in networks. Phys Rev Lett 2002; 89:208701; http://dx.doi.org/10.1103/PhysRevLett.89.208701; PMID: 12443515
  • Ellis JD, Barrios-Rodiles M, Colak R, Irimia M, Kim T, Calarco JA, et al. Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell 2012; 46:884 - 92; http://dx.doi.org/10.1016/j.molcel.2012.05.037; PMID: 22749401
  • Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, et al. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 2012; 46:871 - 83; http://dx.doi.org/10.1016/j.molcel.2012.05.039; PMID: 22749400
  • Murawska M, Brehm A. CHD chromatin remodelers and the transcription cycle. Transcription 2011; 2:244 - 53; http://dx.doi.org/10.4161/trns.2.6.17840; PMID: 22223048
  • Fong YW, Inouye C, Yamaguchi T, Cattoglio C, Grubisic I, Tjian R. A DNA repair complex functions as an Oct4/Sox2 coactivator in embryonic stem cells. Cell 2011; 147:120 - 31; http://dx.doi.org/10.1016/j.cell.2011.08.038; PMID: 21962512

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.