Skip to main content
SpringerLink
Log in

Prediction of Intrinsic Disorder and Its Use in Functional Proteomics

  • Protocol
Gene Function Analysis

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 408))

Abstract

The number of experimentally verified, intrinsically disordered (ID) proteins is rapidly rising. Research is often focused on a structural characterization of a given protein, looking for several key features. However, ID proteins with their dynamic structures that interconvert on a number of time-scales are difficult targets for the majority of traditional biophysical and biochemical techniques. Structural and functional analyses of these proteins can be significantly aided by disorder predictions. The current advances in the prediction of ID proteins and the use of protein disorder prediction in the fields of molecular biology and bioinformatics are briefly overviewed herein. A method is provided to utilize intrinsic disorder knowledge to gain structural and functional information related to individual proteins, protein groups, families, classes, and even entire proteomes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Fischer, E. (1894) Einfluss der configuration auf die wirkung der enzyme. Ber. Dtsch. Chem. Ges. 27, 2985–2993.

    Article  CAS  Google Scholar 

  2. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., and Dunker, A. K. (2003) Predicting intrinsic disorder from amino acid sequence. Proteins 53, 566–572.

    Article  CAS  PubMed  Google Scholar 

  3. Linderstrom-Lang, K. U. and Schellman, J. A. (1959) Protein structure and enzyme activity, in The Enzymes, (Boyer, P. D., Lardy, H., and Myrback, K., eds.), Academic Press, New York, pp. 443–510.

    Google Scholar 

  4. Pullen, R. A., Jenkins, J. A., Tickle, I. J., Wood, S. P., and Blundell, T. L. (1975) The relation of polypeptide hormone structure and flexibility to receptor binding: the relevance of X-ray studies on insulins, glucagon and human placental lactogen. Mol. Cell Biochem. 8, 5–20.

    Article  CAS  PubMed  Google Scholar 

  5. Cary, P. D., Moss, T., and Bradbury, E. M. (1978) High-resolution proton-magneticresonance studies of chromatin core particles. Eur. J. Biochem. 89, 475–482.

    Article  CAS  PubMed  Google Scholar 

  6. Holt, C. and Sawyer, L. (1993) Caseins as rheomorphic proteins: interpretation of primary and secondary structures of the αs1-, β-, and κ-caseins. J. Chem. Soc. Faraday Trans. 89, 2683–269

    Article  CAS  Google Scholar 

  7. Schweers, O., Schoenbrunn-Hanebeck, E., Marx, A., and Mandelkow, E. (1994) Structural studies of tau protein and alzheimer paired helical filaments show no evidence for β-structure. J. Biol. Chem. 269, 24,290–24,297.

    CAS  PubMed  Google Scholar 

  8. Weinreb, P. H., Zhen, W., Poon, A. W., Conway, K. A., and Lansbury, P. T., Jr. (1996) NACP, a protein implicated in Alzheimer’s disease and learning, is natively unfolded. Biochemistry 35, 13,709–13,715.

    Article  CAS  PubMed  Google Scholar 

  9. Wright, P. E. and Dyson, H. J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293, 321–331.

    Article  CAS  PubMed  Google Scholar 

  10. Dunker, A. K., Lawson, J. D., Brown, C. J., et al. (2001) Intrinsically disordered protein. J. Mol. Graph. Model 19, 26–59.

    Article  CAS  PubMed  Google Scholar 

  11. Daughdrill, G. W., Pielak, G. J., Uversky, V. N., Cortese, M. S., and Dunker, A. K. (2005) Natively disordered protein, in Protein Folding Handbook, (Buchner, J. and Kiefhaber, T. eds.), Wiley-VCH: Verlag GmbH & Co., KGaA, Weinheim, pp. 271–353.

    Google Scholar 

  12. Uversky, V. N. (2003) A protein-chameleon: conformational plasticity of alphasynuclein, a disordered protein involved in neurodegenerative disorders. J. Biomol. Struct. Dyn. 21, 211–234.

    CAS  PubMed  Google Scholar 

  13. Uversky, V. N., Oldfield, C. J., and Dunker, A. K. (2005) Showing your ID: intrinsic disorder as an ID for regcognition, regulation, and cell signaling. J. Mol. Recognit. 18, 343–384.

    Article  CAS  PubMed  Google Scholar 

  14. Dunker, A. K. and Obradovic, Z. (2001) The protein trinity-linking function and disorder. Nat. Biotechnol. 19, 805, 806.

    Article  CAS  PubMed  Google Scholar 

  15. Uversky, V. N. (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11, 739–756.

    Article  CAS  PubMed  Google Scholar 

  16. Ringe, D. and Petsko, G. A. (1986) Study of protein dynamics by X-ray diffraction. Methods Enzymol. 131, 389–433.

    Article  CAS  PubMed  Google Scholar 

  17. Dyson, H. J. and Wright, P. E. (2002) Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. Adv. Protein Chem. 62, 311–340.

    Article  CAS  PubMed  Google Scholar 

  18. Bracken, C., Iakoucheva, L. M., Romero, P. R., and Dunker, A. K. (2004) Combining prediction, computation and experiment for the characterization of protein disorder. Curr. Opin. Struct. Biol. 14, 570–576.

    Article  CAS  PubMed  Google Scholar 

  19. Dyson, H. J. and Wright, P. E. (2004) Unfolded proteins and protein folding studied by NMR. Chem. Rev. 104, 3607–3622.

    Article  CAS  PubMed  Google Scholar 

  20. Dyson, H. J. and Wright, P. E. (2005) Elucidation of the protein folding landscape by NMR. Methods Enzymol. 394, 299–321.

    Article  CAS  PubMed  Google Scholar 

  21. Fasman, G. D. (1996) Circular dichroism and the conformational analysis of biomolecules. Plenum Press, New York.

    Google Scholar 

  22. Adler, A. J., Greenfield, N. J., and Fasman, G. D. (1973) Circular dichroism and optical rotatory dispersion of proteins and polypeptides. Methods Enzymol. 27, 675–735.

    Article  CAS  PubMed  Google Scholar 

  23. Provencher, S. W. and Glockner, J. (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20, 33–37.

    Article  CAS  PubMed  Google Scholar 

  24. Woody, R. W. (1995) Circular dichroism. Methods Enzymol. 246, 34–71.

    Article  CAS  PubMed  Google Scholar 

  25. Uversky, V. N., Gillespie, J. R., and Fink, A. L. (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41, 415–427.

    Article  CAS  PubMed  Google Scholar 

  26. Smyth, E., Syme, C. D., Blanch, E. W., Hecht, L., Vasak, M., and Barron, L. D. (2001) Solution structure of native proteins with irregular folds from Raman optical activity. Biopolymers 58, 138–151.

    Article  CAS  PubMed  Google Scholar 

  27. Uversky, V. N. (1999) A multiparametric approach to studies of self-organization of globular proteins. Biochemistry (Mosc) 64, 250–266.

    CAS  Google Scholar 

  28. Receveur-Brechot, V., Bourhis, J. M., Uversky, V. N., Canard, B., and Longhi, S. (2006) Assessing protein disorder and induced folding. Proteins 62, 24–45.

    Article  CAS  PubMed  Google Scholar 

  29. Glatter, O. and Kratky, O. (1982) Small angle X-ray scattering. Academic Press, London.

    Google Scholar 

  30. Markus, G. (1965) Protein substrate conformation and proteolysis. Proc. Natl. Acad. Sci. USA 54, 253–258.

    Article  CAS  PubMed  Google Scholar 

  31. Mikhalyi, E. (1978) Application of proteolytic enzymes to protein structure studies. CRC Press, Boca Raton.

    Google Scholar 

  32. Hubbard, S. J., Eisenmenger, F., and Thornton, J. M. (1994) Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Protein Sci. 3, 757–768.

    Article  CAS  PubMed  Google Scholar 

  33. Fontana, A., de Laureto, P. P., de Filippis, V., Scaramella, E., and Zambonin, M. (1997) Probing the partly folded states of proteins by limited proteolysis. Fold. Des. 2, R17–R26.

    Article  CAS  PubMed  Google Scholar 

  34. Fontana, A., de Laureto, P. P., Spolaore, B., Frare, E., Picotti, P., and Zambonin, M. (2004) Probing protein structure by limited proteolysis. Acta Biochim. Pol. 51, 299–321.

    CAS  PubMed  Google Scholar 

  35. Iakoucheva, L. M., Kimzey, A. L., Masselon, C. D., Smith, R. D., Dunker, A. K., and Ackerman, E. J. (2001) Aberrant mobility phenomena of the DNA repair protein XPA. Protein Sci. 10, 1353–1362.

    Article  CAS  PubMed  Google Scholar 

  36. Tompa, P. (2002) Intrinsically unstructured proteins. Trends Biochem. Sci. 27, 527–533.

    Article  CAS  PubMed  Google Scholar 

  37. Privalov, P. L. (1979) Stability of proteins: small globular proteins. Adv. Protein Chem. 33, 167–241.

    Article  CAS  PubMed  Google Scholar 

  38. Ptitsyn, O. (1995) Molten globule and protein folding. Adv. Protein Chem. 47, 83–229.

    Article  CAS  PubMed  Google Scholar 

  39. Ptitsyn, O. B. and Uversky, V. N. (1994) The molten globule is a third thermodynamical state of protein molecules. FEBS Lett. 341, 15–18.

    Article  CAS  PubMed  Google Scholar 

  40. Uversky, V. N. and Ptitsyn, O. B. (1996) All-or-none solvent-induced transitions between native, molten globule and unfolded states in globular proteins. Fold. Des. 1, 117–122.

    Article  CAS  PubMed  Google Scholar 

  41. Westhof, E., Altschuh, D., Moras, D., et al. (1984) Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature 311, 123–126.

    Article  CAS  PubMed  Google Scholar 

  42. Berzofsky, J. A. (1985) Intrinsic and extrinsic factors in protein antigenic structure. Science 229, 932–940.

    Article  CAS  PubMed  Google Scholar 

  43. Iakoucheva, L. M., Brown, C. J., Lawson, J. D., Obradovic, Z., and Dunker, A. K. (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol. 323, 573–584.

    Article  CAS  PubMed  Google Scholar 

  44. Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., and Uversky, V. N. (2005) Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J. 272, 5129–5148.

    Article  CAS  PubMed  Google Scholar 

  45. Dunker, A. K., Brown, C. J., Lawson, J. D., Iakoucheva, L. M., and Obradovic, Z. (2002) Intrinsic disorder and protein function. Biochemistry 41, 6573–6582.

    Article  CAS  PubMed  Google Scholar 

  46. Xie, H., Vucetic, S., Iakoucheva, L. M., et al. (2007) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 6, 1882–1898.

    Article  CAS  PubMed  Google Scholar 

  47. Vucetic, S., Xie, H., Iakoucheva, L. M., et al. (2007) Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome Res. 6, 1899–1916.

    Article  CAS  PubMed  Google Scholar 

  48. Xie, H., Vucetic, S., Iakoucheva, L. M., et al. (2007) Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications and diseases associated with intrinsically disordered proteins. J. Proteome Res. 6, 1917–1932.

    Article  CAS  PubMed  Google Scholar 

  49. Sim, K. L., Uchida, T., and Miyano, S. (2001) ProDDO: a database of disordered proteins from the Protein Data Bank (PDB). Bioinformatics 17, 379–380.

    Article  CAS  PubMed  Google Scholar 

  50. Vucetic, S., Obradovic, Z., Vacic, V., et al. (2005) DisProt: a database of protein disorder. Bioinformatics 21, 137–140.

    Article  CAS  PubMed  Google Scholar 

  51. Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., and Dunker, A. K. (2001) Sequence complexity of disordered protein. Proteins 42, 38–48.

    Article  CAS  PubMed  Google Scholar 

  52. Wootton, J. C. (1993) Statistic of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17, 149–163.

    Article  CAS  Google Scholar 

  53. Radivojac, P., Obradovic, Z., Smith, D. K., et al. (2004) Protein flexibility and intrinsic disorder. Protein Sci. 13, 71–80.

    Article  CAS  PubMed  Google Scholar 

  54. Romero, P., Obradovic, Z., Kissinger, C. R., Villafranca, J. E., and Dunker, A. K. (1997) Identifying disordered regions in proteins from amino acid sequences. IEEE Int. Conf. Neural Netw. 1, 90–95.

    CAS  Google Scholar 

  55. Lise, S. and Jones, D. T. (2005) Sequence patterns associated with disordered regions in proteins. Proteins 58, 144–150.

    Article  CAS  PubMed  Google Scholar 

  56. Li, X., Romero, P., Rani, M., Dunker, A. K., and Obradovic, Z. (1999) Predicting protein disorder for N-, C-, and internal regions. Genome Inform. Ser. Workshop Genome Inform. 10, 30–40.

    CAS  PubMed  Google Scholar 

  57. Dunker, A. K., Obradovic, Z., Romero, P., Garner, E. C., and Brown, C. J. (2000) Intrinsic protein disorder in complete genomes. Genome Inform. Ser. Workshop Genome Inform. 11, 161–171.

    CAS  PubMed  Google Scholar 

  58. Oldfield, C. J., Cheng, Y., Cortese, M. S., Brown, C. J., Uversky, V. N., and Dunker, A. K. (2005) Comparing and combining predictors of mostly disordered proteins. Biochemistry 44, 1989–2000.

    Article  CAS  PubMed  Google Scholar 

  59. Vucetic, S., Radivojac, P., Obradovic, Z., Brown, C. J., and Dunker, A. K. (2001) Methods for improving protein disorder prediction, in International Joint INNSIEEE Conference on Neural Networks, Washington, DC, pp. 2718–2723.

    Google Scholar 

  60. Vucetic, S., Brown, C. J., Dunker, A. K., and Obradovic, Z. (2003) Flavors of protein disorder. Proteins 52, 573–584.

    Article  CAS  PubMed  Google Scholar 

  61. Melamud, E. and Moult, J. (2003) Evaluation of disorder predictions in CASP5. Proteins 53(Suppl 6), 561–565.

    Article  CAS  PubMed  Google Scholar 

  62. Jin, Y. and Dunbrack, R. L., Jr. (2005) Assessment of disorder predictions in CASP6. Proteins 61(Suppl 7), 167–175.

    Article  CAS  PubMed  Google Scholar 

  63. Jones, D. T. and Ward, J. J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins 53, 573–578.

    Article  CAS  PubMed  Google Scholar 

  64. Jones, D. T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202.

    Article  CAS  PubMed  Google Scholar 

  65. Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., Dunker, A. K., and Obradovic, Z. (2005) Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinformatics Comput. Biol. 3, 35–60.

    Article  CAS  Google Scholar 

  66. Linding, R., Russell, R. B., Neduva, V., and Gibson, T. J. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31, 3701–3708.

    Article  CAS  PubMed  Google Scholar 

  67. Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J., and Russell, R. B. (2003) Protein disorder prediction: implications for structural proteomics. Structure 11, 1453–1459.

    Article  CAS  PubMed  Google Scholar 

  68. Liu, J., Tan, H., and Rost, B. (2002) Loopy proteins appear conserved in evolution. J. Mol. Biol. 322, 53–64.

    Article  CAS  PubMed  Google Scholar 

  69. Liu, J. and Rost, B. (2003) NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res. 31, 3833–3835.

    Article  CAS  PubMed  Google Scholar 

  70. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., and Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337, 635–645.

    Article  CAS  PubMed  Google Scholar 

  71. Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F., and Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics 20, 2138–2139.

    Article  CAS  PubMed  Google Scholar 

  72. Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I. (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol. 347, 827–839.

    Article  CAS  PubMed  Google Scholar 

  73. Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21, 3433–3434.

    Article  CAS  PubMed  Google Scholar 

  74. Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., et al. (2005) FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21, 3435–3438.

    Article  CAS  PubMed  Google Scholar 

  75. Yang, Z. R., Thomson, R., McNeil, P., and Esnouf, R. M. (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21, 3369–3376.

    Article  CAS  PubMed  Google Scholar 

  76. Coeytaux, K. and Poupon, A. (2005) Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics 21, 1891–1900.

    Article  CAS  PubMed  Google Scholar 

  77. Cheng, J., Sweredoski, M. J., and Baldi, P. (2005) Accurate prediction of protein disordered regions by mining protein structure data. Data Mining Knowledge Disc. 11, 213–222.

    Article  Google Scholar 

  78. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., and Dunker, A. K. (2005) Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 61(Suppl 7), 176–182.

    Article  CAS  PubMed  Google Scholar 

  79. Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K., and Obradovic, Z. (2006) Lengthdependent prediction of protein intrinsic disorder. BMC Bioinformatics 7, 208.

    Article  PubMed  Google Scholar 

  80. Vullo, A., Bortolami, O., Pollastri, G., and Tosatto, S. C. (2006) Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res. 34, W164–W168.

    Article  CAS  PubMed  Google Scholar 

  81. Garner, E., Romero, P., Dunker, A. K., Brown, C., and Obradovic, Z. (1999) Predicting binding regions within disordered proteins. Genome Inform. Ser. Workshop Genome Inform. 10, 41–50.

    CAS  PubMed  Google Scholar 

  82. Oldfield, C. J., Cheng, Y., Cortese, M. S., Romero, P., Uversky, V. N., and Dunker, A. K. (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44, 12,454–12,470.

    Article  CAS  PubMed  Google Scholar 

  83. Iakoucheva, L. M., Radivojac, P., Brown, C. J., et al. (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32, 1037–1049.

    Article  CAS  PubMed  Google Scholar 

  84. Ritter, L. M., Arakawa, T., and Goldberg, A. F. (2005) Predicted and measured disorder in peripherin/rds, a retinal tetraspanin. Protein Pept. Lett. 12, 677–686.

    Article  CAS  PubMed  Google Scholar 

  85. Kukhtina, V., Kottwitz, D., Strauss, H., et al. (2005) Intracellular domain of nicotinic acetylcholine receptor: the importance of being unfolded. J. Neurochem.

    Google Scholar 

  86. Yiu, C. P., Beavil, R. L., and Chan, H. Y. (2006) Biophysical characterisation reveals structural disorder in the nucleolar protein, Dribble. Biochem. Biophys. Res. Commun. 343, 311–318.

    Article  CAS  PubMed  Google Scholar 

  87. Hinds, M. G., Smits, C., Fredericks-Short, R., et al. (2007) Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change on binding to prosurvival Bcl-2 targets. Cell Death Differ. 14, 128–136.

    Article  CAS  PubMed  Google Scholar 

  88. Nardini, M., Svergun, D., Konarev, P. V., et al. (2006) The C-terminal domain of the transcriptional corepressor CtBP is intrinsically unstructured. Protein Sci. 15, 1042–1050.

    Article  CAS  PubMed  Google Scholar 

  89. Roy, S., Schnell, S., and Radivojac, P. (2007) Unraveling the nature of the segmentation clock: intrinsic disorder of clock proteins and their interaction map. Comput. Biol. Chem. 30, 241–248.

    Article  Google Scholar 

  90. Popovic, M., Coglievina, M., Guarnaccia, C., et al. (2006) Gene synthesis, expression, purification, and characterization of human Jagged-1 intracellular region. Protein Expr. Purif. 47, 398–404.

    Article  CAS  PubMed  Google Scholar 

  91. Cheng, Y., Le Gall, T., Oldfield, C. J., Dunker, A. K., and Uversky, V. N. (2006) Abundance of intrinsic disorder in proteins associated with cardiovascular disease. Biochemistry 45, 10,448–10,460.

    Article  CAS  PubMed  Google Scholar 

  92. Liu, J., Perumal, N. B., Oldfield, C. J., Su, E. W., Uversky, V. N., and Dunker, A. K. (2006) Intrinsic disorder in transcription factors. Biochemistry 45, 6873–6888.

    Article  CAS  PubMed  Google Scholar 

  93. Singh, G. P., Ganapathi, M., Sandhu, K. S., and Dash, D. (2006) Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes. Proteins 62, 309–315.

    Article  CAS  PubMed  Google Scholar 

  94. Hansen, J. C., Lu, X., Ross, E. D., and Woody, R. W. (2006) Intrinsic protein disorder, amino acid composition, and histone terminal domains. J. Biol. Chem. 281, 1853–1856.

    Article  CAS  PubMed  Google Scholar 

  95. Haynes, C. and Iakoucheva, L. M. (2006) Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins. Nucleic Acids Res. 34, 305–312.

    Article  CAS  PubMed  Google Scholar 

  96. Bustos, D. M. and Iglesias, A. A. (2006) Intrinsic disorder is a key characteristic in partners that bind 14-3-3 proteins. Proteins 63, 35–42.

    Article  CAS  PubMed  Google Scholar 

  97. Denning, D. P., Patel, S. S., Uversky, V., Fink, A. L., and Rexach, M. (2003) Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc. Natl. Acad. Sci. USA 100, 2450–2455.

    Article  CAS  PubMed  Google Scholar 

  98. Boeckmann, B., Bairoch, A., Apweiler, R., et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370.

    Article  CAS  PubMed  Google Scholar 

  99. Daily, K. M., Radivojac, P., and Dunker, A. K. (2005) Intrinsic disorder and protein modifications: building an SVM predictor for methylation, in IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, San Diego, California, CA, pp.475–481.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Medicine, Indiana University, Indianapolis, IN

    Vladimir N. Uversky & A. Keith Dunker

  2. Russian Academy of Sciences, Moscow Region, Russia

    Vladimir N. Uversky

  3. School of Informatics, Indiana University, Bloomington, IN

    Predrag Radivojac

  4. The Rockefeller University New York, NY

    Lilia M. Iakoucheva

  5. Temple University, Philadelphia, PA

    Zoran Obradovic

Authors
  1. Vladimir N. Uversky
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Predrag Radivojac
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lilia M. Iakoucheva
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zoran Obradovic
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. Keith Dunker
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD

    Michael F. Ochs

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Humana Press Inc.

About this protocol

Cite this protocol

Uversky, V.N., Radivojac, P., Iakoucheva, L.M., Obradovic, Z., Keith Dunker, A. (2007). Prediction of Intrinsic Disorder and Its Use in Functional Proteomics. In: Ochs, M.F. (eds) Gene Function Analysis. Methods in Molecular Biology™, vol 408. Humana Press. https://doi.org/10.1007/978-1-59745-547-3_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-547-3_5

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-734-1

  • Online ISBN: 978-1-59745-547-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation