The contribution of intrinsic disorder prediction to the elucidation of protein function

Current Opinion in Structural Biology

Volumn 23, Issue 3, 2013, Pages 467-472

  Cozzetto, Domenico ^a   Jones, David T ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

HUMAN; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; REVIEW; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; INTRINSICALLY DISORDERED PROTEINS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEOME; SEQUENCE ANALYSIS, PROTEIN;

EID: 84879144696     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2013.02.001     Document Type: Review

References (42)

1. Anfinsen C.B., Haber E., Sela M., White F.H. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A 1961, 47:1309-1314.
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
3. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucl Acids Res 2012, 40:D71-D75.
4. Wright P.E., Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999, 293:321-331.
5. Ward J.J., Sodhi J.S., McGuffin L.J., Buxton B.F., Jones D.T. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337:635-645.
6. Romero P., Obradovic Z., Li X., Garner E.C., Brown C.J., Dunker A.K. Sequence complexity of disordered protein. Proteins 2001, 42:38-48.
7. Uversky V.N. What does it mean to be natively unfolded?. Eur J Biochem 2002, 269:2-12.
8. Garner E., Cannon P., Romero P., Obradovic Z., Dunker A.K. Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Inform Workshop Genome Inform 1998, 9:201-213.
9. Radivojac P., Obradovic Z., Smith D.K., Zhu G., Vucetic S., Brown C.J., Lawson J.D., Dunker A.K. Protein flexibility and intrinsic disorder. Protein Sci 2004, 13:71-80.
10. Li X., Romero P., Rani M., Dunker A.K., Obradovic Z. Predicting protein disorder for N-, C-, and internal regions. Genome Inform Workshop Genome Inform 1999, 10:30-40.
11. Orosz F., Ovadi J. Proteins without 3D structure: definition, detection and beyond. Bioinformatics 2011, 27:1449-1454.
12. Monastyrskyy B., Fidelis K., Moult J., Tramontano A., Kryshtafovych A. Evaluation of disorder predictions in CASP9. Proteins 2011, 79(Suppl 10):107-118.
13. Vucetic S., Brown C.J., Dunker A.K., Obradovic Z. Flavors of protein disorder. Proteins 2003, 52:573-584.
14. Bellay J., Han S., Michaut M., Kim T., Costanzo M., Andrews B.J., Boone C., Bader G.D., Myers C.L., Kim P.M. Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol 2011, 12:R14.
15. Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci 2002, 27:527-533.
16. Dunker A.K., Brown C.J., Lawson J.D., Iakoucheva L.M., Obradovic Z. Intrinsic disorder and protein function. Biochemistry 2002, 41:6573-6582.
17. Lobley A., Swindells M.B., Orengo C.A., Jones D.T. Inferring function using patterns of native disorder in proteins. PLoS Comput Biol 2007, 3:e162.
18. Lobley A.E., Nugent T., Orengo C.A., Jones D.T. FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 2008, 36:W297-W302.
19. Vacic V., Oldfield C.J., Mohan A., Radivojac P., Cortese M.S., Uversky V.N., Dunker A.K. Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res 2007, 6:2351-2366.
20. Disfani F.M., Hsu W.L., Mizianty M.J., Oldfield C.J., Xue B., Dunker A.K., Uversky V.N., Kurgan L. MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics 2012, 28:i75-i83.
21. Meszaros B., Simon I., Dosztanyi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput Biol 2009, 5:e1000376.
22. Fuxreiter M., Tompa P., Simon I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 2007, 23:950-956.
23. Davey N.E., Edwards R.J., Shields D.C. Computational identification and analysis of protein short linear motifs. Front Biosci 2010, 15:801-825.
24. Nguyen Ba A.N., Yeh B.J., van Dyk D., Davidson A.R., Andrews B.J., Weiss E.L., Moses A.M. Proteome-wide discovery of evolutionary conserved sequences in disordered regions. Sci Signal 2012, 5:rs1.
25. Davey N.E., Cowan J.L., Shields D.C., Gibson T.J., Coldwell M.J., Edwards R.J. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Res 2012, 40:10628-10641.
26. Meszaros B., Dosztanyi Z., Simon I. Disordered binding regions and linear motifs-bridging the gap between two models of molecular recognition. PLoS One 2012, 7:e46829.
27. Romero P.R., Zaidi S., Fang Y.Y., Uversky V.N., Radivojac P., Oldfield C.J., Cortese M.S., Sickmeier M., LeGall T., Obradovic Z., et al. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci U S A 2006, 103:8390-8395.
28. Pentony M.M., Jones D.T. Modularity of intrinsic disorder in the human proteome. Proteins 2010, 78:212-221.
29. Buljan M., Chalancon G., Eustermann S., Wagner G.P., Fuxreiter M., Bateman A., Babu M.M. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 2012, 46:871-883.
30. Midic U., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. Protein disorder in the human diseasome: unfoldomics of human genetic diseases. BMC Genomics 2009, 10(Suppl 1):S12.
31. Pentony M.M., Ward J., Jones D.T. Computational resources for the prediction and analysis of native disorder in proteins. Methods Mol Biol 2010, 604:369-393.
32. Gsponer J., Futschik M.E., Teichmann S.A., Babu M.M. Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 2008, 322:1365-1368.
33. Edwards Y.J., Lobley A.E., Pentony M.M., Jones D.T. Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol 2009, 10:R50.
34. Haynes C., Oldfield C.J., Ji F., Klitgord N., Cusick M.E., Radivojac P., Uversky V.N., Vidal M., Iakoucheva L.M. Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2006, 2:e100.
35. Radivojac P., Clark W.T., Oron T.R., Schnoes A.M., Wittkop T., Sokolov A., Graim K., Funk C., Verspoor K., Ben-Hur A., et al. A large-scale evaluation of computational protein function prediction. Nat Methods 2013, (Epub ahead of print).
36. Cozzetto D., Buchan D., Bryson K., Jones D. Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics 2013, 14:S1.
37. Chen J. Towards the physical basis of how intrinsic disorder mediates protein function. Arch Biochem Biophys 2012, 524:123-131.
38. Marsh J.A., Teichmann S.A., Forman-Kay J.D. Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol 2012, 22:643-650.
39. Fuxreiter M., Simon I., Friedrich P., Tompa P. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J Mol Biol 2004, 338:1015-1026.
40. Knott M., Best R.B. A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations. PLoS Comput Biol 2012, 8:e1002605.
41. Lindorff-Larsen K., Trbovic N., Maragakis P., Piana S., Shaw D.E. Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. J Am Chem Soc 2012, 134:3787-3791.
42. Shan Y., Eastwood M.P., Zhang X., Kim E.T., Arkhipov A., Dror R.O., Jumper J., Kuriyan J., Shaw D.E. Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell 2012, 149:860-870.