High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder

Nucleic Acids Research

Volumn 43, Issue 18, 2015, Pages

  Peng, Zhenling ^a,b   Kurgan, Lukasz ^b  

^a TIANJIN UNIVERSITY   (China)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; INTRINSICALLY DISORDERED PROTEIN; RNA BINDING PROTEIN; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; CRYSTAL STRUCTURE; DNA BINDING; DROSOPHILA MELANOGASTER; HUMAN; MUS MUSCULUS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEOMICS; RNA BINDING; SEQUENCE ALIGNMENT; ANIMAL; BINDING SITE; BIOLOGY; CHEMISTRY; METABOLISM; MOUSE; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE; STATISTICAL MODEL; VALIDATION STUDY;

ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; HUMANS; INTRINSICALLY DISORDERED PROTEINS; MICE; MODELS, STATISTICAL; PROTEOME; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84983734659     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv585     Document Type: Article

References (63)

1. Peng, Z., Yan, J., Fan, X., Mizianty, M.J., Xue, B., Wang, K., Hu, G., Uversky, V.N. and Kurgan, L. (2015) Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. Cell. Mol. Life Sci., 72, 137-151.
2. van der Lee, R., Buljan, M., Lang, B., Weatheritt, R.J., Daughdrill, G.W., Dunker, A.K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D.T. et al. (2014) Classification of intrinsically disordered regions and proteins. Chem. Rev., 114, 6589-6631.
3. Habchi, J., Tompa, P., Longhi, S. and Uversky, V.N. (2014) Introducing protein intrinsic disorder. Chem. Rev., 114, 6561-6588.
4. Dosztanyi, Z., Meszaros, B. and Simon, I. (2010) Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. Brief Bioinform., 11, 225-243.
5. He, B., Wang, K., Liu, Y., Xue, B., Uversky, V.N. and Dunker, A.K. (2009) Predicting intrinsic disorder in proteins: an overview. Cell Res., 19, 929-949.
6. Peng, Z.L. and Kurgan, L. (2012) Comprehensive comparative assessment of in-silico predictors of disordered regions. Curr. Protein Pept. Sci., 13, 6-18.
7. 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.
8. Xue, B., Dunker, A.K. and Uversky, V.N. (2012) Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J. Biomol. Struct. Dyn., 30, 137-149.
9. Galea, C.A., High, A.A., Obenauer, J.C., Mishra, A., Park, C.G., Punta, M., Schllessinger, A., Ma, J., Rost, B., Slaughter, C.A. et al. (2009) Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J. Proteome Res., 8, 211-226.
10. Tompa, P., Dosztanyi, Z. and Simon, I. (2006) Prevalent structural disorder in E-coli and S-cerevisiae proteomes. J. Proteome Res., 5, 1996-2000.
11. Cumberworth, A., Lamour, G., Babu, M.M. and Gsponer, J. (2013) Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes. Biochem. J., 454, 361-369.
12. Haynes, C., Oldfield, C.J., Ji, F., Klitgord, N., Cusick, M.E., Radivojac, P., Uversky, V.N., Vidal, M. and Iakoucheva, L.M. (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput. Biol., 2, 890-901.
13. Fuxreiter, M., Toth-Petroczy, A., Kraut, D.A., Matouschek, A.T., Lim, R.Y.H., Xue, B., Kurgan, L. and Uversky, V.N. (2014) Disordered proteinaceous machines. Chem. Rev., 114, 6806-6843.
14. Dyson, H.J. (2012) Roles of intrinsic disorder in protein-nucleic acid interactions. Mol. Biosyst., 8, 97-104.
15. Chen, J.W., Romero, P., Uversky, V.N. and Dunker, A.K. (2006) Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder. J. Proteome Res., 5, 888-898.
16. Tompa, P. and Csermely, P. (2004) The role of structural disorder in the function of RNA and protein chaperones. FASEB J., 18, 1169-1175.
17. Puton, T., Kozlowski, L., Tuszynska, I., Rother, K. and Bujnicki, J.M. (2012) Computational methods for prediction of protein-RNA interactions. J. Struct. Biol., 179, 261-268.
18. Zhao, H.Y., Yang, Y.D. and Zhou, Y.Q. (2013) Prediction of RNA binding proteins comes of age from low resolution to high resolution. Mol. Biosyst., 9, 2417-2425.
19. Kauffman, C. and Karypis, G. (2012) Computational tools for protein-DNA interactions. Wires Data Min. Knowl., 2, 14-28.
20. Gromiha, M.M. and Nagarajan, R. (2013) Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. Adv. Protein Chem. Str., 91, 65-99.
21. Shen, J., Zhang, J., Luo, X., Zhu, W., Yu, K., Chen, K., Li, Y. and Jiang, H. (2007) Predicting protein-protein interactions based only on sequences information. Proc. Natl. Acad. Sci. U.S.A., 104, 4337-4341.
22. Zhang, Q.C., Petrey, D., Deng, L., Qiang, L., Sin, Y., Thu, C.A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T. et al. (2013) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature, 495, 127-127.
23. Sharma, A., Dehzangi, A., Lyons, J., Imoto, S., Miyano, S., Nakai, K. and Patil, A. (2014) Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function. PLoS One, 9, e89890.
24. Meszaros, B., Simon, I. and Dosztanyi, Z. (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol., 5, e1000376.
25. Khan, W., Duffy, F., Pollastri, G., Shields, D.C. and Mooney, C. (2013) Predicting binding within disordered protein regions to structurally characterised peptide-binding domains. PloS One, 8, e72838.
26. Disfani, F.M., Hsu, W.L., Mizianty, M.J., Oldfield, C.J., Xue, B., Dunker, A.K., Uversky, V.N. and Kurgan, L. (2012) MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics, 28, i75-i83.
27. Jones, D.T. and Cozzetto, D. (2014) DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics, 31, 857-863.
28. Sickmeier, M., Hamilton, J.A., LeGall, T., Vacic, V., Cortese, M.S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V.N. et al. (2007) DisProt: the database of disordered proteins. Nucleic Acids Res., 35, D786-D793.
29. 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.
30. Monastyrskyy, B., Fidelis, K., Moult, J., Tramontano, A. and Kryshtafovych, A. (2011) Evaluation of disorder predictions in CASP9. Proteins-Struct. Funct. Genet., 79, 107-118.
31. Monastyrskyy, B., Kryshtafovych, A., Moult, J., Tramontano, A. and Fidelis, K. (2014) Assessment of protein disorder region predictions in CASP10. Proteins, 82(Suppl 2), 127-137.
32. Huang, Y., Niu, B., Gao, Y., Fu, L. and Li, W. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
33. Anderson, T.W. and Darling, D.A. (1952) Asymptotic theory of certain goodness of fit criteria based on stochastic processes. Ann. Math. Stat., 23, 193-212.
34. Wilcoxon, F. (1945) Individual comparisons by ranking methods. Biometrics Bull., 1, 80-83.
35. Xue, L.C., Dobbs, D. and Honavar, V. (2011) HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinform., 12, 244.
36. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
37. Peng, Z.L., Mizianty, M.J. and Kurgan, L. (2014) Genome-scale prediction of proteins with long intrinsically disordered regions. Proteins-Struct. Funct. Bioinform., 82, 145-158.
38. Walia, R.R., Caragea, C., Lewis, B.A., Towfic, F., Terribilini, M., El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2012) Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinform., 13, 89.
39. Ma, X., Guo, J., Liu, H.D., Xie, J.M. and Sun, X. (2012) Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information. IEEE/ACM Trans. Comput. Biol. Bioinform., 9, 1766-1775.
40. Kawashima, S. and Kanehisa, M. (2000) AAindex: amino acid index database. Nucleic Acids Res., 28, 374.
41. Dunker, A.K., Lawson, J.D., Brown, C.J., Williams, R.M., Romero, P., Oh, J.S., Oldfield, C.J., Campen, A.M., Ratliff, C.R., Hipps, K.W. et al. (2001) Intrinsically disordered protein. J. Mol. Graph. Model, 19, 26-59.
42. Romero, P., Obradovic, Z., Li, X.H., Garner, E.C., Brown, C.J. and Dunker, A.K. (2001) Sequence complexity of disordered protein. Proteins-Struct. Funct. Genet., 42, 38-48.
43. Liu, J.F., Tan, H.P. and Rost, B. (2002) Loopy proteins appear conserved in evolution. J. Mol. Biol., 322, 53-64.
44. Dyson, H.J. andWright, P.E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell. Biol., 6, 197-208.
45. Lobley, A., Swindells, M.B., Orengo, C.A. and Jones, D.T. (2007) Inferring function using patterns of native disorder in proteins. PLoS Comput. Biol., 3, 1567-1579.
46. 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.
47. Mizianty, M.J., Stach, W., Chen, K., Kedarisetti, K.D., Disfani, F.M. and Kurgan, L. (2010) Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Bioinformatics, 26, i489-i496.
48. Kuznetsov, I.B., Gou, Z.K., Li, R. and Hwang, S.W. (2006) Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. Proteins-Struct. Funct. Bioinform., 64, 19-27.
49. Hwang, S., Gou, Z.K. and Kuznetsov, I.B. (2007) DP-Bind: a Web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics, 23, 634-636.
50. Bader, J.S., Chaudhuri, A., Rothberg, J.M. and Chant, J. (2004) Gaining confidence in high-throughput protein interaction networks. Nat. Biotechn., 22, 78-85.
51. Lin, N., Wu, B.L., Jansen, R., Gerstein, M. and Zhao, H.Y. (2004) Information assessment on predicting protein-protein interactions. BMC Bioinform., 5, 154.
52. Consortium, U. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
53. Blake, J.A. and Harris, M.A. (2008) The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Curr Protoc Bioinformatics, doi:10.1002/0471250953.bi0702s23.
54. Cook, K.B., Kazan, H., Zuberi, K., Morris, Q. and Hughes, T.R. (2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res., 39, D301-D308.
55. Zhang, H.M., Chen, H., Liu, W., Liu, H., Gong, J., Wang, H. and Guo, A.Y. (2012) AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res., 40, D144-D149.
56. Baltz, A.G., Munschauer, M., Schwanhausser, B., Vasile, A., Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M. et al. (2012) The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell, 46, 674-690.
57. Kwon, S.C., Yi, H., Eichelbaum, K., Fohr, S., Fischer, B., You, K.T., Castello, A., Krijgsveld, J., Hentze, M.W. and Kim, V.N. (2013) The RNA-binding protein repertoire of embryonic stem cells. Nat. Struct. Mol. Biol., 20, 1122-1130.
58. Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K.R., Rastas, P., Morgunova, E., Enge, M., Taipale, M., Wei, G. et al. (2013) DNA-binding specificities of human transcription factors. Cell, 152, 327-339.
59. Calderone, A., Castagnoli, L. and Cesareni, G. (2013) mentha: a resource for browsing integrated protein-interaction networks. Nat. Methods, 10, 690-691.
60. Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., Speck, T., Kruger, D., Grebnev, G., Kuban, M. et al. (2014) The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res., 42, D259-D266.
61. Patil, A., Kinoshita, K. and Nakamura, H. (2010) Hub promiscuity in protein-protein interaction networks. Int. J. Mol. Sci., 11, 1930-1943.
62. Wang, L., Huang, C., Yang, M. and Yang, J. (2010) BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst. Biol., 4, S3.
63. Ma, X., Guo, J., Liu, H.D., Xie, J.M. and Sun, X. (2012) Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information. IEEE/ACM Trans. Comput. Biol. Bioinform., 9, 1766-1775.