Sequence patterns associated with disordered regions in proteins

Proteins: Structure, Function and Genetics

Volumn 58, Issue 1, 2005, Pages 144-150

  Lise, S ^a   Jones, D T ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Disordered proteins; Sequence patterns; Structure prediction; Structure function paradigm

Indexed keywords

AMINO ACID; GLUTAMIC ACID; LYSINE; PROLINE;

AMINO ACID SEQUENCE; ARTICLE; PEPTIDE MAPPING; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 10844222539     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20279     Document Type: Article

References (27)

1. Jones DT. Protein structure prediction in the postgenomic era. Curr Opin Struct Biol 2000;10:371-379.
2. Brenner SE. A tour of structural genomics. Nat Rev Genet 2001;2:801-809.
3. Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999;293:321-331.
4. Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z. Intrinsic disorder and protein function. Biochemistry 2002;41:6573-6582.
5. Iakoucheva LM, Kimzey AL, Masselon CD, Bruce JE, Garner EC, Brown CJ, Dunker AK, Smith RD, Ackerman EJ. Identification of intrinsic order and disorder in the DNA repair protein XPA. Protein Sci 2001;10:560-571.
6. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang CH, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z. Intrinsically disordered protein. J Mol Graph Mod 2001;19:26-59.
7. Namba K. Roles of partly unfolded conformations in macromolecular self-assembly. Genes Cells 2001;6:1-12.
8. Dyson HJ, Wright PE. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 2002;12:54-60.
9. Uversky V. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002;11:739-756.
10. Uversky VN, Gillespie JR, Fink AL. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 2000;41:415-427.
11. Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK. Sequence complexity of disordered protein. Proteins 2001;42:38-48.
12. Li X, Obradovic Z, Brown CJ, Garner EC, Dunker AK. Comparing predictors of disordered protein. Genome Inform 2000;11:172-184.
13. Dunker AK, Brown CJ, Obradovic Z. Identification and functions of usefully disordered proteins. Adv Protein Chem 2002;62:25-49.
14. Vucetic S, Brown CJ, Dunker AK, Obradovic Z. Flavors of protein disorder. Proteins 2003;52:573-584.
15. Jones DT, Ward JJ. Prediction of disordered regions in proteins from position specific scoring matrices. Proteins 2003;53:573-578.
16. 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.
17. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russel RB. Protein disorder prediction: implications for structural proteomics. Structure 2003;11:1453-1459.
18. Rooman MJ, Wodak SJ. Identification of predictive sequence motifs limited by protein structure data base size. Nature 1988;335:45-49.
19. Rooman MJ, Rodriguez J, Wodak SJ. Relations between protein sequence and structure and their significance. J Mol Biol 1990;213:337-350.
20. Rooman MJ, Wodak SJ. Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins. Proteins 1991;9:69-78.
21. Available online at http://compbio.iupui.edu/dunker/html/www/ Datasets/ALL_dis.htm
22. Available online at http://compbio.iupui.edu/dunker/html/www/Datasets/ O_PDB_S25_Aug99.htm
23. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524
24. Hulo N, Sigrist CJA, Le Saux V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, Bairoch A. Recent improvements to the PROSITE database. Nucleic Acids Res 2004;32:D134-D137.
25. Schneider TD, Stephens RM. Sequence Logos: A new way to display consensus sequences. Nucleic Acids Res 1990;18:6097-6100.
26. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004;14:1188-1190.
27. Ferreon JC, Hilser VJ. The effect of the polyproline II (PPII) conformation on the denatured state entropy. Protein Sci 2003;12:447-457.