Folded-unfolded cross-predictions and protein evolution: The case study of coiled-coils

FEBS Letters

Volumn 584, Issue 8, 2010, Pages 1623-1627

  Szappanos, Balázs ^a,c   Süveges, Dániel ^a   Nyitray, László ^a   Perczel, András ^a,b   Gáspári, Zoltán ^a  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b MTA ELTE Protein Modeling Research Group and Laboratory of Structural Chemistry and Biology   (Hungary)

^c INSTITUTE OF BIOCHEMISTRY   (Hungary)

Author keywords

Coiled coil; Intrinsically disordered protein; Protein evolution; Structure prediction

Indexed keywords

ACCURACY; ALGORITHM; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; MOLECULAR EVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 77951295640     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2010.03.026     Document Type: Article

References (41)

1. Lupas A.N., Gruber M. The structure of alpha-helical coiled coils. Adv. Protein Chem. 2005, 70:37-78.
2. Woolfson D.N. The design of coiled-coil structures and assemblies. Adv. Protein Chem. 2005, 70:79-112.
3. Grigoryan G., Keating A.E. Structural specificity in coiled-coil interactions. Curr. Opin. Struct. Biol. 2008, 18:477-483.
4. Rose A., Meier I. Scaffolds, levers, rods and springs: diverse cellular functions of long coiled-coil proteins. Cell Mol. Life Sci. 2004, 61:1996-2009.
5. Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci. 2002, 27:527-533.
6. Dunker A.K., Obradovic Z., Romero P., Garner E.C., Brown C.J. Intrinsic protein disorder in complete genomes. Genome Inform. Ser. Workshop Genome Inform. 2000, 11:161-171.
7. Liu J., Rost B. Comparing function and structure between entire proteomes. Protein Sci. 2001, 10:1970-1979.
8. Li Y., Brown J.H., Reshetnikova L., Blazsek A., Farkas L., Nyitray L., Cohen C. Visualization of an unstable coiled coil from the scallop myosin rod. Nature 2003, 424:341-345.
9. Burkhard P., Stetefeld J., Strelkov S.V. Coiled coils: a highly versatile protein folding motif. Trends Cell Biol. 2001, 11:82-88.
10. Suveges D., Gaspari Z., Toth G., Nyitray L. Charged single alpha-helix: a versatile protein structural motif. Proteins 2009, 74:905-916.
11. Morii H., Takenawa T., Arisaka F., Shimizu T. Identification of kinesin neck region as a stable alpha-helical coiled coil and its thermodynamic characterization. Biochemistry 1997, 36:1933-1942.
12. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science 1991, 252:1162-1164.
13. Delorenzi M., Speed T. An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics 2002, 18:617-625.
14. Wolf E., Kim P.S., Berger B. MultiCoil: a program for predicting two- and three-stranded coiled coils. Protein Sci. 1997, 6:1179-1189.
15. McDonnell A.V., Jiang T., Keating A.E., Berger B. Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics 2006, 22:356-358.
16. Gruber M., Soding J., Lupas A.N. REPPER-repeats and their periodicities in fibrous proteins. Nucleic Acids Res. 2005, 33:W239-W243.
17. Linding R., Jensen L.J., Diella F., Bork P., Gibson T.J., Russell R.B. Protein disorder prediction: implications for structural proteomics. Structure 2003, 11:1453-1459.
18. Prilusky J., Felder C.E., Zeev-Ben-Mordehai T., Rydberg E.H., Man O., Beckmann J.S., Silman I., Sussman J.L. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 2005, 21:3435-3438.
19. Linding R., Russell R.B., Neduva V., Gibson T.J. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 2003, 31:3701-3708.
20. Dosztanyi Z., Csizmok V., Tompa P., Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol. 2005, 347:827-839.
21. Yang Z.R., Thomson R., McNeil P., Esnouf R.M. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 2005, 21:3369-3376.
22. Obradovic Z., Peng K., Vucetic S., Radivojac P., Dunker A.K. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 2005, 61(Suppl. 7):176-182.
23. Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 1994, 3:522-524.
24. Walshaw J., Woolfson D.N. Socket: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol. 2001, 307:1427-1450.
25. Testa O.D., Moutevelis E., Woolfson D.N. CC+: a relational database of coiled-coil structures. Nucleic Acids Res. 2009, 37:D315-D322.
26. Sickmeier M., et al. DisProt: the database of disordered proteins. Nucleic Acids Res. 2007, 35:D786-D793.
27. Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
28. Rost B., Sander C., Schneider R. Redefining the goals of protein secondary structure prediction. J. Mol. Biol. 1994, 235:13-26.
29. Iakoucheva L.M., Brown C.J., Lawson J.D., Obradovic Z., Dunker A.K. Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol. 2002, 323:573-584.
30. 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.
31. Gazi A.D., Bastaki M., Charova S.N., Gkougkoulia E.A., Kapellios E.A., Panopoulos N.J., Kokkinidis M. Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems. J. Biol. Chem. 2008, 283:34062-34068.
32. Barbar E. Dynein light chain LC8 is a dimerization hub essential in diverse protein networks. Biochemistry 2008, 47:503-508.
33. Hodi Z., Nemeth A.L., Radnai L., Hetenyi C., Schlett K., Bodor A., Perczel A., Nyitray L. Alternatively spliced exon B of myosin Va is essential for binding the tail-associated light chain shared by dynein. Biochemistry 2006, 45:12582-12595.
34. Hodi Z., et al. The LC8 family of dynein light chains: multifunctional chaperon-like proteins. FEBS J. 2007, 274:106.
35. Meszaros B., Simon I., Dosztanyi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol. 2009, 5:e1000376.
36. Tompa P. Intrinsically unstructured proteins evolve by repeat expansion. Bioessays 2003, 25:847-855.
37. Gaspari Z., Ortutay C., Toth G. Divergent microsatellite evolution in the human and chimpanzee lineages. FEBS Lett. 2007, 581:2523-2526.
38. Tóth-Petróczy Á., Mészáros B., Simon I., Dunker A.K., Uversky V.N., Fuxreiter M. Assessing conservation of disordered regions in proteins. Open Proteom. J. 2008, 1:46-53.
39. Pal C., Papp B., Lercher M.J. An integrated view of protein evolution. Nat. Rev. Genet. 2006, 7:337-348.
40. Szilagyi A., Gyorffy D., Zavodszky P. The twilight zone between protein order and disorder. Biophys. J. 2008, 95:1612-1626.
41. Tokuriki N., Tawfik D.S. Protein dynamism and evolvability. Science 2009, 324:203-207.