From protein sequence to dynamics and disorder with DynaMine

Nature Communications

Volumn 4, Issue , 2013, Pages

  Cilia, Elisa ^a,b   Pancsa, Rita ^c,d   Tompa, Peter ^b,c,d   Lenaerts, Tom ^a,b,c   Vranken, Wim F ^b,c,d  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b Interuniversity Institute of Bioinformatics in Brussels (IB)2   (Belgium)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^d DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BIOCHEMISTRY; DATA SET; MOLECULAR ANALYSIS; PROTEIN; VIRUS;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; DYNAMINE; HYDROGEN BOND; HYDROPHOBICITY; LINEAR REGRESSION ANALYSIS; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE DATABASE; TRANSACTIVATION;

DYNAMINE; HUMAN ADENOVIRUS TYPE 5;

ALGORITHMS; AMINO ACID SEQUENCE; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84889560142     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3741     Document Type: Article

References (53)

1. Tompa, P. Intrinsically unstructured proteins. Trends Biochem. Sci. 27, 527-533 (2002). (Pubitemid 35279598)
2. Uversky, V. N. Intrinsic disorder in proteins associated with neurodegenerative diseases. Front. Biosci. 14, 5188-5238 (2009).
3. Schweitzer-Stenner, R. Conformational propensities and residual structures in unfolded peptides and proteins. Mol. Biosyst. 8, 122-133 (2012).
4. Sickmeier, M. et al. DisProt: the database of disordered proteins. Nucleic Acids Res. 35, D786-D793 (2007). (Pubitemid 46056310)
5. Zhang, Y., Stec, B. &Godzik, A. Between order and disorder in protein structures: analysis of dual personality fragments in proteins. Structure 15, 1141-1147 (2007). (Pubitemid 47362692)
6. Fuxreiter, M., Simon, I., Friedrich, P. &Tompa, P. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J. Mol. Biol. 338, 1015-1026 (2004). (Pubitemid 38542830)
7. Mohan, A. et al. Analysis of molecular recognition features (MoRFs). J. Mol. Biol. 362, 1043-1059 (2006). (Pubitemid 44353519)
8. Lee, S. H. et al. Understanding pre-structured motifs (PreSMos) in intrinsically unfolded proteins. Curr. Protein Pept. Sci. 13, 34-54 [pii] (2012).
9. Deng, X., Eickholt, J. &Cheng, J. A comprehensive overview of computational protein disorder prediction methods. Mol. Biosyst. 8, 114-121 (2012).
10. Teilum, K., Olsen, J. G. &Kragelund, B. B. Functional aspects of protein flexibility. cel. Mol. Life Sci. 66, 2231-2247 (2009).
11. Lange, O. F. et al. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (New York, NY) 320, 1471-1475 (2008). (Pubitemid 351929422)
12. Kutyshenko, V. P. et al. Solution structure and dynamics of the chimeric SH3 domains, SHH- and SHA-";Bergeracs". Biochim. Biophys. Acta 1794, 1813-1822 (2009).
13. Liang, S. et al. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry (John Wiley &Sons) 48, 399-414 (2009).
14. Li, L., Uversky, V. N., Dunker, A. K. &Meroueh, S. O. A computational investigation of allostery in the catabolite activator protein. J. Am. Chem. Soc. 129, 15668-15676 (2007).
15. Henzler-Wildman, K. A. et al. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913-916 (2007). (Pubitemid 350231333)
16. Markwick, P. R. L., Malliavin, T. &Nilges, M. Structural biology by NMR: structure, dynamics, and interactions. PLoS Comput. Biol. 4, e1000168 (2008).
17. Zhang, F. &Bruschweiler, R. Contact model for the prediction of NMR N-H order parameters in globular proteins. J. Am. Chem. Soc. 124, 12654-12655 (2002). (Pubitemid 35215977)
18. Ota, M. et al. An assignment of intrinsically disordered regions of proteins based on NMR structures. J. Struct. Biol. 181, 29-36 (2013).
19. Daughdrill, G. W., Borcherds, W. M. &Wu, H. Disorder predictors also predict backbone dynamics for a family of disordered proteins. PloS One 6, e29207 (2011).
20. Dyson, H. J. Expanding the proteome: disordered and alternatively folded proteins. Q. Rev. Biophys. 44, 467-518 (2011).
21. Berjanskii, M. V. &Wishart, D. S. Application of the random coil index to studying protein flexibility. J.Biomol. NMR 40, 31-48 (2008).
22. Ulrich, E. et al. BioMagResBank. Nucleic Acids Res. 36, D402-D408 (2008).
23. Dunker, A. K. et al. Intrinsically disordered protein. J. Mol. Graph. Model. 19, 26-59 (2001). (Pubitemid 32411501)
24. Dunker, A. K. et al. The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 9(Suppl 2): S1 (2008).
25. Linding, R., Russell, R. B., Neduva, V. &Gibson, T. J. GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31, 3701-3708 (2003). (Pubitemid 37442227)
26. Holladay, N. B., Kinch, L. N. &Grishin, N. V. Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity. Protein Sci. 16, 2140-2152 (2007). (Pubitemid 47481649)
27. Uversky, V. N. Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11, 739-756 (2002). (Pubitemid 34241284)
28. Dosztanyi, Z., Csizmok, V., Tompa, P. &Simon, I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21, 3433-3434 (2005). (Pubitemid 41222453)
29. Ishida, T. &Kinoshita, K. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res. 35, W460-W464 (2007).
30. 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 21, 3369-3376 (2005). (Pubitemid 41222441)
31. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P. &Dunker, A. K. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 61(Suppl 7): 176-182 (2005). (Pubitemid 43069972)
32. Prilusky, J. et al. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21, 3435-3438 (2005). (Pubitemid 41222454)
33. Walsh, I., Martin, A. J., Di Domenico, T. &Tosatto, S. C. ESpritz: accurate and fast prediction of protein disorder. Bioinformatics 28, 503-509 (2012).
34. Olson, K. E. et al. Secondary structure and dynamics of an intrinsically unstructured linker domain. J. Biomol. Struct. Dyn. 23, 113-124 (2005). (Pubitemid 41346030)
35. Gu, J. &Hilser, V. J. Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome. Structure 16, 1627-1637 (2008).
36. Lindorff-Larsen, K., Best, R. B., Depristo, M. A., Dobson, C. M. &Vendruscolo, M. Simultaneous determination of protein structure and dynamics. Nature 433, 128-132 (2005).
37. Dunker, A. K. &Obradovic, Z. The protein trinity-linking function and disorder. Nat. Biotechnol. 19, 805-806 (2001).
38. Diella, F. et al. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci. 13, 6580-6603 [pii] (2008).
39. Davey, N. E., Shields, D. C. &Edwards, R. J. SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34, 3546-3554 (2006).
40. Dinkel, H. et al. ELM-the database of eukaryotic linear motifs. Nucleic Acids Res. 40, D242-D251 (2012).
41. Rajasekaran, S. et al. Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res. 37, D185-D190 (2009).
42. Hensen, U. et al. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PloS One 7, e33931 (2012).
43. Uversky, V. N. A protein-chameleon: conformational plasticity of alphasynuclein, a disordered protein involved in neurodegenerative disorders. J. Biomol. Struct. Dyn. 21, 211-234 (2003). (Pubitemid 37204199)
44. Uversky, V. N., Oldfield, C. J. &Dunker, A. K. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu. Rev. Biophys. 37, 215-246 (2008).
45. Vranken, W. et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-696 (2005). (Pubitemid 40695845)
46. Rieping, W. &Vranken, W. F. Validation of archived chemical shifts through atomic coordinates. Proteins 78, 2482-2489 (2010).
47. Wang, B., Wang, Y. &Wishart, D. S. A probabilistic approach for validating protein NMR chemical shift assignments. J. Biomol. NMR 47, 85-99 (2010).
48. Goodman, J. L., Pagel, M. D. &Stone, M. J. Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters. J. Mol. Biol. 295, 963-978 (2000).
49. Gibrat, J. F., Garnier, J. &Robson, B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol. 198, 425-443 (1987). (Pubitemid 18017815)
50. Mark Hall, E. F., Holmes, G., Pfahringer, B., Reutemann, P. &Witten, I. H The WEKA data mining software: an update. ACM SIGKDD Explor. Newslett. In SIGKDD Explorations. Vol. 11, 10-18 (2009).
51. Li, X., Romero, P., Rani, M., Dunker, A. K. &Obradovic, Z. Predicting protein disorder for N-, C-, and internal regions. Genome Inform. Ser. Workshop Genome Inform. 10, 30-40 (1999).
52. Pentony, M. M. &Jones, D. T. Modularity of intrinsic disorder in the human proteome. Proteins 78, 212-221 (2010).
53. Heinig, M. &Frishman, D. STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res. 32, W500-W502 (2004). (Pubitemid 38997383)