Toward a quantitative theory of intrinsically disordered proteins and their function

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 47, 2009, Pages 19819-19823

  Liu, Jintao ^a   Faeder, James R ^a   Camacho, Carlos J ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Binding; Catalysis; Intrinsic disorder; Specificity; Transcription

Indexed keywords

ADULT; ARTICLE; CATALYSIS; FEMALE; GENOME; HUMAN; HUMAN EXPERIMENT; MALE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; THERMODYNAMICS; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EUKARYOTA; PROKARYOTA;

EID: 73949144611     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0907710106     Document Type: Article

References (37)

1. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. J Mol Biol 293:321-331.
2. Dunker AK, Obradovic Z, Romero P, Garner EC, Brown CJ (2000) Intrinsic protein disorder in complete genomes. Genome Informatics 11:161-171.
3. Haynes C, et al. (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2:e100.
4. Romero PR, et al. (2006) Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci USA 103:8390-8395.
5. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337:635-645.
6. Xie H, et al. (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 6:1882-1898.
7. Iakoucheva LM, Brown CJ, Lawson JD, Obradovic Z, Dunker AK (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 323:573-584.
8. Shoemaker BA, Portman JJ, Wolynes PG (2000) Speeding molecular recognition by using the folding funnel: The fly-casting mechanism. Proc Natl Acad Sci USA 97:8868-8873.
9. Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6:197-208.
10. Schulz GE (1979) In Molecular Mechanism of Biological Recognition (Elsevier, Amsterdam), pp. 79-94.
11. Ashburner M, et al. (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25:25-29.
12. Zwanzig R (1997) Two-state models of protein folding kinetics. Proc Natl Acad Sci USA 94:148-150.
13. Tsai CJ, Ma B, Sham YY, Kumar S, Nussinov R (2001) Structured disorder and conformational selection. Proteins 44:418-427.
14. Spolar RS, Record Jr MT (1994) Coupling of local folding to site-specific binding of proteins to DNA. Science 263:777-784.
15. Rajamani D, Thiel S, Vajda S, Camacho CJ (2004) Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 101:11287-11292.
16. Camacho CJ, Katsumata Y, Ascherman DP (2008) Structural and thermodynamic approach to peptide immunogenicity. PLoS Comput Biol 4:e1000231.
17. Dunker AK,et al. (1998) Protein disorder and the evolution of molecular recognition: Theory, predictions and observations. Pac Symp Biocomput 473-484.
18. Pauling L (1948) Nature of forces between large molecules of biological interest. Nature 161:707-709.
19. Yang LW, Bahar I (2005) Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure 13:893-904.
20. Shoichet BK, Baase WA, Kuroki R, Matthews BW (2005) A relationship between protein stability and protein function. Proc Natl Acad Sci USA 92:452-456.
21. Ladbury JE, Arold S (2000) Searching for specificity in SH domains. Chem Biol 7:R3-R8.
22. Wang R, Fang X, Lu Y, Yang CY, Wang S (2005) The PDBbind database: Methodologies and updates. J Med Chem 48:4111-4119.
23. Barrell D, et al. (2009) The GOA database in 2009 - An integrated gene ontology annotation resource. Nucl Acids Res 37:D396-D403.
24. UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190-D195.
25. Hong EL, et al. (2008) Gene ontology annotations at SGD: New data sources and annotation methods. Nucleic Acids Res 36:D577-D581.
26. Keseler IM, et al. (2009) EcoCyc: A comprehensive view of Escherichia coli biology. Nucl Acids Res 37:D464-D470.
27. Liang C, et al. (2008) Gramene: A growing plant comparative genomics resource. Nucl Acids Res 36:D947-D953.
28. Drysdale R, FlyBase Consortium (2008) FlyBase: A database for the Drosophila research community. Methods Mol Biol 420:45-59.
29. Bieri T, et al. (2007) WormBase: New content and better access. Nucleic Acids Res 35:D506-D510.
30. Fey P, et al. (2009) dictyBase - A Dictyostelium bioinformatics resource update. Nucleic Acids Res 37:D515-D519.
31. Aslett M, Wood V (2006) Gene ontology annotation status of the fission yeast genome: Preliminary coverage approaches 100%. Yeast 13:913-919.
32. Haft DH, Selengut JD, White O (2003) The TIGRFAMs database of protein families. Nucleic Acids Res 31:371-373.
33. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7:208.
34. Prilusky J, et al. (2005) FoldIndex: A simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21:3435-3438.
35. Linding R, et al. (2003) Protein disorder prediction: Implications for structural proteomics. Structure 11:1453-1459.
36. Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28:235-242.
37. DeGroot MH (1991) In Probability and Statistics. (Addison-Wesley, Reading, MA), 3rd Ed.