How is functional specificity achieved through disordered regions of proteins?

BioEssays

Volumn 35, Issue 1, 2013, Pages 17-22

  Das, Rahul K ^a   Mittal, Anuradha ^a   Pappu, Rohit V ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

Disordered regions; Motifs

Indexed keywords

CALCIUM CHANNEL N TYPE; DNA TOPOISOMERASE (ATP HYDROLYSING); GLYCINE; LIGAND; POTASSIUM CHANNEL; SHAKER POTASSIUM CHANNEL; VOLTAGE DEPENDENT ANION CHANNEL;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CYTOSOLIC FRACTION; FUZZY SYSTEM; MOLECULAR BIOLOGY; MOLECULAR DOCKING; MOLECULAR RECOGNITION; POLARIZATION AND DEPOLARIZATION; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN MOTIF; QUANTITATIVE ANALYSIS; REGULATORY SEQUENCE; THERMODYNAMICS;

AMINO ACID SEQUENCE; BINDING SITES; MODELS, MOLECULAR; POTASSIUM CHANNELS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84871012320     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201200115     Document Type: Article

References (37)

1. Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, et al. 2002. Intrinsic disorder and protein function. Biochemistry 41: 6573- 82.
2. Dyson HJ, Wright PE. 2005. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197- 208.
3. Gonzalez-Perez V, Zeng XH, Henzler-Wildman K, Lingle CJ. 2012. Stereospecific binding of a disordered peptide segment mediates BK channel inactivation. Nature 485: 133- 6.
4. Kriwacki RW, Hengst L, Tennant L, Reed SI, et al. 1996. Structural studies of p21(Waf1/Cip1/Sdi1) in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proc Natl Acad Sci USA 93: 11504- 9.
5. Dyson HJ, Wright PE. 2002. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12: 54- 60.
6. Sickmeier M, Hamilton JA, LeGall T, Vacic V, et al. 2007. DisProt: the database of disordered proteins. Nucleic Acids Res 35: D786- 93.
7. Zhou HX, Pang XD, Lu C. 2012. Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets. Phys Chem Chem Phys 14: 10466- 76.
8. von Hippel PH. 2007. From "simple" DNA-protein interactions to the macromolecular machines of gene expression. Annu Rev Biophys Biomol Struct 36: 79- 105.
9. Ou L, Ferreira AM, Otieno S, Xiao LM, et al. 2011. Incomplete folding upon binding mediates Cdk4/Cyclin D complex activation by tyrosine phosphorylation of inhibitor p27 protein. J Biol Chem 286: 30142- 51.
10. Mittag T, Marsh J, Orlicky S, Borg M, et al. 2010. " Fuzzy" complexes: how much disorder can a biologically relevant complex tolerate, and can it even be beneficial? Biochem Cell Biol 88: 403.
11. Fuxreiter M. 2012. Fuzziness: linking regulation to protein dynamics. Mol Biosys 8: 168- 77.
12. Fuxreiter M, Simon I, Bondos S. 2011. Dynamic protein-DNA recognition: beyond what can be seen. Trends Biochem Sci 36: 415- 23.
13. Tompa P, Fuxreiter M. 2008. Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci 33: 2- 8.
14. Hansen J-P, McDonald I. 2006. Theory of Simple Liquids. Amsterdam, The Netherlands: Academic Press.
15. Hammes GG, Chang YC, Oas TG. 2009. Conformational selection or induced fit: a flux description of reaction mechanism. Proc Natl Acad Sci USA 106: 13737- 41.
16. Garcia-Garcia C, Draper DE. 2003. Electrostatic interactions in a peptide-RNA complex. J Mol Biol 331: 75- 88.
17. Zhang WH, Ganguly D, Chen JH. 2012. Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. PLoS Comp Biol 8: e1002353.
18. Aldrich RW. 1990. Potassium channels - mixing and matching. Nature 345: 475- 6.
19. Aldrich RW. 2001. Fifty years of inactivation. Nature 411: 643- 4.
20. Hoshi T, Zagotta WN, Aldrich RW. 1990. Biophysical and molecular mechanisms of Shaker potassium channel inactivation. Science 250: 533- 8.
21. Li WY, Aldrich RW. 2006. State-dependent block of BK channels by synthesized shaker ball peptides. J Gen Physiol 128: 423- 41.
22. Mackinnon R, Aldrich RW, Lee AW. 1993. Functional stoichiometry of shaker potassium channel inactivation. Science 262: 757- 9.
23. Murrell-Lagnado RD, Aldrich RW. 1993. Interactions of amino-terminal domains of shaker K-channels with a pore blocking site studied with synthetic peptides. J Gen Physiol 102: 949- 75.
24. Murrell-Lagnado RD, Aldrich RW. 1993. Energetics of shaker K-channels block by inactivation peptides. J Gen Physiol 102: 977- 1003.
25. Zeng XH, Benzinger GR, Xia XM, Lingle CJ. 2007. BK channels with beta3a subunits generate use-dependent slow afterhyperpolarizing currents by an inactivation-coupled mechanism. J Neurosci 27: 4707- 15.
26. Hu T, Chang S, Hsieh TS. 1998. Identifying Lys(359) as a critical residue for the ATP dependent reactions of Drosophila DNA topoisomerase II. J Biol Chem 273: 9586- 92.
27. Davey NE, Van Roey K, Weatheritt RJ, Toedt G, et al. 2012. Attributes of short linear motifs. Mol Biosys 8: 268- 81.
28. Nguyen Ba AN, Yeh BJ, van Dyk D, Davidson AR, et al. 2012. Proteome-wide discovery of evolutionary conserved sequences in disordered regions. Sci Signal 5: rs1.
29. Shereda RD, Kozlov AG, Lohman TM, Cox MM, et al. 2008. SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 43: 289- 318.
30. Bertagna A, Toptygin D, Brand L, Barrick D. 2008. The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder. Biochem Soc Trans 36: 157- 66.
31. Mao AH, Crick SL, Vitalis A, Chicoine CL, et al. 2010. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci USA 107: 8183- 8.
32. Muller-Spath S, Soranno A, Hirschfeld V, Hofmann H, et al. 2010. Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci USA 107: 14609- 14.
33. Marsh JA, Forman-Kay JD. 2010. Sequence determinants of compaction in intrinsically disordered proteins. Biophys J 98: 2383- 90.
34. Vuzman D, Levy Y. 2010. DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail. Proc Natl Acad Sci USA 107: 21004- 9.
35. Das RK, Crick SL, Pappu RV. 2012. N-terminal segments modulate the alpha-helical propensities of the intrinsically disordered basic regions of bZIP proteins. J Mol Biol 416: 287- 99.
36. Das RK, Mao AH, Pappu RV. 2012. Unmasking functional motifs within disordered regions of proteins. Sci Signal 5: pe17.
37. Babu MM, Kriwacki RW, Pappu RV. 2012. Versatility from protein disorder. Science 337: 1460- 1.