The disordered amino-terminus of SIMPL interacts with members of the 70-kDa heat-shock protein family

DNA and Cell Biology

Volumn 25, Issue 12, 2006, Pages 704-714

  Breese, Erin Haag ^a   Uversky, Vladimir N ^a   Georgiadis, Millie M ^a   Harrington, Maureen A ^a,b  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK COGNATE PROTEIN 70; HEAT SHOCK PROTEIN; HEAT SHOCK PROTEIN 70; PROTEIN; PROTEIN SIMPL; SYNAPTOTAGMIN I; TUMOR NECROSIS FACTOR ALPHA; UNCLASSIFIED DRUG;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; ANTIGEN ANTIBODY COMPLEX; ARTICLE; CHARGE HYDROPATHY PLOT; CONTROLLED STUDY; CUMULATIVE DISTRIBUTION FUNCTION; EMBRYO; ENTROPY; FUNCTIONAL PROTEOMICS; HUMAN; HUMAN CELL; MASS SPECTROMETRY; MATHEMATICAL ANALYSIS; METHODOLOGY; MOLECULAR BIOLOGY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; ANIMALS; CARRIER PROTEINS; CELLS, CULTURED; COMPUTATIONAL BIOLOGY; HSP70 HEAT-SHOCK PROTEINS; HUMANS; MASS SPECTROMETRY; MICE; MUTANT PROTEINS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN; TRANSFECTION;

EID: 33846027092     PISSN: 10445498     EISSN: None     Source Type: Journal    
DOI: 10.1089/dna.2006.25.704     Document Type: Article

References (48)

1. BERMAN, H.M., WESTBROOK, J., FENG, Z., GILLILAND, G., BHAT, T.N., WEISSIG, H., SHINDYALOV, I.N., and BOURNE, P.E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
2. BOECKMANN, B., BAIROCH, A., APWEILER, R., BLATTER, M.C., ESTREICHER, A., GASTEIGER, E., MARTIN, M.J., MICHOUD, K., O'DONOVAN, C., PHAN, L, et al. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365-370.
3. CALLAGHAN, A.J., AURIKKO, J.P., ILAG, L.L., GUNTER GROSSMANN, J., CHANDRAN, V., KUHNEL, K., POLJAK, L., CARPOUSIS, A.J., ROBINSON, C.V., SYMMONS, M.F., et al. (2004). Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 340, 965-979.
4. DUNKER, A.K., GARNER, E., GUILLIOT, S., ROMERO, P., ALBRECHT, K., HART, J., OBRADOVIC, Z., KISSINGER, C., and VILLAFRANCA, J.E. (1998). Protein disorder and the evolution of molecular recognition: Theory, predictions and observations. Pac. Symp. Biocomput. 473-484.
5. DUNKER, A.K., and OBRADOVIC, Z. (2001). The protein trinity-Linking function and disorder. Nat. Biotechnol. 19, 805-806.
6. DUNKER, A.K., OBRADOVIC, Z., ROMERO, P., GARNER, E.C., and BROWN, C.J. (2000). Intrinsic protein disorder in complete genomes. Genome Inform. Ser. Workshop Genome Inform. 11, 161-171.
7. DUNKER, A.K., LAWSON, J.D., BROWN, C.J., WILLIAMS, R.M., ROMERO, P., OH, J.S., OLDFIELD, C.J., CAMPEN, A.M., RATLIFF, C.M., HIPPS, K.W., et al. (2001). Intrinsically disordered protein. J. Mol. Graph. Model 19, 26-59.
8. DUNKER, A.K., BROWN, C.J., and OBRADOVIC, Z. (2002a). Identification and functions of usefully disordered proteins. Adv. Protein Chem. 62, 25-49.
9. DUNKER, A.K., BROWN, C.J., LAWSON, J.D., IAKOUCHEVA, L.M., and OBRADOVIC, Z. (2002b). Intrinsic disorder and protein function. Biochemistry 41, 6573-6582.
10. DUNKER, A.K., CORTESE, M.S., ROMERO, P., IAKOUCHEVA, L.M., and UVERSKY, V.N. (2005). Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J. 272, 5129-5148.
11. DYSON, H.J., and WRIGHT, P.E. (2002). Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12, 54-60.
12. DYSON, H.J., and WRIGHT, P.E. (2005). Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell. Biol. 6, 197-208.
13. FINK, A.L. (2005). Natively unfolded proteins. Curr. Opin. Struct. Biol. 15, 35-41.
14. GARNER, E., ROMERO, P., DUNKER, A.K., BROWN, C. and OBRADOVIC, Z. (1999). Predicting binding regions within disordered proteins. Genome Inform. Ser. Workshop Genome Inform. 10, 41-50.
15. GUINEZ, C., MORELLE, W., MICHALSKI, J.C., and LEFEBVRE, T. (2005). O-GlcNAc glycosylation: A signal for the nuclear transport of cytosolic proteins? The Inter. J. Biochem. Cell Biol. 37, 765-774.
16. GUNASEKARAN, K., TSAI, C.J., KUMAR, S., ZANUY, D., and NUSSINOV, R. (2003). Extended disordered proteins: Targeting function with less scaffold. Trends Biochem. Sci. 28, 81-85.
17. IAKOUCHEVA, L.M., BROWN, C.J., LAWSON, J.D., OBRADOVIC, Z., and DUNKER, A.K. (2002). Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol. 323, 573-584.
18. KELLER, A., NESVIZHSKII, A.I., KOLKER, E., and AEBERSOLD, R. (2002). Emperical statistical model to estimate the accuracy of peptide identification made by MS/MS and database search. Anal. Chem. 74, 5383-5392.
19. KIANG, J.G. and TSOKOS, G.C. (1998). Heat shock protein 70 kDa: Molecular biology, biochemistry, and physiology. Pharmacol. Ther. 80, 183-201.
20. KWON, H.J., BREESE, E.H., VIG-VARGA, E., LUO, Y., LEE, Y., GOEBL, M.G., and HARRINGTON, M.A. (2004). Tumor necrosis factor alpha induction of NF-κB requires the novel coactivator SIMPL. Mol. Cell. Biol. 24, 9317-9326.
21. KYTE, J. and DOOLITTLE, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
22. LI, X., ROMERO, P., RAMI, M., DUNKER, A.K., and OBRADOVIC, Z. (1999). Predicting protein disorder for N-. C-. and internal regions. Genome Inform. Ser. Workshop Genome Inform. 10, 30-40.
23. MEADOR, W.E., MEANS, A.R., and QUIOCHO, F.A. (1992). Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. Science 257, 1251-1255.
24. MONSIGNY, M., RONDANINO, C., DUVERGER, E., FAJAC, I., and ROCH, A.-C. (2004). Glyco-dependent nuclear import of glycoproteins, glycoplexes and glycosylated plasmids. Biochim Biophys Acta 1673, 94-103.
25. NESVIZHSKII, A.I., KELLER, A., KOLKER, E., and AEBERSOLD, R. (2003). A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658.
26. OBRADOVIC, Z., PENG, K., VUCETIC, S., RADIVOJAC, P. BROWN, C.J., and DUNKER, A.K. (2003). Predicting intrinsic disorder from amino acid sequence. Proteins 53(Suppl. 6), 566-572.
27. OLDFIELD, C.J., CHENG, Y., CORTESE, M.S., BROWN, C.J., UVERSKY, V.N., and DUNKER, A.K. (2005a). Comparing and combining predictors of mostly disordered proteins. Biochemistry 44, 1989-2000.
28. OLDFIELD, C.J., CHENG, Y. CORTESE, M.S. ROMERO, P., UVERSKY, V.N., and DUNKER, A.K. (2005b). Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44, 12454-12470.
29. RAN, R., LU, A., ZHANG, L., TANG, Y., ZHU, H., XU, H., FENG, Y., HAN, C., ZHOU, G., RIGBY, A.C., et al. (2004). Hsp70 promotes TNF-mediated apoptosis by binding IKKγ and impairing NF-κB survival signaling. Genes Dev. 18, 1466-4481.
30. ROHDE, M. DAUGAARD, M., JENSEN, M.H. HELIN, K., NYLANDSTE, J., and JÄÄTTELÄ, M. (2006). Members of the heat-shock protein 70 family promote cancer cell growth by distinct mechanisms. Genes Dev. 19, 570-582.
31. ROMERO, P., OBRADOVIC, Z., and DUNKER, A.K. (1997a) Sequence data analysis for long disordered regions prediction in the calcineurin family. Genome Inform 8, 110-124.
32. ROMERO, P., OBRADOVIC, Z., KISSINGER, C. VILLAFRANCA, J.E., and DUNKER, A.K. (1997b). Identifying disordered regions in proteins from ammo acid sequence. Proc Int Conf Neural Networks 1, 90-95.
33. ROMERO, P., OBRADOVIC, Z., LI, X., GARNER, E.C., BROWN, C.J., and DUNKER, A.K. (2001). Sequence complexity of disordered protein. Proteins 42, 38-48.
34. SHI, X. and THOMAS, J.O. (1992). The transport of proteins into the nucleus requires the 70-kilodalton heat shock protein or its cytosolic cognate. Mol. Cell. Biol. 12, 2186-2192.
35. SPRENT, P. (1993). Allied Nonparametric Statistical Methods. 2nd ed. (Chapman and Hall, London).
36. THULASIRAMAN, V., YUN, B.-G., UMA, S., GU, Y., SCROGGINS, B.T., and MATTS, R.L. (2002). Differential inhibition of Hsc70 activities by two Hsc70 binding peptides. Biochemistry 41, 3742-3753.
37. TOMPA, P. (2002). Intrinsically unstructured proteins. Trends Biochem Sci. 27, 527-533.
38. TOMPA, P. (2003). The functional benefits of disorder. J. Mol. Struct. (Theochem.) 666-667, 361-371.
39. TSUKAHARA, F., and MARU, Y. (2004). Identification of novel nuclear export and nuclear localization-related signals in human heat shock cognate protein 70. J Biol Chem 279, 8867-8872.
40. UVERSKY, V.N. (2002a). Natively unfolded proteins: A point where biology waits for physics. Protein Sci. 11, 739-756.
41. UVERSKY, V.N. (2002b). What does it mean to he natively unfolded? Eur. J. Biochem. 269, 2-12.
42. UVERSKY, V.N., GILLESPIEM, J.R., and FINK, A.L. (2000). Why are "natively-unfolded" proteins unstructured under physiologic conditions? Proteins 41, 415-427.
43. UVERSKY, V.N., OLDFIELD, C.J., and DUNKER, A.K. (2005). Showing your ID: Intrinsic disorder as an ID for recognition, regulation and cell signaling. J. Mol. Recognit. 18, 343-384.
44. VIG, E., GREEN, M., LIU, Y., YU, K.Y., KWON, H.-J., GOEBL, M.G., and HARRINGTON, M.A. (2001). SIMPL is a tumor necrosis factor-specific regulator of nuclear factor kappaB activity. J. Biol. Chem. 276, 7859-7866.
45. VUCETIC, S., BROWN, C.J., DUNKER, A.K., and OBRADOVIC, Z. (2003). Flavors of protein disorder. Proteins 52, 573-584.
46. WARD, J.J., SODHI, J.S., MCGUFFIN, L.J., BUXTON, B.F., and JONES, D.T. (2004). Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337, 635-645.
47. WRIGHT, P.E., and DYSON, H.J. (1999). Intrinsically unstructured proteins: Reassessing the protein structure-function paradigm. J. Mol. Biol. 293, 321-331.
48. YATES, J.R., ENG, J.K., MCCORMACK, A.L., and SCHIELTZ, D. (1995). Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436.