Structure and intrinsic disorder in protein autoinhibition

Structure

Volumn 21, Issue 3, 2013, Pages 332-341

  Trudeau, Travis ^a   Nassar, Roy ^a   Cumberworth, Alexander ^a   Wong, Eric T C ^a   Woollard, Geoffrey ^a   Gsponer, Jörg ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOINHIBITION; CONTROLLED STUDY; INHIBITION KINETICS; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN STRUCTURE;

ALTERNATIVE SPLICING; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PHOSPHORYLATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 84874828251     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.12.013     Document Type: Article

References (58)

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
2. S. Bhattacharya, Z. Dai, J. Li, S. Baxter, D.J.E. Callaway, D. Cowburn, and Z. Bu A conformational switch in the scaffolding protein NHERF1 controls autoinhibition and complex formation J. Biol. Chem. 285 2010 9981 9994
3. M. Buck, W. Xu, and M.K. Rosen A two-state allosteric model for autoinhibition rationalizes WASP signal integration and targeting J. Mol. Biol. 338 2004 271 285
4. M. Buljan, G. Chalancon, S. Eustermann, G.P. Wagner, M. Fuxreiter, A. Bateman, and M.M. Babu Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks Mol. Cell 46 2012 871 883
5. B. Catimel, T. Teh, M.R.M. Fontes, I.G. Jennings, D.A. Jans, G.J. Howlett, E.C. Nice, and B. Kobe Biophysical characterization of interactions involving importin-α during nuclear import J. Biol. Chem. 276 2001 34189 34198
6. P.M. Chan, S. Ilangumaran, J. La Rose, A. Chakrabartty, and R. Rottapel Autoinhibition of the kit receptor tyrosine kinase by the cytosolic juxtamembrane region Mol. Cell. Biol. 23 2003 3067 3078
7. J.W. Chen, P. Romero, V.N. Uversky, and A.K. Dunker Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions J. Proteome Res. 5 2006 879 887
8. L.L. Chen, M. Sabripour, E.F. Wu, V.G. Prieto, G.N. Fuller, and M.L. Frazier A mutation-created novel intra-exonic pre-mRNA splice site causes constitutive activation of KIT in human gastrointestinal stromal tumors Oncogene 24 2005 4271 4280
9. J.-H. Cho, V. Muralidharan, M. Vila-Perello, D.P. Raleigh, T.W. Muir, and A.G. Palmer 3rd Tuning protein autoinhibition by domain destabilization Nat. Struct. Mol. Biol. 18 2011 550 555
10. J.A. Clapperton, S.R. Martin, S.J. Smerdon, S.J. Gamblin, and P.M. Bayley Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism Biochemistry 41 2002 14669 14679
11. A.J. Dombroski, W.A. Walter, and C.A. Gross Amino-terminal amino acids modulate σ-factor DNA-binding activity Genes Dev. 7 12A 1993 2446 2455
12. Z. Dosztányi, V. Csizmok, P. Tompa, and I. Simon IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content Bioinformatics 21 2005 3433 3434
13. J. Eder, M. Rheinnecker, and A.R. Fersht Folding of subtilisin BPN': role of the pro-sequence J. Mol. Biol. 233 1993 293 304
14. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
15. L. Falzon, S. Patel, Y.J. Chen, and M. Inouye Autotomic behavior of the propeptide in propeptide-mediated folding of prosubtilisin E J. Mol. Biol. 366 2007 494 503
16. R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunasekaran, G. Ceric, and K. Forslund The Pfam protein families database Nucleic Acids Res. 38 Database issue 2010 D211 D222
17. P. Flicek, M.R. Amode, D. Barrell, K. Beal, S. Brent, D. Carvalho-Silva, P. Clapham, G. Coates, S. Fairley, and S. Fitzgerald Ensembl 2012 Nucleic Acids Res. 40 Database issue 2012 D84 D90
18. J. Gsponer, and M.M. Babu The rules of disorder or why disorder rules Prog. Biophys. Mol. Biol. 99 2009 94 103
19. J. Gsponer, M.E. Futschik, S.A. Teichmann, and M.M. Babu Tight regulation of unstructured proteins: from transcript synthesis to protein degradation Science 322 2008 1365 1368
20. P.V. Hornbeck, J.M. Kornhauser, S. Tkachev, B. Zhang, E. Skrzypek, B. Murray, V. Latham, and M. Sullivan PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse Nucleic Acids Res. 40 Database issue 2012 D261 D270
21. S.R. Hubbard Juxtamembrane autoinhibition in receptor tyrosine kinases Nat. Rev. Mol. Cell Biol. 5 2004 464 471
22. L.M. Iakoucheva, C.J. Brown, J.D. Lawson, Z. Obradović, and A.K. Dunker Intrinsic disorder in cell-signaling and cancer-associated proteins J. Mol. Biol. 323 2002 573 584
23. R. Ihaka, and R. Gentleman R: a language for data analysis and graphics J. Comput. Graph. Statist. 5 1996 299 314
24. B. Jayaraman, and L.K. Nicholson Thermodynamic dissection of the Ezrin FERM/CERMAD interface Biochemistry 46 2007 12174 12189
25. A.S. Kim, L.T. Kakalis, N. Abdul-Manan, G.A. Liu, and M.K. Rosen Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein Nature 404 2000 151 158
26. L.J. Ko, and C. Prives p53: puzzle and paradigm Genes Dev. 10 1996 1054 1072
27. B. Kobe, J. Heierhorst, S.C. Feil, M.W. Parker, G.M. Benian, K.R. Weiss, and B.E. Kemp Giant protein kinases: domain interactions and structural basis of autoregulation EMBO J. 15 1996 6810 6821
28. T. Kortemme, and D. Baker A simple physical model for binding energy hot spots in protein-protein complexes Proc. Natl. Acad. Sci. USA 99 2002 14116 14121
29. L.F. Lareau, R.E. Green, R.S. Bhatnagar, and S.E. Brenner The evolving roles of alternative splicing Curr. Opin. Struct. Biol. 14 2004 273 282
30. A. Leaver-Fay, M. Tyka, S.M. Lewis, O.F. Lange, J. Thompson, R. Jacak, K. Kaufman, P.D. Renfrew, C.A. Smith, and W. Sheffler ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules Methods Enzymol. 487 2011 545 574
31. B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
32. G.M. Lee, L.W. Donaldson, M.A. Pufall, H.-S. Kang, I. Pot, B.J. Graves, and L.P. McIntosh The structural and dynamic basis of Ets-1 DNA binding autoinhibition J. Biol. Chem. 280 2005 7088 7099
33. P. Li, I.R. Martins, G.K. Amarasinghe, and M.K. Rosen Internal dynamics control activation and activity of the autoinhibited Vav DH domain Nat. Struct. Mol. Biol. 15 2008 613 618
34. X. Li, P. Romero, M. Rani, A.K. Dunker, and Z. Obradovic Predicting Protein Disorder for N-, C-, and Internal Regions Genome Inform. Ser. Workshop Genome Inform. 10 1999 30 40
35. N. London, D. Movshovitz-Attias, and O. Schueler-Furman The structural basis of peptide-protein binding strategies Structure 18 2010 188 199
36. C. Marie-Claire, Y. Yabuta, K. Suefuji, H. Matsuzawa, and U. Shinde Folding pathway mediated by an intramolecular chaperone: the structural and functional characterization of the aqualysin I propeptide J. Mol. Biol. 305 2001 151 165
37. I.K. McDonald, and J.M. Thornton Satisfying hydrogen bonding potential in proteins J. Mol. Biol. 238 1994 777 793
38. B. Mészáros, A. Tompa, I. Simon, and Z. Dosztányi Molecular principles of the interaction of disordered proteins J. Mol. Biol. 372 2007 549 561
39. A. Mohan, C.J. Oldfield, P. Radivojac, V. Vacic, M.S. Cortese, A.K. Dunker, and V.N. Uversky Analysis of molecular recognition features (MoRFs) J. Mol. Biol. 362 2006 1043 1059
40. C.D. Mol, D.R. Dougan, T.R. Schneider, R.J. Skene, M.L. Kraus, D.N. Scheibe, G.P. Snell, H. Zou, B.C. Sang, and K.P. Wilson Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase J. Biol. Chem. 279 2004 31655 31663
41. A. Morreale, M. Venkatesan, H.R. Mott, D. Owen, D. Nietlispach, P.N. Lowe, and E.D. Laue Structure of Cdc42 bound to the GTPase binding domain of PAK Nat. Struct. Biol. 7 2000 384 388
42. I.M. Nooren, and J.M. Thornton Structural characterisation and functional significance of transient protein-protein interactions J. Mol. Biol. 325 2003 991 1018
43. G. Ostlund, T. Schmitt, K. Forslund, T. Köstler, D.N. Messina, S. Roopra, O. Frings, and E.L. Sonnhammer InParanoid 7: new algorithms and tools for eukaryotic orthology analysis Nucleic Acids Res. 38 Database issue 2010 D196 D203
44. S.B. Padrick, and M.K. Rosen Physical mechanisms of signal integration by WASP family proteins Annu. Rev. Biochem. 79 2010 707 735
45. M.A. Pearson, D. Reczek, A. Bretscher, and P.A. Karplus Structure of the ERM protein moesin reveals the FERM domain fold masked by an extended actin binding tail domain Cell 101 2000 259 270
46. M.A. Pufall, and B.J. Graves Autoinhibitory domains: modular effectors of cellular regulation Annu. Rev. Cell Dev. Biol. 18 2002 421 462
47. M.A. Pufall, G.M. Lee, M.L. Nelson, H.S. Kang, A. Velyvis, L.E. Kay, L.P. McIntosh, and B.J. Graves Variable control of Ets-1 DNA binding by multiple phosphates in an unstructured region Science 309 2005 142 145
48. D. Rajamani, S. Thiel, S. Vajda, and C.J. Camacho Anchor residues in protein-protein interactions Proc. Natl. Acad. Sci. USA 101 2004 11287 11292
49. P. Romero, Z. Obradovic, X. Li, E.C. Garner, C.J. Brown, and A.K. Dunker Sequence complexity of disordered protein Proteins 42 2001 38 48
50. P.R. Romero, S. Zaidi, Y.Y. Fang, V.N. Uversky, P. Radivojac, C.J. Oldfield, M.S. Cortese, M. Sickmeier, T. LeGall, Z. Obradovic, and A.K. Dunker Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms Proc. Natl. Acad. Sci. USA 103 2006 8390 8395
51. V. Rousseau, O. Goupille, N. Morin, and J. Barnier A new consitutively active brain PAKB isoform displays modified specificities toward Rac and Cdc42 GTPases J. Biol. Chem. 278 2003 3912 3920
52. R.J. Siezen, and J.A. Leunissen Subtilases: the superfamily of subtilisin-like serine proteases Protein Sci. 6 1997 501 523
53. S. Stöven, I. Ando, L. Kadalayil, Y. Engström, and D. Hultmark Activation of the Drosophila NF-kappaB factor Relish by rapid endoproteolytic cleavage EMBO Rep. 1 2000 347 352
54. I. Walsh, A.J. Martin, T. Di Domenico, and S.C. Tosatto ESpritz: accurate and fast prediction of protein disorder Bioinformatics 28 2012 503 509
55. J.J. Ward, J.S. Sodhi, L.J. McGuffin, B.F. Buxton, and D.T. Jones Prediction and functional analysis of native disorder in proteins from the three kingdoms of life J. Mol. Biol. 337 2004 635 645
56. D.L. Wheeler, T. Barrett, D.A. Benson, S.H. Bryant, K. Canese, D.M. Church, M. DiCuccio, R. Edgar, S. Federhen, and W. Helmberg Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 34 Database issue 2006 D173 180
57. L.E. Wybenga-Groot, B. Baskin, S.H. Ong, J. Tong, T. Pawson, and F. Sicheri Structural basis for autoinhibition of the Ephb2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region Cell 106 2001 745 757
58. B. Yu, I.R. Martins, P. Li, G.K. Amarasinghe, J. Umetani, M.E. Fernandez-Zapico, D.D. Billadeau, M. Machius, D.R. Tomchick, and M.K. Rosen Structural and energetic mechanisms of cooperative autoinhibition and activation of Vav1 Cell 140 2010 246 256