Substrate specificity of protein kinases and computational prediction of substrates

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1754, Issue 1-2, 2005, Pages 200-209

  Kobe, Boštjan ^a   Kampmann, Thorsten ^a   Forwood, Jade K ^a   Listwan, Pawel ^a   Brinkworth, Ross I ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Bioinformatics; Phosphorylation; Protein kinase; Protein structure; Signal transduction; Substrate specificity

Indexed keywords

PEPTIDE; PHOSPHATASE; PROTEIN KINASE;

AMINO ACID SEQUENCE; CONFERENCE PAPER; ENZYME ACTIVITY; ENZYME SPECIFICITY; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

BINDING SITES; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PEPTIDES; PHOSPHOPROTEIN PHOSPHATASE; PHOSPHORYLATION; PROTEIN KINASES; PROTEIN STRUCTURE, SECONDARY; SUBSTRATE SPECIFICITY;

EID: 29144510554     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2005.07.036     Document Type: Conference Paper

References (95)

1. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, and R.A. Holt The sequence of the human genome Science 291 2001 1304 1351
2. T. Hunter Signaling-2000 and beyond Cell 100 2000 113 127
3. G. Manning, D.B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam The protein kinase complement of the human genome Science 298 2002 1912 1934
4. L.A. Pinna, and M. Ruzzene How do protein kinases recognize their substrates? Biochim. Biophys. Acta 1314 1996 191 225
5. A. Kreegipuu, N. Blom, and S. Brunak PhosphoBase, a database of phosphorylation sites: release 2.0 Nucleic Acids Res. 27 1999 237 239
6. P.G. Besant, E. Tan, and P.V. Attwood Mammalian protein histidine kinases Int. J. Biochem. Cell Biol. 35 2003 297 309
7. S.K. Hanks, and A.M. Quinn Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family members Methods Enzymol. 200 1991 38 62
8. R.I. Brinkworth, R.A. Breinl, and B. Kobe Conserved sequence motifs in protein kinase families M.M. Gromiha S. Selvaraj Recent Research Developments in Protein Folding, Stability and Design, Research Signpost, Trivandrum, Kerala, India 2002 67 77
9. D.R. Knighton, J. Zheng, L.F. Ten Eyck, V.A. Ashford, N.-H. Xuong, S.S. Taylor, and J.M. Sowadski Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase Science 253 1991 407 414
10. B. Kobe, T. Gleichmann, T. Teh, J. Heierhorst, and B.E. Kemp Crystallization of protein kinases and phosphatases D.G. Hardie Protein Phosphorylation: A Practical Approach vol. 2 1999 Oxford Univ. Press Oxford 387 421
11. M. Huse, and J. Kuriyan The conformational plasticity of protein kinases Cell 109 2002 275 282
12. G.M. Cheetham Novel protein kinases and molecular mechanisms of autoinhibition Curr. Opin. Struct. Biol. 14 2004 700 705
13. E.H. Walker, O. Perisic, C. Ried, L. Stephens, and R.L. Williams Structural insights into phosphoinositide 3-kinase catalysis and signalling Nature 402 1999 313 320
14. D.R. Knighton, J. Zheng, L.F. Ten Eyck, N.-H. Xuong, S.S. Taylor, and J.M. Sowadski Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase Science 253 1991 414 420
15. E.D. Lowe, M.E. Noble, V.T. Skamnaki, N.G. Oikonomakos, D.J. Owen, and L.N. Johnson The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition EMBO J. 16 1997 6646 6658
16. N.R. Brown, M.E. Noble, J.A. Endicott, and L.N. Johnson The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases Nat. Cell Biol. 1 1999 438 443
17. S.R. Hubbard Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog EMBO J. 16 1997 5572 5581
18. J. Yang, P. Cron, V.M. Good, V. Thompson, B.A. Hemmings, and D. Barford Crystal structure of an activated Akt/protein kinase B ternary complex with GSK3-peptide and AMP-PNP Nat. Struct. Biol. 9 2002 940 944
19. R.I. Brinkworth, R.A. Breinl, and B. Kobe Structural basis and prediction of substrate specificity in protein serine/threonine kinases Proc. Natl. Acad. Sci. U. S. A. 100 2003 74 79
20. I. Schechter, and A. Berger On the size of the active site in proteases: I. Papain Biochem. Biophys. Res. Commun. 27 1967 157 162
21. B.E. Kemp, D.J. Graves, E. Benjamini, and E.G. Krebs Role of multiple basic residues in determining the substrate specificity of cyclic AMP-dependent protein kinase J. Biol. Chem. 252 1977 4888 4894
22. G.W. Tessmer, J.R. Skuster, L.B. Tabatabai, and D.J. Graves Studies on the specificity of phosphorylase kinase using peptide substrates J. Biol. Chem. 252 1977 5666 5671
23. B.E. Kemp, and R.B. Pearson Protein kinase recognition sequence motifs Trends Biochem. Sci. 15 1990 342 346
24. R.B. Pearson, and B.E. Kemp Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations Methods Enzymol. 200 1991 62 81
25. A. Kreegipuu, N. Blom, S. Brunak, and J. Jarv Statistical analysis of protein kinase specificity determinants FEBS Lett. 430 1998 45 50
26. G. Zhu, Y. Liu, and S. Shaw Protein kinase specificity. A strategic collaboration between kinase peptide specificity and substrate recruitment Cell Cycle 4 2005 52 56
27. T. Lee, A.N. Hoofnagle, Y. Kabuyama, J. Stroud, X. Min, E.J. Goldsmith, L. Chen, K.A. Resing, and N.G. Ahn Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry Mol. Cell 14 2004 43 55
28. M.C. Faux, and J.D. Scott More on target with protein phosphorylation: conferring specificity by location Trends Biochem. Sci. 21 1996 312 315
29. M.A. Lemmon, and J. Schlessinger Regulation of signal transduction and signal diversity by receptor oligomerization Trends Biochem. Sci. 19 1994 459 463
30. H.M. Sauro, and B.N. Kholodenko Quantitative analysis of signaling networks Prog. Biophys. Mol. Biol. 86 2004 5 43
31. O. Mayans, P.F.M. van der Ven, M. Wilm, A. Mues, P. Young, D. Furst, M. Wilmanns, and M. Gautel Structural basis for activation of the titin kinase domain during myofibrillogenesis Nature 395 1998 863 869
32. N.R. Brown, M.E. Noble, A.M. Lawrie, M.C. Morris, P. Tunnah, G. Divita, L.N. Johnson, and J.A. Endicott Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity J. Biol. Chem. 274 1999 8746 8756
33. S. Favelyukis, J.H. Till, S.R. Hubbard, and W.T. Miller Structure and autoregulation of the insulin-like growth factor 1 receptor kinase Nat. Struct. Biol. 8 2001 1058 1063
34. Z. Songyang, and L.C. Cantley Recognition and specificity in protein tyrosine kinase-mediated signalling Trends Biochem. Sci. 20 1995 470 475
35. M.W. Wooten In-gel kinase assay as a method to identify kinase substrates Science STKE 153 2002 PL15
36. A. Knebel, N. Morrice, and P. Cohen A novel method to identify protein kinase substrates: eEF2 kinase is phosphorylated and inhibited by SAPK4/p38delta EMBO J. 20 2001 4360 4369
37. R. Fukunaga, and T. Hunter Identification of MAPK substrates by expression screening with solid-phase phosphorylation Methods Mol. Biol. 250 2004 211 236
38. R. Fukunaga, and T. Hunter MNK1, a new MAP kinase-activated protein kinase, isolated by a novel expression screening method for identifying protein kinase substrates EMBO J. 16 1997 1921 1933
39. T.P. Cujec, P.F. Medeiros, P. Hammond, C. Rise, and B.L. Kreider Selection of v-abl tyrosine kinase substrate sequences from randomized peptide and cellular proteomic libraries using mRNA display Chem. Biol. 9 2002 253 264
40. A.C. Bishop, J.A. Ubersax, D.T. Petsch, D.P. Matheos, N.S. Gray, J. Blethrow, E. Shimizu, J.Z. Tsien, P.G. Schultz, and M.D. Rose A chemical switch for inhibitor-sensitive alleles of any protein kinase Nature 407 2000 395 401
41. K. Shah, and K.M. Shokat A chemical genetic approach for the identification of direct substrates of protein kinases Methods Mol. Biol. 233 2003 253 271
42. H. Zhu, J.F. Klemic, S. Chang, P. Bertone, A. Casamayor, K.G. Klemic, D. Smith, M. Gerstein, M.A. Reed, and M. Snyder Analysis of yeast protein kinases using protein chips Nat. Genet. 26 2000 283 289
43. H.K. Kole, M. Abdel-Ghany, and E. Racker Specific dephosphorylation of phosphoproteins by protein-serine and -tyrosine kinases Proc. Natl. Acad. Sci. U. S. A. 85 1988 5849 5853
44. D.C. Berwick, and J.M. Tavare Identifying protein kinase substrates: hunting for the organ-grinder's monkeys Trends Biochem. Sci. 29 2004 227 232
45. H. Zhang, X. Zha, Y. Tan, P.V. Hornbeck, A.J. Mastrangelo, D.R. Alessi, R.D. Polakiewicz, and M.J. Comb Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs J. Biol. Chem. 277 2002 39379 39387
46. A. Pandey, A.V. Podtelejnikov, B. Blagoev, X.R. Bustelo, M. Mann, and H.F. Lodish Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors Proc. Natl. Acad. Sci. U. S. A. 97 2000 179 184
47. M. Gronborg, T.Z. Kristiansen, A. Stensballe, J.S. Andersen, O. Ohara, M. Mann, O.N. Jensen, and A. Pandey A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate Mol. Cell. Proteomics 1 2002 517 527
48. S.B. Ficarro, M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowitz, D.F. Hunt, and F.M. White Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat. Biotechnol. 20 2002 301 305
49. Y. Oda, T. Nagasu, and B.T. Chait Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat. Biotechnol. 19 2001 379 382
50. H. Zhou, J.D. Watts, and R. Aebersold A systematic approach to the analysis of protein phosphorylation Nat. Biotechnol. 19 2001 375 378
51. M. Mann, S.E. Ong, M. Gronborg, H. Steen, O.N. Jensen, and A. Pandey Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome Trends Biotechnol. 20 2002 261 268
52. D.T. McLachlin, and B.T. Chait Analysis of phosphorylated proteins and peptides by mass spectrometry Curr. Opin. Chem. Biol. 5 2001 591 602
53. D.G. Campbell, and N.A. Morrice Identification of protein phosphorylation sites by a combination of mass spectrometry and solid phase Edman sequencing J. Biomol. Tech. 13 2002 119 130
54. A.J. Mackey, T.A. Haystead, and W.R. Pearson CRP: cleavage of radiolabeled phosphoproteins Nucleic Acids Res. 31 2003 3859 3861
55. Z.A. Knight, B. Schilling, R.H. Row, D.M. Kenski, B.W. Gibson, and K.M. Shokat Phosphospecific proteolysis for mapping sites of protein phosphorylation Nat. Biotechnol. 21 2003 1047 1054
56. S.A. Beausoleil, M. Jedrychowski, D. Schwartz, J.E. Elias, J. Villen, J. Li, M.A. Cohn, L.C. Cantley, and S.P. Gygi Large-scale characterization of HeLa cell nuclear phosphoproteins Proc. Natl. Acad. Sci. U. S. A. 101 2004 12130 12135
57. K. Godl, J. Wissing, A. Kurtenbach, P. Habenberger, S. Blencke, H. Gutbrod, K. Salassidis, M. Stein-Gerlach, A. Missio, and M. Cotton An efficient proteomics method to identify the cellular targets of protein kinase inhibitors Proc. Natl. Acad. Sci. U. S. A. 100 2003 15434 15439
58. S.A. Johnson, and T. Hunter Kinomics: methods for deciphering the kinome Nat. Methods 2 2005 17 25
59. C.E. Sims, and N.L. Allbritton Single-cell kinase assays: opening a window onto cell behavior Curr. Opin. Biotechnol. 14 2003 23 28
60. O.D. Perez, and G.P. Nolan Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry Nat. Biotechnol. 20 2002 155 162
61. P.J. Verveer, F.S. Wouters, A.R. Reynolds, and P.I. Bastiaens Quantitative imaging of lateral ErbB1 receptor signal propagation in the plasma membrane Science 290 2000 1567 1570
62. A. Miyawaki Visualization of the spatial and temporal dynamics of intracellular signaling Dev. Cell 4 2003 295 305
63. E. Oancea, M.N. Teruel, A.F. Quest, and T. Meyer Green fluorescent protein (GFP)-tagged cysteine-rich domains from protein kinase C as fluorescent indicators for diacylglycerol signaling in living cells J. Cell Biol. 140 1998 485 498
64. A. Toutchkine, V. Kraynov, and K. Hahn Solvent-sensitive dyes to report protein conformational changes in living cells J. Am. Chem. Soc. 125 2003 4132 4145
65. Z. Songyang, S. Blechner, N. Hoagland, M.F. Hoekstra, H. Piwnica-Worms, and L.C. Cantley Use of an oriented peptide library to determine the optimal substrates of protein kinases Curr. Biol. 4 1994 973 982
66. K. Fujii, G. Zhu, Y. Liu, J. Hallam, L. Chen, J. Herrero, and S. Shaw Kinase peptide specificity: improved determination and relevance to protein phosphorylation Proc. Natl. Acad. Sci. U. S. A. 101 2004 13744 13749
67. U. Reimer, U. Reineke, and J. Schneider-Mergener Peptide arrays: from macro to micro Curr. Opin. Biotechnol. 13 2002 315 320
68. L. Rychlewski, M. Kschischo, L. Dong, M. Schutkowski, and U. Reimer Target specificity analysis of the Abl kinase using peptide microarray data J. Mol. Biol. 336 2004 307 311
69. A.M. Wollacott, and J.R. Desjarlais Virtual interaction profiles of proteins J. Mol. Biol. 313 2001 317 342
70. B. Brannetti, A. Via, G. Cestra, G. Cesareni, and M. Helmer-Citterich SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family J. Mol. Biol. 298 2000 313 328
71. P. Aloy, and R.B. Russell Interrogating protein interaction networks through structural biology Proc. Natl. Acad. Sci. U. S. A. 99 2002 5896 5901
72. T. Kortemme, and D. Baker Computational design of protein-protein interactions Curr. Opin. Chem. Biol. 8 2004 91 97
73. A. Bairoch, P. Bucher, and K. Hofmann The PROSITE database, its status in 1997 Nucleic Acids Res. 25 1997 217 221
74. P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D.M. Martin, G. Ausiello, B. Brannetti, and A. Costantini ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res. 31 2003 3625 3630
75. C.M. Smith, I.N. Shindyalov, S. Veretnik, M. Gribskov, S.S. Taylor, L.F. Ten Eyck, and P.E. Bourne The protein kinase resource Trends Biochem. Sci. 22 1997 444 446
76. S. Peri, J.D. Navarro, R. Amanchy, T.Z. Kristiansen, C.K. Jonnalagadda, V. Surendranath, V. Niranjan, B. Muthusamy, T.K. Gandhi, and M. Gronborg Development of human protein reference database as an initial platform for approaching systems biology in humans Genome Res. 13 2003 2363 2371
77. J.S. Garavelli The RESID database of protein modifications: 2003 developments Nucleic Acids Res. 31 2003 499 501
78. N. Blom, S. Gammeltoft, and S. Brunak Sequence and structure-based prediction of eukaryotic protein phosphorylation sites J. Mol. Biol. 294 1999 1351 1362
79. M. Hjerrild, A. Stensballe, T.E. Rasmussen, C.B. Kofoed, N. Blom, T. Sicheritz-Ponten, M.R. Larsen, S. Brunak, O.N. Jensen, and S. Gammeltoft Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry J. Proteome Res. 3 2004 426 433
80. M.B. Yaffe, G.G. Leparc, J. Lai, T. Obata, S. Volinia, and L.C. Cantley A motif-based profile scanning approach for genome-wide prediction of signaling pathways Nat. Biotechnol. 19 2001 348 353
81. J.C. Obenauer, L.C. Cantley, and M.B. Yaffe Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs Nucleic Acids Res. 31 2003 3635 3641
82. J.H. Kim, J. Lee, B. Oh, K. Kimm, and I. Koh Prediction of phosphorylation sites using SVMs Bioinformatics 20 2004 3179 3184
83. D. Plewczynski, A. Tkacz, L.S. Wyrwicz, and L. Rychlewski AutoMotif server: prediction of single residue post-translational modifications in proteins Bioinformatics 21 2005 2525 2527
84. F.F. Zhou, Y. Xue, G.L. Chen, and X. Yao GPS: a novel group-based phosphorylation predicting and scoring method Biochem. Biophys. Res. Commun. 325 2004 1443 1448
85. Z. Songyang, K.P. Lu, Y.T. Kwon, L.-H. Tsai, O. Filhol, C. Cochet, D.A. Brickey, T.R. Soderling, C. Bartleson, and D.J. Graves A structural basis for substrate specificities of protein Ser/Thr kinases: primary sequence preference of casein kinases I and II, NIMA, phosphorylase kinase, calmodulin-dependent kinase II, CDK5, and Erk1 Mol. Cell. Biol. 16 1996 6486 6493
86. R.I. Brinkworth, J. Horne, and B. Kobe A computational analysis of substrate binding strength by phosphorylase kinase and protein kinase A J. Mol. Recognit. 15 2002 104 111
87. M. Sun, X.H. Liu, S.H. Ji, and Y.F. Zhao Modeling kinase-substrate specificity: implication of the distance between substrate nucleophilic oxygen and attacked phosphorus of ATP analog on binding affinity J. Mol. Graphics Modell. 23 2005 433 438
88. L. Li, E.I. Shakhnovich, and L.A. Mirny Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases Proc. Natl. Acad. Sci. U. S. A. 100 2003 4463 4468
89. J.W. Scott, D.G. Norman, S.A. Hawley, L. Kontogiannis, and D.G. Hardie Protein kinase substrate recognition studied using the recombinant catalytic domain of AMP-activated protein kinase and a model substrate J. Mol. Biol. 317 2002 309 323
90. A. Dinudom, A.B. Fotia, R.J. Lefkowitz, J.A. Young, S. Kumar, and D.I. Cook The kinase Grk2 regulates Nedd4/Nedd4-2-dependent control of epithelial Na+ channels Proc. Natl. Acad. Sci. U. S. A. 101 2004 11886 11890
91. A. Kelner, I. Pekala, S. Kaczanowski, G. Muszynska, D.G. Hardie, and G. Dobrowolska Biochemical characterization of the tobacco 42-kD protein kinase activated by osmotic stress Plant Physiol. 136 2004 3255 3265
92. N.W. Court, I. Kuo, O. Quigley, and M.A. Bogoyevitch Phosphorylation of the mitochondrial protein Sab by stress-activated protein kinase 3 Biochem. Biophys. Res. Commun. 319 2004 130 137
93. J.L. Sussman, D. Lin, J. Jiang, N.O. Manning, J. Prilusky, O. Ritter, and E.E. Abola Protein data bank (PDB): database of three-dimensional structural information of biological macromolecules Acta Crystallogr., D Biol. Crystallogr. 54 1998 1078 1084
94. Madhusudan, E.A. Trafny, N.-H. Xuong, J.A. Adams, L.F. Ten Eyck, S.S. Taylor, and J.M. Sowadski cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer Protein Sci. 3 1994 176 187
95. B. Boeckmann, A. Bairoch, R. Apweiler, M.C. Blatter, A. Estreicher, E. Gasteiger, M.J. Martin, K. Michoud, C. O'Donovan, and I. Phan The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res. 31 2003 365 370