GPS: A novel group-based phosphorylation predicting and scoring method

Biochemical and Biophysical Research Communications

Volumn 325, Issue 4, 2004, Pages 1443-1448

  Zhou, Feng Feng ^a   Xue, Yu ^a   Chen, Guo Liang ^a   Yao, Xuebiao ^a,b  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b MOREHOUSE SCHOOL OF MEDICINE   (United States)

Author keywords

Aurora B; GPS; Phosphorylation; PKA; Protein kinases

Indexed keywords

ISOLEUCINE; POLYPEPTIDE; PROTEIN KINASE; SERINE; THREONINE; VALINE;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; COMPUTER PREDICTION; DIAGNOSTIC ACCURACY; ENZYME SUBSTRATE COMPLEX; GLOBAL POSITIONING SYSTEM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; SCORING SYSTEM; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS;

ALGORITHMS; BINDING SITES; CONSERVED SEQUENCE; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN KINASES; PROTEIN-SERINE-THREONINE KINASES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 8844284560     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.11.001     Document Type: Article

References (38)

1. Y. Lou, J. Yao, A. Zereshki, Z. Dou, K. Ahmed, H. Wang, J. Hu, Y. Wang, and X. Yao NEK2A interacts with MAD1 and possibly functions as a novel integrator of the spindle checkpoint signaling J. Biol. Chem. 279 2004 20049 20057
2. S. Uddin, F. Lekmine, A. Sassano, H. Rui, E.N. Fish, and L.C. Platanias Role of Stat5 in type I interferon-signaling and transcriptional regulation Biochem. Biophys. Res. Commun. 308 2003 325 330
3. F. Yoshizawa, E. Watanabe, K. Sugahara, and Y. Natori Translational initiation regulators are hypophosphorylated in rat liver during ethionine-mediated ATP depletion Biochem. Biophys. Res. Commun. 298 2002 235 239
4. A.J. Meijer, and P.F. Dubbelhuis Amino acid signalling and the integration of metabolism Biochem. Biophys. Res. Commun. 313 2004 397 403
5. S. Choudhary, A. Kumar, R.K. Kale, L.G. Raisz, and C.C. Pilbeam Extracellular calcium induces COX-2 in osteoblasts via a PKA pathway Biochem. Biophys. Res. Commun. 322 2004 395 402
6. P.K. Dash, S.A. Orsi, M. Moody, and A.N. Moore A role for hippocampal Rho-ROCK pathway in long-term spatial memory Biochem. Biophys. Res. Commun. 322 2004 893 898
7. 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
8. S. Caenepeel, G. Charydczak, S. Sudarsanam, T. Hunter, and G. Manning The mouse kinome: discovery and comparative genomics of all mouse protein kinases Proc. Natl. Acad. Sci. USA 101 2004 11707 11712
9. 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
10. B.A. Ballif, J. Villen, S.A. Beausoleil, D. Schwartz, S.P. Gygi, Phosphoproteomic analysis of the developing mouse brain, Mol. Cell. Proteomics (2004) [Epub ahead of print]
11. 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. USA 101 2004 2130 2135
12. Y.P. Lim, L.S. Diong, R. Qi, B.J. Druker, and R.J. Epstein Phosphoproteomic fingerprinting of epidermal growth factor signaling and anticancer drug action in human tumor cells Mol. Cancer Ther. 2 2003 1369 1377
13. T.S. Nuhse, A. Stensballe, O.N. Jensen, and S.C. Peck Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database Plant Cell 16 2004 2394 2405
14. C. Kraft, F. Herzog, C. Gieffers, K. Mechtler, A. Hagting, J. Pines, and J.M. Peters Mitotic regulation of the human anaphase-promoting complex by phosphorylation EMBO J. 22 2003 6598 6609
15. 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
16. Z.A. Knight, B. Schilling, R.H. Row, D.M. Kenski, B.W. Gibson, K.M. Shokat, Phosphospecific proteolysis for mapping sites of protein phosphorylation, Nat. Biotechnol. 21 (2003) 1047-1054. Erratum in: Nat. Biotechnol. 21 (2003) 1396.
17. A. Kreegipuu, N. Blom, S. Brunak, and J. Jarv Statistical analysis of protein kinase specificity determinants FEBS Lett. 430 1998 45 50
18. N. Blom, S. Gammeltoft, and S. Brunak Sequence and structure-based prediction of eukaryotic protein phosphorylation sites J. Mol. Biol. 294 1999 1351 1362
19. N. Blom, T. Sicheritz-Ponten, R. Gupta, S. Gammeltoft, and S. Brunak Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence Proteomics 4 2004 1633 1649
20. 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
21. J.H. Kim, J. Lee, B. Oh, K. Kimm, I. Koh, Prediction of phosphorylation sites using SVMs, Bioinformatics (2004) [Epub ahead of print]
22. 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. USA 100 2003 74 79
23. 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. USA 100 2003 4463 4468
24. F. Diella, S. Cameron, C. Gemund, R. Linding, A. Via, B. Kuster, T. Sicheritz-Ponten, N. Blom, and T.J. Gibson Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins BMC Bioinformatics 5 2004 79
25. A. Kreegipuu, N. Blom, and S. Brunak PhosphoBase, a database of phosphorylation sites: release 2.0 Nucleic Acids Res. 27 1999 237 239
26. S. Henikoff, and J.G. Henikoff Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. USA 89 1992 10915 10919
27. Stijn van Dongen, Graph Clustering by Flow Simulation, PhD thesis, University of Utrecht, May 2000
28. A.J. Enright, S. Van Dongen, and C.A. Ouzounis An efficient algorithm for large-scale detection of protein families Nucleic Acids Res. 30 2002 1575 1584
29. Y.W. Ke, Z. Dou, J. Zhang, and X.B. Yao Function and regulation of Aurora/Ipl1p kinase family in cell division Cell Res. 13 2003 69 81
30. P. Meraldi, R. Honda, and E.A. Nigg Aurora kinases link chromosome segregation and cell division to cancer susceptibility Curr. Opin. Genet. Dev. 14 2004 29 36
31. A. Kawajiri, Y. Yasui, H. Goto, M. Tatsuka, M. Takahashi, K. Nagata, and M. Inagaki Functional significance of the specific sites phosphorylated in desmin at cleavage furrow: Aurora-B may phosphorylate and regulate type III intermediate filaments during cytokinesis coordinatedly with Rho-kinase Mol. Biol. Cell 14 2003 1489 1500
32. R. Gassmann, A. Carvalho, A.J. Henzing, S. Ruchaud, D.F. Hudson, R. Honda, E.A. Nigg, D.L. Gerloff, and W.C. Earnshaw Borealin: a novel chromosomal passenger required for stability of the bipolar mitotic spindle J. Cell Biol. 166 2004 179 191
33. A.R. Skop, H. Liu, J. Yates III, B.J. Meyer, and R. Heald Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms Science 305 2004 61 66
34. R.R. Adams, D.M. Eckley, P. Vagnarelli, S.P. Wheatley, D.L. Gerloff, A.M. Mackay, P.A. Svingen, S.H. Kaufmann, and W.C. Earnshaw Human INCENP colocalizes with the Aurora-B/AIRK2 kinase on chromosomes and is overexpressed in tumour cells Chromosoma 110 2001 65 74
35. H. Katayama, W.R. Brinkley, and S. Sen The Aurora kinases: role in cell transformation and tumorigenesis Cancer Metastasis Rev. 22 2003 451 464
36. G.J. Gorbsky Mitosis: MCAK under the aura of Aurora B Curr. Biol. 14 2004 R346 R348
37. W. Lan, X. Zhang, S.L. Kline-Smith, S.E. Rosasco, G.A. Barrett-Wilt, J. Shabanowitz, D.F. Hunt, C.E. Walczak, and P.T. Stukenberg Aurora B phosphorylates centromeric MCAK and regulates its localization and microtubule depolymerization activity Curr. Biol. 14 2004 273 286
38. R. Ohi, T. Sapra, J. Howard, and T.J. Mitchison Differentiation of cytoplasmic and meiotic spindle assembly MCAK functions by Aurora B-dependent phosphorylation Mol. Biol. Cell 15 2004 2895 2906