Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions

Molecular BioSystems

Volumn 8, Issue 10, 2012, Pages 2771-2782

  Naegle, Kristen M ^a,b,c   White, Forest M ^a,b   Lauffenburger, Douglas A ^a,b   Yaffe, Michael B ^a,b,c  

^a WASHINGTON UNIVERSITY   (United States)

^b Department of Biological Engineering ^*  (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN BINDING PROTEIN; EGFR PROTEIN, HUMAN; EPIDERMAL GROWTH FACTOR RECEPTOR; LIGAND; LIM PROTEIN; PDLIM1 PROTEIN, HUMAN; PHOSPHOPROTEIN; TYROSINE;

ARTICLE; CYTOLOGY; DATA MINING; EPITHELIUM CELL; FEMALE; GENETICS; HUMAN; IMMUNOHISTOCHEMISTRY; IMMUNOPRECIPITATION; LIQUID CHROMATOGRAPHY; MAMMARY GLAND; METABOLISM; PHOSPHORYLATION; PRIMARY CELL CULTURE; PROTEIN ANALYSIS; PROTEIN BINDING; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY;

CHROMATOGRAPHY, LIQUID; DATA MINING; EPITHELIAL CELLS; FEMALE; HUMANS; IMMUNOHISTOCHEMISTRY; IMMUNOPRECIPITATION; LIGANDS; LIM DOMAIN PROTEINS; MAMMARY GLANDS, HUMAN; MICROFILAMENT PROTEINS; PHOSPHOPROTEINS; PHOSPHORYLATION; PRIMARY CELL CULTURE; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; RECEPTOR, EPIDERMAL GROWTH FACTOR; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; TYROSINE;

EID: 84865803278     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c2mb25200g     Document Type: Article

References (31)

1. Y. Yarden M. X. Sliwkowski Untangling the ErbB signalling network Nat. Rev. Mol. Cell Biol. 2001 2 2 127 137
2. T. Pawson J. D. Scott Signaling through scaffold, anchoring, and adaptor proteins Science 1997 278 5346 2075 2080
3. M. B. Yaffe Phosphotyrosine-binding domains in signal transduction Nat. Rev. Mol. Cell Biol. 2002 3 3 177 186
4. M. Mann O. N. Jensen Proteomic analysis of post-translational modifications Nat. Biotechnol. 2003 21 3 255 261
5. A. Nita-Lazar H. Saito-Benz F. M. White Quantitative phosphoproteomics by mass spectrometry: past, present, and future Proteomics 2008 8 21 4433 4443
6. M. B. Yaffe F. M. White Signaling networks get the global treatment Genome Biol. 2007 8 1 202
7. Y. Zhang et al., Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules Mol. Cell. Proteomics 2005 4 9 1240 1250
8. J. V. Olsen et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks Cell 2006 127 3 635 648
9. K. M. Naegle et al., MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets PLoS Comput. Biol. 2011 7 7 e1002119
10. A. Wolf-Yadlin et al., Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks Proc. Natl. Acad. Sci. U. S. A. 2007 104 14 5860 5865
11. K. M. Naegle et al., PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies Mol. Cell. Proteomics 2010 9 11 2558 2570
12. B. Turner et al., iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence Database 2010 2010 baq023
13. M. P. Oksvold et al., Serine mutations that abrogate ligand-induced ubiquitination and internalization of the EGF receptor do not affect c-Cbl association with the receptor Oncogene 2003 22 52 8509 8518
14. A. G. Batzer et al., The phosphotyrosine interaction domain of Shc binds an LXNPXY motif on the epidermal growth factor receptor Mol. Cell. Biol. 1995 15 8 4403 4409
15. T. Vallenius K. Luukko T. P. Makela CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4 J. Biol. Chem. 2000 275 15 11100 11105
16. T. Vallenius T. P. Makela Clik1: a novel kinase targeted to actin stress fibers by the CLP-36 PDZ-LIM protein J. Cell Sci. 2002 115 Pt 10 2067 2073
17. O. Soderberg et al., Direct observation of individual endogenous protein complexes in situ by proximity ligation Nat. Methods 2006 3 12 995 1000
18. A. Vinayagam et al., A directed protein interaction network for investigating intracellular signal transduction Sci. Signal 2011 4 189 rs8
19. J. Zhang S. Lautar A yeast three-hybrid method to clone ternary protein complex components Anal. Biochem. 1996 242 1 68 72
20. G. Rigaut et al., A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 1999 17 10 1030 1032
21. M. P. Williamson M. J. Sutcliffe Protein-protein interactions Biochem. Soc. Trans. 2010 38 4 875 878
22. X. Xu et al., The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification Protein Expression Purif. 2010 72 2 149 156
23. C. Guerrero et al., An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network Mol. Cell. Proteomics 2006 5 2 366 378
24. G. D. Bader et al., BIND - The Biomolecular Interaction Network Database Nucleic Acids Res. 2001 29 1 242 245
25. C. Stark et al., BioGRID: a general repository for interaction datasets Nucleic Acids Res. 2006 34 Database issue D535 D539
26. A. Chatr-aryamontri et al., MINT: the Molecular INTeraction database Nucleic Acids Res. 2007 35 Database issue D572 D574
27. I. Xenarios et al., DIP: the database of interacting proteins Nucleic Acids Res. 2000 28 1 289 291
28. B. Snel et al., STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene Nucleic Acids Res. 2000 28 18 3442 3444
29. J. C. Obenauer L. C. Cantley M. B. Yaffe et al., Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs Nucleic Acids Res. 2003 31 13 3635 3641
30. Y. Hochberg Y. Benjamini More powerful procedures for multiple significance testing Stat Med. 1990 9 7 811 818
31. R. A. Dickins et al., Probing tumor phenotypes using stable and regulated synthetic microRNA precursors Nat. Genet. 2005 37 11 1289 1295