Phosphospecific proteolysis for mapping sites of protein phosphorylation

Nature Biotechnology

Volumn 21, Issue 9, 2003, Pages 1047-1054

  Knight, Zachary A ^a   Schilling, Birgit ^b   Row, Richard H ^b   Kenski, Denise M ^a   Gibson, Bradford W ^a,b   Shokat, Kevan M ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BUCK INSTITUTE FOR RESEARCH ON AGING   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MASS SPECTROMETRY; PROTEINS;

PHOSPHORYLATION;

BIOTECHNOLOGY;

AMINOETHYLCYSTEINE; BETA METHYLAMINOETHYLCYSTEINE; LYSINE; LYSINE DERIVATIVE; PHOSPHOPEPTIDE; PHOSPHOSERINE; PHOSPHOTHREONINE; PROTEINASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CHEMICAL MODIFICATION; CHEMICAL REACTION; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN PHOSPHORYLATION; SOLID; TANDEM MASS SPECTROMETRY;

BETA-ADRENERGIC RECEPTOR KINASE; CYCLIC AMP-DEPENDENT PROTEIN KINASES; ENDOPEPTIDASES; ENZYME-LINKED IMMUNOSORBENT ASSAY; PEPTIDE HYDROLASES; PHOSPHOAMINO ACIDS; PHOSPHOPEPTIDES; PHOSPHORYLATION; PHOSPHOSERINE; PHOSPHOTHREONINE; PHOSPHOTRANSFERASES; PROTEIN INTERACTION MAPPING; PROTEOME; PROTEOMICS; TUBULIN;

EID: 0042861519     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt863     Document Type: Article

References (38)

1. Venter, J.C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
2. Manning, G., Whyte, D.B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912-1934 (2002).
3. Shah, K. & Shokat, K.M. A chemical genetic screen for direct v-Src substrates reveals ordered assembly of a retrograde signaling pathway. Chem. Biol. 9, 35-47 (2002).
4. Bishop, A.C. et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407, 395-401 (2000).
5. McLachlin, D.T. & Chait, B.T. Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 5, 591-602 (2001).
6. Mann, M. et al. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 20, 261-268 (2002).
7. Zhou, H., Watts, J.D. & Aebersold, R. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19, 375-378 (2001).
8. Oda, Y., Nagasu, T. & Chait, B.T. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19, 379-382 (2001).
9. Steen, H. & Mann, M. A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode. J. Am. Soc. Mass Spectrom. 13, 996-1003 (2002).
10. Ficarro, S.B. et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20, 301-305 (2002).
11. Meyer, H.E., Hoffmann-Posorske, E., Korte, H. & Heilmeyer, L.M. Jr. Sequence analysis of phosphoserine-containing peptides. Modification for picomolar sensitivity. FEBS Lett. 204, 61-66 (1986).
12. Simpson, D.L., Hranisavljevic, J. & Davidson, E.A. Elimination and sulfite addition as a means of localization and identification of substituted seryl and threonyl residues in proteins and proteoglycans. Biochemistry 11, 1849-1856 (1972).
13. Byford, M.F. Rapid and selective modification of phosphoserine residues catalysed by Ba2+ ions for their detection during peptide microsequencing. Biochem. J. 280 (Pt 1), 261-265 (1991).
14. Adamczyk, M., Gebler, J.C. & Wu, J. Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry. Rapid Commun. Mass Spectrom. 15, 1481-1488 (2001).
15. Goshe, M.B. et al. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal. Chem. 73, 2578-2586 (2001).
16. Jaffe, H., Veeranna & Pant, H.C. Characterization of serine and threonine phosphorylation sites in beta-elimination/ethanethiol addition-modified proteins by electrospray tandem mass spectrometry and database searching. Biochemistry 37, 16211-16224 (1998).
17. Annan, R.S., Huddleston, M.J., Verma, R., Deshaies, R.J. & Carr, S.A. A multidimensional electrospray MS-based approach to phosphopeptide mapping. Anal. Chem. 73, 393-404 (2001).
18. Janek, K., Wenschuh, H., Bienert, M. & Krause, E. Phosphopeptide analysis by positive and negative ion matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 15, 1593-1599 (2001).
19. Limas, C.J. & Limas, C. Involvement of microtubules in the isoproterenol-induced 'down'-regulation of myocardial beta-adrenergic receptors. Biochim. Biophys. Acta 735, 181-184 (1983).
20. Haga, K., Ogawa, H., Haga, T. & Murofushi, H. GTP-binding-protein-coupled receptor kinase 2 (GRK2) binds and phosphorylates tubulin. Eur. J. Biochem. 255, 363-368 (1998).
21. Pitcher, J.A. et al. The G protein-coupled receptor kinase 2 is a microtubule-associated protein kinase that phosphorylates tubulin. J. Biol. Chem. 273, 12316-12324 (1998).
22. Carman, C.V., Som, T., Kim, C.M. & Benovic, J.L. Binding and phosphorylation of tubulin by G protein-coupled receptor kinases. J. Biol. Chem. 273, 20308-20316 (1998).
23. Banerjee, A. Coordination of posttranslational modifications of bovine brain alpha-tubulin. Polyglycylation of delta2 tubulin. J. Biol. Chem. 277, 46140-46144 (2002).
24. Alexander, J.E. et al. Characterization of posttranslational modifications in neuron-specific class III beta-tubulin by mass spectrometry. Proc. Natl. Acad. Sci. USA 88, 4685-4689 (1991).
25. Yoshida, N., Haga, K. & Haga, T. Identification of sites of phosphorylation by G-protein-coupled receptor kinase 2 in beta-tubulin. Eur. J. Biochem. 270, 1154-1163 (2003).
26. Pitcher, J.A. et al. Feedback inhibition of G protein-coupled receptor kinase 2 (GRK2) activity by extracellular signal-regulated kinases. J. Biol. Chem. 274, 34531-34534 (1999).
27. Beardsley, R.L., Karty, J.A. & Reilly, J.P. Enhancing the intensities of lysine-terminated tryptic peptide ions in matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 14, 21417-2153 (2000).
28. Beardsley, R.L. & Reilly, J.P. Optimization of guanidination procedures for MALDI mass mapping. Anal. Chem. 74, 1884-1890 (2002).
29. Brancia, F.L., Oliver, S.G. & Gaskell, S.J. Improved matrix-assisted laser desorption/ionization mass spectrometric analysis of tryptic hydrolysates of proteins following guanidination of lysine-containing peptides. Rapid Commun. Mass Spectrom. 14, 2070-2073 (2000).
30. Cupo, P., El-Deiry, W., Whitney, P.L. & Awad, W.M. Jr. Stabilization of proteins by guanidination. J. Biol. Chem. 255, 10828-10833 (1980).
31. Kimmel, J.R. Guanidination of Proteins. Methods Enzymol, 11, 584-589 (1967).
32. Mega, T., Nakamura, N. & Ikenaka, T. Modifications of substituted seryl and threonyl residues in phosphopeptides anda polysialoglycoprotein by beta-elimination and nucleophile additions. J. Biochem. (Tokyo) 107, 68-72 (1990).
33. Wells, L.V. et al. Mapping sites of O-GicNAc modification using affinity tags for serine and threonine post-translational modifications. Molecular and Cellular Proteomics 1, 791-804 (2002).
34. Greis, K.D. et al. Selective detection and site-analysis of O-GlcNAc-modified glycopeptides by beta-elimination and tandem electrospray mass spectrometry. Anal. Biochem. 234, 38-49 (1996).
35. Meldal, M. & Breddam, K. Anthranilamide and nitrotyrosine as a donor-acceptor pair in internally quenched fluorescent substrates for endopeptidases: multicolumn peptide synthesis of enzyme substrates for subtilisin Carlsberg and pepsin. Anal. Biochem. 195, 141-147 (1991).
36. Bonetto, V., Bergman, A.C., Jornvall, H. & Sillard, R. C-terminal sequence analysis of peptides and proteins using carboxypeptidases and mass spectrometry after derivatization of Lys and Cys residues. Anal. Chem. 69, 1315-1319 (1997).
37. Kim, C.M., Dion, S.B., Onorato, J.J. & Benovic, J.L. Expression and characterization of two beta-adrenergic receptor kinase isoforms using the baculovirus expression system. Receptor 3, 39-55 (1993).
38. Dorff, P.a.H. & Hauske, J.R. A Solid Phase CBZ Chloride Equivalent - A New Matrix Specific Linker. Tetrahedron Lett. 36, 1589-1592 (1995).