Dynamic changes in protein-protein interaction and protein phosphorylation probed with amine-reactive isotope tag

Molecular and Cellular Proteomics

Volumn 4, Issue 9, 2005, Pages 1358-1369

  Smolka, Marcus B ^a   Albuquerque, Claudio P ^a   Chen, Sheng Hong ^a   Schmidt, Kristina H ^a   Wei, Xiao X ^a   Kolodner, Richard D ^a   Zhou, Huilin ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINE; AMINE REACTIVE ISOTOPE TAG; CHECKPOINT KINASE 2; DNA; HISTONE; ISOTOPE; PEPTIDE; PROTEIN; REAGENT; SERINE; UNCLASSIFIED DRUG;

ARTICLE; CELL STIMULATION; DNA DAMAGE; INTRACELLULAR TRANSPORT; ISOTOPE LABELING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DETERMINATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE;

ALANINE; AMINO ACID SUBSTITUTION; BINDING SITES; BLOTTING, WESTERN; CELL CYCLE PROTEINS; CHROMATOGRAPHY, ION EXCHANGE; DEUTERIUM; DNA DAMAGE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HYDROGEN; ISOTOPE LABELING; METHYL METHANESULFONATE; MUTAGENESIS, SITE-DIRECTED; MUTAGENS; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN-SERINE-THREONINE KINASES; RECOMBINANT PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES;

EID: 24944451331     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M500115-MCP200     Document Type: Article

References (36)

1. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Seraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032
2. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147
3. Archambault, V., Chang, E. J., Drapkin, B. J., Cross, F. R., Chait, B. T., and Rout, M. P. (2004) Targeted proteomic study of the cyclin-Cdk module. Mol. Cell 14, 699-711
4. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A. R., Sassi, H., Nielsen, P. A., Rasmussen, K. J., Andersen, J. R., Johansen, L. E., Hansen, L. H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B. D., Matthiesen, J., Hendrickson, R. C., Gleeson, F., Pawson, T., Moran, M. F., Durocher, D., Mann, M., Hogue, C. W., Figeys, D., and Tyers, M. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183
5. Ranish, J. A., Yi, E. C., Leslie, D. M., Purvine, S. O., Goodlett, D. R., Eng, J., and Aebersold, R. (2003) The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349-355
6. McLachlin, D. T., and Chait, B. T. (2001) Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 5, 591-602
7. Loughrey Chen, S., Huddleston, M. J., Shou, W., Deshaies, R. J., Annan, R. S., and Carr, S. A. (2002) Mass spectrometry-based methods for phosphorylation site mapping of hyperphosphorylated proteins applied to Net1, a regulator of exit from mitosis in yeast. Mol. Cell. Proteomics 1, 186-196
8. Oda, Y., Huang, K., Cross, F. R., Cowburn, D., and Chait, B. T. (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U. S. A. 96, 6591-6596
9. Blagoev, B., Ong, S. E., Kratchmarova, I., and Mann, M. (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 22, 1139-1145
10. Cagney, G., and Emili, A. (2002) De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nat. Biotechnol. 20, 163-170
11. Munchbach, M., Quadroni, M., Miotto, G., and James, P. (2000) Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal. Chem. 72, 4047-4057
12. Sanchez, Y., Desany, B. A., Jones, W. J., Liu, Q., Wang, B., and Elledge, S. J. (1996) Regulation of RAD53 by the ATM-like kinases MEC1 and TEL1 in yeast cell cycle checkpoint pathways. Science 271, 357-360
13. Sun, Z., Fay, D. S., Marini, F., Foiani, M., and Stern, D. F. (1996) Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways. Genes Dev. 10, 395-406
14. Emili, A. (1998) MEC1-dependent phosphorylation of Rad9p in response to DNA damage. Mol. Cell 2, 183-189
15. Gilbert, C. S., Green, C. M., and Lowndes, N. F. (2001) Budding yeast Rad9 is an ATP-dependent Rad53 activating machine. Mol. Cell 8, 129-136
16. Schwartz, M. F., Duong, J. K., Sun, Z., Morrow, J. S., Pradhan, D., and Stern, D. F. (2002) Rad9 phosphorylation sites couple Rad53 to the Saccharomyces cerevisiae DNA damage checkpoint. Mol. Cell 9, 1055-1065
17. Sun, Z., Hsiao, J., Fay, D. S., and Stern, D. F. (1998) Rad53 FHA domain associated with phosphorylated Rad9 in the DNA damage checkpoint. Science 281, 272-274
18. Vialard, J. E., Gilbert, C. S., Green, C. M., and Lowndes, N. F. (1998) The budding yeast Rad9 checkpoint protein is subjected to Mec1/Tel1-dependent hyperphosphorylation and interacts with Rad53 after DNA damage. EMBO J. 17, 5679-5688
19. Emili, A., Schieltz, D. M., Yates, J. R., III, and Hartwell, L. H. (2001) Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor Asf1. Mol. Cell 7, 13-20
20. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741
21. Longtine, M. S., McKenzie, A., III, Demarini, D. J., Shah, N. G., Wach, A., Brachat, A., Philippsen, P., and Pringle, J. R. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953-961
22. Zhou, W., Ryan, J. J., and Zhou, H. (2004) Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J. Biol. Chem. 279, 32262-32268
23. Stensballe, A., Andersen, S., and Jensen, O. N. (2001) Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off-line mass spectrometry analysis. Proteomics 1, 207-222
24. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951
25. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
26. Zhou, H., Ranish, J. A., Wafts, J. D., and Aebersold, R. (2002) Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20, 512-515
27. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., III (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol. 17, 676-682
28. Gunjan, A., and Verreault, A. (2003) A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell 115, 537-549
29. Gilchrist, D., Mykytka, B., and Rexach, M. (2002) Accelerating the rate of disassembly of karyopherin cargo complexes. J. Biol. Chem. 277, 18161-18172
30. Chook, Y. M., and Blobel, G. (2001) Karyopherins and nuclear import. Curr. Opin. Struct. Biol. 11, 703-715
31. 2/M cell cycle progression in Saccharomyces cerevisiae. Mol. Cell. Biol. 24, 2779-2788
32. Bashkirov, V. I., Bashkirova, E. V., Haghnazari, E., and Heyer, W. D. (2003) Direct kinase-to-kinase signaling mediated by the FHA phosphoprotein recognition domain of the Dun1 DNA damage checkpoint kinase. Mol. Cell. Biol. 23, 1441-1452
33. Duncker, B. P., Shimada, K., Tsai-Pflugfelder, M., Pasero, P., and Gasser, S. M. (2002) An N-terminal domain of Dbf4p mediates interaction with both origin recognition complex (ORC) and Rad53p and can deregulate late origin firing. Proc. Natl. Acad. Sci. U. S. A. 99, 16087-16092
34. Sidorova, J. M., and Breeden, L. L. (2003) Rad53 checkpoint kinase phosphorylation site preference identified in the Swi6 protein of Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 3405-3416
35. Lee, S. J., Schwartz, M. F., Duong, J. K., and Stern, D. F. (2003) Rad53 phosphorylation site clusters are important for Rad53 regulation and signaling. Mol. Cell. Biol. 23, 6300-6314
36. Kim, S. T., Lim, D. S., Canman, C. E., and Kastan, M. B. (1999) Substrate specificities and identification of putative substrates of ATM kinase family members. J. Biol. Chem. 274, 37538-37543