An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

Nature Methods

Volumn 3, Issue 12, 2006, Pages 1013-1019

  Bürckstümmer, Tilmann ^a   Bennett, Keiryn L ^a   Preradovic, Adrijana ^a   Schütze, Gregor ^a   Hantschel, Oliver ^a   Superti Furga, Giulio ^a   Bauch, Angela ^a  

^a ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; KU ANTIGEN; PROTEIN G; STREPTAVIDIN;

ARTICLE; BINDING AFFINITY; CELL STRAIN HEK293; COMPLEX FORMATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; MAMMAL CELL; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEOMICS;

AFFINITY LABELS; CELL PHYSIOLOGY; CHROMATOGRAPHY, AFFINITY; MASS SPECTROMETRY; PROTEIN INTERACTION MAPPING; PROTEOME; PROTEOMICS;

MAMMALIA;

EID: 33751211249     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth968     Document Type: Article

References (35)

1. Alberts, B. The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 92, 291-294 (1998).
2. Papin, J.A., Hunter, T., Palsson, B.O. & Subramaniam, S. Reconstruction of cellular signalling networks and analysis of their properties. Nat. Rev. Mol. Cell Biol. 6, 99-111 (2005).
3. Bauch, A. & Superti-Furga, G. Charting protein complexes, signaling pathways, and networks in the immune system. Immunol. Rev. 210, 187-207 (2006).
4. Hinsby, A.M. et al. A wiring of the human nucleolus. Mol. Cell 22, 285-295 (2006).
5. Fox, A.H. & Lamond, A.I. Nuclear processes controlled by molecular machines. Genome Biol. 3 REPORTS4016 (2002).
6. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
7. Puig, O. et al. The tandem affinity purification (TAP) method: A general procedure of protein complex purification. Methods 24, 218-229 (2001).
8. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032 (1999).
9. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
10. Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
11. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
12. Bouwmeester, T. et al. A physical and functional map of the human TNF-atpha/NF-kappa B signal transduction pathway. Nat. Cell Biol. 6, 97-105 (2004).
13. Butland, G. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537 (2005).
14. Brajenovic, M., Joberty, G., Kuster, B., Bouwmeester, T. & Drewes, G. Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network. J. Biol. Chem. 279, 12804-12811 (2004).
15. Terpe, K. Overview of tag protein fusions: From molecular and biochemical fundamentals to commercial systems. Appl. Microbiol. Biotechnol. 60, 523-533 (2003).
16. Ghosh, S. & Karin, M. Missing pieces in the NF-kappaB puzzle. Cell 109, S81-S96 (2002).
17. Sjobring, U., Bjorck, L. & Kastern, W. Streptococcal protein G. Gene structure and protein binding properties. J. Biol. Chem. 266, 399-405 (1991).
18. Sauer-Eriksson, A.E., Kleywegt, G.J., Uhlen, M. & Jones, T.A. Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. Structure 3, 265-278 (1995).
19. Keefe, A.D., Wilson, D.S., Seelig, B. & Szostak, J.W. One-step purification of recombinant proteins using a nanomolar-affinity streptavidin-binding peptide, the SBP-Tag. Protein Expr. Purif. 23, 440-446 (2001).
20. Collis, S.J., DeWeese, T.L., Jeggo, P.A. & Parker, A.R. The Life and death of DNA-PK. Oncogene 24, 949-961 (2005).
21. Gottlieb, T.M. & Jackson, S.P. The DNA-dependent protein kinase: requirement for DNA ends and association with Ku antigen. Cell 72, 131-142 (1993).
22. Li, B. & Comai, L. Functional interaction between Ku and the werner syndrome protein in DNA end processing. J. Biol. Chem. 275, 28349-28352 (2000).
23. Aoki, Y., Zhao, G., Qiu, D., Shi, L. & Kao, P.N. CsA-sensitive purine-box transcriptional regulator in bronchial epithelial cells contains NF45, NF90, and Ku. Am. J. Physiol. 275, L1164-L1172 (1998).
24. Crevel, G., Ivetic, A., Ohno, K., Yamaguchi, M. & Cotterill, S. Nearest neighbour analysis of MCM protein complexes in Drosophila melanogaster. Nucleic Acids Res. 29, 4834-4842 (2001).
25. Fouraux, M.A., Bouvet, P., Verkaart, S., van Venrooij, W.J. & Pruijn, G.J. Nucleolin associates with a subset of the human Ro ribonucleoprotein complexes. J. Mol. Biol. 320, 475-488 (2002).
26. Park, J., Wood, M.A. & Cole, M.D. BAF53 forms distinct nuclear complexes and functions as a critical c-Myc-interacting nuclear cofactor for oncogenic transformation. Mol. Cell. Biol. 22, 1307-1316 (2002).
27. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
28. Brown, D. & Superti-Furga, G. Rediscovering the sweet spot in drug discovery. Drug Discov. Today 8, 1067-1077 (2003).
29. Fishman, M.C. & Porter, J.A. Pharmaceuticals: A new grammar for drug discovery. Nature 437, 491-493 (2005).
30. Cheeseman, I.M. & Desai, A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE 2005, pl1 (2005).
31. Bertwistle, D., Sugimoto, M. & Sherr, C.J. Physical and functional interactions of the Arf tumor suppressor protein with nucleophosmin/B23. Mol. Cell. Biol. 24, 985-996 (2004).
32. Canton, D.A. et al. The pleckstrin homology domain-containing protein CKIP-1 is involved in regulation of cell morphology and the actin cytosketeton and interaction with actin capping protein. Mol. Cell. Biol. 25, 3519-3534 (2005).
33. Hacker, H. et al. Specificity in Toll-Like receptor signalling through distinct effector functions of TRAF3 and TRAF6. Nature 439, 204-207 (2006).
34. Naviaux, R.K., Costanzi, E., Haas, M. & Verma, I.M. The pCL vector system: Rapid production of helper-free, high-titer, recombinant retroviruses. J. Virol. 70, 5701-5705 (1996).
35. Kinsella, T.M. & Nolan, G.P. Episomal vectors rapidly and stably produce high-titer recombinant retrovirus. Hum. Gene Ther. 7, 1405-1413 (1996).