Chapter 38: Tandem Affinity Purification Strategy for Protein Complex Characterization—References

Aebersold R. and Mann M. 2003. Mass spectrometry-based proteomics. Nature 422: 198–207.

Aloy P., Bottcher B., Ceulemans H., Leutwein C., Mellwig C., Fischer S., Gavin A.C., Bork P., Superti-Furga G., Serrano L., and Russell R.B. 2004. Structure-based assembly of protein complexes in yeast. Science 303: 2026–2029.

Baudin A., Ozier K.O., Denouel A., Lacroute F., and Cullin C. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21: 3329–3330.

Bouveret E., Rigaut G., Shevchenko A., Wilm M., and Séraphin B. 2000. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 19: 1661–1671.

Bouwmeester T., Bauch A., Ruffner H., Angrand P.O., Bergamini G., Croughton K., Cruciat C., Eberhard D., Gagneur J., Ghidelli S., et al. 2004. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nat. Cell Biol. 6: 97–105.

Brizzard B.L., Chubet R.G., and Vizard D.L. 1994. Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution. Biotechniques 16: 730–735.

Bushnell D.A. and Kornberg R.D. 2003. Complete, 12-subunit RNA polymerase II at 4.1-Å resolution: Implications for the initiation of transcription. Proc. Natl. Acad. Sci. 100: 6969–6973.

Caspary F., Shevchenko A., Wilm M., and Séraphin B. 1999. Partial purification of the yeast U2 snRNP reveals a novel yeast pre- mRNA splicing factor required for pre-spliceosome assembly. EMBO J. 18: 3463–3474.

Chong S., Mersha F.B., Comb D.G., Scott M.E., Landry D., Vence L.M., Perler F.B., Benner J., Kucera R.B., Hirvonen C.A., et al. 1997. Single-column purification of free recombinant proteins using a self-cleavable affinity tag derived from a protein splicing element. Gene 192: 271–281.

Deutscher M.P. 1990. Guide to protein purification. Academic Press, San Diego, California.

Dougherty W.G., Cary S.M., and Parks T.D. 1989. Molecular genetic analysis of a plant virus polyprotein cleavage site: A model. Virology 171: 356–364.

Dziembowski A., Ventura A.P., Rutz B., Caspary F., Faux C., Halgand F., Laprevote O., and Séraphin B. 2004. Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J. 23: 4847–4856.

Forler D., Kocher T., Rode M., Gentzel M., Izaurralde E., and Wilm M. 2003. An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nat. Biotechnol. 21: 89–92.

Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147.

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.

Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y.L., Ooi C.E., Godwin B., Vitols E., et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302: 1727–1736.

Gully D., Moinier D., Loiseau L., and Bouveret E. 2003. New partners of acyl carrier protein detected in Escherichia coli by tandem affinity purification. FEBS Lett. 548: 90–96.

Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., and Aebersold R. 2000. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. 97: 9390–9395.

Harlow E. and Lane D. 1988. Antibodies: A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

Hartmuth K., Urlaub H., Vornlocher H.P., Will C.L., Gentzel M., Wilm M., and Lührmann R. 2002. Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc. Natl. Acad. Sci. 99: 16719–16724.

Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.

Hochuli E., Bannwarth W., Döbeli H., Gentz R., and Stüber D. 1988. Genetic approach to facilitate purification of recombinant proteins with a novel metal chelate adsorbent. Biotechnology 6: 1321–1325.

Honey S., Schneider B.L., Schieltz D.M., Yates J.R., Futcher B. 2001. A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-CDK complex. Nucleic Acids Res. 29: E24.

Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., Yamamoto K., Kuhara S., and Sakaki Y. 2000. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. 97: 1143–1147.

Jurica M.S., Licklider L.J., Gygi S.R., Grigorieff N., and Moore M.J. 2002. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8: 426–443.

Lamond A.I. and Mann M. 1997. Cell biology and the genome projects—A concerted strategy for characterizing multi-protein complexes using mass-spectrometry. Trends Cell Biol. 7: 139–142.

Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., Vidalain P.O., Han J.D., Chesneau A., Hao T., et al. 2004. A map of the interactome network of the metazoan C. elegans. Science 303: 540–543.

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.

Lohman T.M., Chao K., Green J.M., Sage S., and Runyon G.T. 1989. Large-scale purification and characterization of the Escherichia coli rep gene product. J. Biol. Chem. 264: 10139–10147.

Ozols J. 1990. Amino acid analysis. Methods Enzymol. 182: 587–601.

Puig O., Rutz B., Luukkonen B.G., Kandels L.S., Bragado N.E., and Séraphin B. 1998. New constructs and strategies for efficient PCR-based gene manipulations in yeast. Yeast 14: 1139–1146.

Puig O., Caspary F., Rigaut G., Rutz B., Bouveret E., Bragado-Nilsson E., Wilm M., and Séraphin B. 2001. The tandem affinity purification (TAP) method: A general procedure of protein complex purification. Methods 24: 218–229.

Ranish J.A., Hahn S., Lu Y., Yi E.C., Li X.J., Eng J., and Aebersold R. 2004. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat. Genet. 36: 707–713.

Rappsilber J., Ryder U., Lamond A.I., and Mann M. 2002. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12: 1231–1245.

Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., and Séraphin B. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17: 1030–1032.

Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., and Séraphin B. 1999. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J. 18: 3451–3462.

Schmidt T.G. and Skerra A. 1993. The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment. Protein Eng. 6: 109–122.

Schmitt C., von Kobbe C., Bachi A., Pante N., Rodrigues J.P., Boscheron C., Rigaut G., Wilm M., Séraphin B., Carmo-Fonseca M., and Izaurralde E. 1999. Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p. EMBO J. 18: 4332–4347.

Séraphin B. 1995. Sm and Sm-like proteins belong to a large family: Identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J. 14: 2089–2098.

Shevchenko A., Jensen O.N., Podtelejnikov A.V., Sagliocco F., Wilm M., Vorm O., Mortensen P., Shevchenko A., Boucherie H., and Mann M. 1996. Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. 93: 14440–14445.

Stofko-Hahn R.E., Carr D.W., and Scott J.D. 1992. A single step purification for recombinant proteins. Characterization of a microtubule associated protein (MAP 2) fragment which associates with the type II cAMP-dependent protein kinase. FEBS Lett. 302: 274–278.

Swaffield J.C., Melcher K., and Johnston S.A. 1995. A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein. Nature 374: 88–91.

Swaffield J.C., Melcher K., and Johnston S.A. 1996. A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein (correction). Nature 379: 658.

Tasto J.J., Carnahan R.H., McDonald W.H., and Gould K.L. 2001. Vectors and gene targeting modules for tandem affinity purification in Schizosaccharomyces pombe. Yeast 18: 657–662.

Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623–627.

Washburn M.P., Wolters D., and Yates J.R., III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19: 242–247.

Wasinger V.C., Cordwell S.J., Cerpa-Poljak A., Yan J.X., Gooley A.A., Wilkins M.R., Duncan M.W., Harris R., Williams K.L., and Humphery-Smith I. 1995. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16: 1090–1094.

Wessel D. and Flugge U.I. 1984. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138: 141–143.

Wilkins M.R., Pasquali C., Appel R.D., Ou K., Golaz O., Sanchez J.C., Yan J.X., Gooley A.A., Hughes G., Humphery-Smith I., et al. 1996. From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14: 61–65.

Wilm M., Shevchenko A., Houthaeve T., Breit S., Schweigerer L., Fotsis T., and Mann M. 1996. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379: 466–469.

Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S., Houfek T., et al. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101–2105.

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