Preparation of recombinant protein spotted arrays for proteome-wide identification of kinase targets

Current Protocols in Protein Science

Volumn , Issue SUPPL.72, 2013, Pages

  Im, Hogune ^a   Snyder, Michael ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Kinase; Phosphorylation; Post translation; Protein array

Indexed keywords

BUFFER; PHOSPHOTRANSFERASE; PROTEIN HYDROLYSATE; PROTEOME; RECOMBINANT PROTEIN; TRITON X 100; FUNGAL PROTEIN;

ARTICLE; ENZYME ACTIVITY; ENZYME SUBSTRATE; EUKARYOTE; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN TARGETING; RADIOACTIVITY; YEAST; ANIMAL; CHEMISTRY; HUMAN; METABOLISM; METHODOLOGY; PHOSPHORYLATION; PROTEIN PROCESSING; FUNGAL STRAIN; PROTEIN INDUCTION; PROTEIN MODIFICATION; PROTEIN NUCLEIC ACID INTERACTION;

ANIMALS; FUNGAL PROTEINS; HUMANS; PHOSPHORYLATION; PHOSPHOTRANSFERASES; PROTEIN ARRAY ANALYSIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; RECOMBINANT PROTEINS;

EID: 84883199598     PISSN: 19343655     EISSN: 19343663     Source Type: Journal    
DOI: 10.1002/0471140864.ps2704s72     Document Type: Article

References (22)

1. Balboni, I., Limb, C., Tenenbaum, J.D., and Utz, P.J. 2008. Evaluation of microarray surfaces and arraying parameters for autoantibody profiling. Proteomics 8:3443-3449.
2. Brizuela, L., Braun, P., and LaBaer, J. 2001. FLEXGene repository: From sequenced genomes to gene repositories for high-throughput functional biology and proteomics. Mol. Biochem. Parasitol. 118:155-165.
3. Bussow, K., Nordhoff, E., Lubbert, C., Lehrach, H., andWalter, G. 2000. A human cDNA library for high-throughput protein expression screening. Genomics 65:1-8.
4. Cheung, K.H., Hager, J., Nelson, K., White, K., Li, Y., Snyder, M., Williams, K., and Miller, P. 2002. A dynamic approach to mapping coordinates between microplates and microarrays. J. Biomed. Informatics 35:306-312.
5. Fasolo, J., Sboner, A., Sun, M.G., Yu, H., Chen, R., Sharon, D., Kim, P.M., Gerstein, M., and Snyder, M. 2011. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev. 25:767-778.
6. Gelperin, D.M., White, M.A., Wilkinson, M.L., Kon, Y., Kung, L.A., Wise, K.J., Lopez-Hoyo, N., Jiang, L., Piccirillo, S., Yu, H., Gerstein, M., Dumont, M.E., Phizicky, E.M., Snyder, M., and Grayhack, E.J. 2005. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev. 19:2816-2826.
7. Graslund, S., Nordlund, P., Weigelt, J., Hallberg, B.M., Bray, J., Gileadi, O., Knapp, S., Oppermann, U., Arrowsmith, C., Hui, R.,Ming, J., dhe-Paganon, S., Park, H.W., Savchenko, A., Yee, A., Edwards, A., Vincentelli, R.,Cambillau, C., Kim, R., Kim, S.H., Rao, Z., Shi, Y., Terwilliger, T.C., Kim, C.Y., Hung, L.W., Waldo, G.S., Peleg, Y., Albeck, S., Unger, T., Dym, O., Prilusky, J., Sussman, J.L., Stevens, R.C., Lesley, S.A., Wilson, I.A., Joachimiak, A., Collart, F., Dementieva, I., Donnelly, M.I., Eschenfeldt, W.H., Kim, Y., Stols, L., Wu, R., Zhou, M., Burley, S.K., Emtage, J.S., Sauder, J.M., Thompson, D., Bain, K., Luz, J., Gheyi, T., Zhang, F., Atwell, S., Almo, S.C., Bonanno, J.B., Fiser, A., Swaminathan, S., Studier, F.W., Chance, M.R., Sali, A., Acton, T.B., Xiao, R., Zhao, L., Ma, L.C., Hunt, J.F., Tong, L., Cunningham, K., Inouye, M., Anderson, S., Janjua, H., Shastry, R., Ho, C.K., Wang, D., Wang, H., Jiang, M., Montelione, G.T., Stuart, D.I., Owens, R.J., Daenke, S., Schutz, A., Heinemann, U., Yokoyama, S., Bussow, K., and Gunsalus, K.C. 2008. Protein production and purification. Nat. Methods 5:135-146.
8. Hu, S., Xie, Z., Onishi, A., Yu, X., Jiang, L., Lin, J., Rho, H.S., Woodard, C., Wang, H., Jeong, J.S., Long, S., He, X., Wade, H., Blackshaw, S., Qian, J., and Zhu, H. 2009. Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139:610-622.
9. Hudson, J.R., Jr., Dawson, E.P., Rushing, K.L., Jackson, C.H., Lockshon, D., Conover, D., Lanciault, C., Harris, J.R., Simmons, S.J., Rothstein, R., and Fields, S. 1997. The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 7:1169-1173.
10. Lennon, G., Auffray, C., Polymeropoulos, M., and Soares, M.B. 1996. The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics 33:151-152.
11. MacBeath, G. and Schreiber, S.L. 2000. Printing proteins as microarrays for high-throughput function determination. Science 289:1760-1763.
12. Meng, L., Michaud, G.A., Merkel, J.S., Zhou, F., Huang, J., Mattoon, D.R., and Schweitzer, B. 2008. Protein kinase substrate identification on functional protein arrays. BMC Biotechnol. 8:22.
13. Popescu, S.C., Popescu, G.V., Bachan, S., Zhang, Z., Seay, M., Gerstein, M., Snyder, M., and Dinesh-Kumar, S.P. 2007. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc. Natl. Acad. Sci. U.S.A. 104:4730-4735.
14. Ptacek, J., Devgan, G., Michaud, G., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Jona, G., Breitkreutz, A., Sopko, R.,McCartney, R.R., Schmidt, M.C., Rachidi, N., Lee, S.J., Mah, A.S., Meng, L., Stark, M.J., Stern, D.F., De Virgilio, C., Tyers, M., Andrews, B., Gerstein, M., Schweitzer, B., Predki, P.F., and Snyder, M. 2005. Global analysis of protein phosphorylation in yeast. Nature 438:679-684.
15. Reboul, J., Vaglio, P., Rual, J.F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R., Moore, T., Hudson, J.R., Jr., Hartley, J.L., Brasch, M.A., Vandenhaute, J., Boulton, S., Endress, G.A., Jenna, S., Chevet, E., Papasotiropoulos, V., Tolias, P.P., Ptacek, J., Snyder, M., Huang, R., Chance, M.R., Lee, H., Doucette-Stamm, L., Hill, D.E., and Vidal, M. 2003. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34:35-41.
16. Schweitzer, B. and Kingsmore, S.F. 2002. Measuring proteins on microarrays. Curr. Opin. Biotechnol. 13:14-19.
17. Strausberg, R.L., Feingold, E.A., Klausner, R.D., and Collins, F.S. 1999. The mammalian gene collection. Science 286:455-457.
18. Strausberg, R.L., Feingold, E.A., Grouse, L.H., Derge, J.G., Klausner, R.D., Collins, F.S., Wagner, L., Shenmen, C.M., Schuler, G.D., Altschul, S.F., Zeeberg, B., Buetow, K.H., Schaefer, C.F., Bhat, N.K., Hopkins, R.F., Jordan, H., Moore, T., Max, S.I., Wang, J., Hsieh, F., Diatchenko, L.,Marusina, K., Farmer, A.A., Rubin, G.M., Hong, L., Stapleton, M., Soares, M.B., Bonaldo, M.F., Casavant, T.L., Scheetz, T.E., Brownstein, M.J., Usdin, T.B., Toshiyuki, S., Carninci, P., Prange, C., Raha, S.S., Loquellano, N.A., Peters, G.J., Abramson, R.D., Mullahy, S.J., Bosak, S.A., McEwan, P.J., McKernan, K.J., Malek, J.A., Gunaratne, P.H., Richards, S., Worley, K.C., Hale, S., Garcia, A.M., Gay, L.J., Hulyk, S.W., Villalon, D.K., Muzny, D.M., Sodergren, E.J., Lu, X., Gibbs, R.A., Fahey, J., Helton, E., Ketteman, M., Madan, A., Rodrigues, S., Sanchez, A.,Whiting, M., Madan, A., Young, A.C., Shevchenko, Y., Bouffard, G.G., Blakesley, R.W., Touchman, J.W., Green, E.D., Dickson, M.C., Rodriguez, A.C., Grimwood, J., Schmutz, J., Myers, R.M., Butterfield, Y.S., Krzywinski, M.I., Skalska, U., Smailus, D.E., Schnerch, A., Schein, J.E., Jones, S.J., and Marra, M.A. 2002. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl. Acad. Sci. U.S.A. 99:16899-16903.
19. Tabakman, S.M., Lau, L., Robinson, J.T., Price, J., Sherlock, S.P., Wang, H., Zhang, B., Chen, Z., Tangsombatvisit, S., Jarrell, J.A., Utz, P.J., and Dai, H. 2011. Plasmonic substrates for multiplexed protein microarrays with femtomolar sensitivity and broad dynamic range. Nat. Communications 2:466.
20. Tsvetanova, N.G., Klass, D.M., Salzman, J., and Brown, P.O. 2010. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One 5:e12671.
21. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R.A., Gerstein, M., and Snyder, M. 2001. Global analysis of protein activities using proteome chips. Science 293:2101-2105.
22. Zhu, X., Gerstein, M., and Snyder, M. 2006. ProCAT: a data analysis approach for protein microarrays. Genome Biol. 7:R110.