A hexylchloride-based catch-And-release system for chemical proteomic applications

ACS Chemical Biology

Volumn 8, Issue 4, 2013, Pages 691-699

  Brigham, Jennifer L ^a   Perera, B Gayani K ^a   Maly, Dustin J ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CHLORIDE; CHLOROHEXANE; HALOTAG PROTEIN; HYBRID PROTEIN; PROTEIN; PROTEIN KINASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL LYSATE; CHEMICAL BINDING; CHEMICAL STRUCTURE; CONTROLLED STUDY; COVALENT BOND; ENZYME ACTIVE SITE; FEMALE; FLUORESCENCE ANALYSIS; HUMAN; HUMAN CELL; MAMMAL CELL; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN IMMOBILIZATION;

CHLORIDES; HELA CELLS; HUMANS; PROTEOMICS;

MAMMALIA;

EID: 84876520136     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb300623a     Document Type: Article

References (44)

1. Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S., Boesche, M., Hobson, S., Mathieson, T., Perrin, J., Raida, M., Rau, C., Reader, V., Sweetman, G., Bauer, A., Bouwmeester, T., Hopf, C., Kruse, U., Neubauer, G., Ramsden, N., Rick, J., Kuster, B., and Drewes, G. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors Nat. Biotechnol. 25, 1035-1044
2. Daub, H., Olsen, J. V., Bairlein, M., Gnad, F., Oppermann, F. S., Korner, R., Greff, Z., Keri, G., Stemmann, O., and Mann, M. (2008) Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle Mol. Cell 31, 438-448
3. Dulla, K., Daub, H., Hornberger, R., Nigg, E. A., and Korner, R. (2010) Quantitative site-specific phosphorylation dynamics of human protein kinases during mitotic progression Mol. Cell Proteomics 9, 1167-1181
4. Oppermann, F. S., Gnad, F., Olsen, J. V., Hornberger, R., Greff, Z., Keri, G., Mann, M., and Daub, H. (2009) Large-scale proteomics analysis of the human kinome Mol. Cell Proteomics 8 (7) 1751-64
5. Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p Science 272, 408-411
6. Ong, S. E., Schenone, M., Margolin, A. A., Li, X., Do, K., Doud, M. K., Mani, D. R., Kuai, L., Wang, X., Wood, J. L., Tolliday, N. J., Koehler, A. N., Marcaurelle, L. A., Golub, T. R., Gould, R. J., Schreiber, S. L., and Carr, S. A. (2009) Identifying the proteins to which small-molecule probes and drugs bind in cells Proc. Natl. Acad. Sci. U.S.A. 106, 4617-4622
7. Rix, U. and Superti-Furga, G. (2009) Target profiling of small molecules by chemical proteomics Nat. Chem. Biol. 5, 616-624
8. Evans, M. J. and Cravatt, B. F. (2006) Mechanism-based profiling of enzyme families Chem. Rev. 106, 3279-3301
9. Taylor, M. T., Blackman, M. L., Dmitrenko, O., and Fox, J. M. (2011) Design and synthesis of highly reactive dienophiles for the tetrazine-trans- cyclooctene ligation J. Am. Chem. Soc. 133, 9646-9649
10. Blackman, M. L., Royzen, M., and Fox, J. M. (2008) Tetrazine ligation: fast bioconjugation based on inverse-electron-demand Diels-Alder reactivity J. Am. Chem. Soc. 130, 13518-13519
11. Mahal, L. K., Yarema, K. J., and Bertozzi, C. R. (1997) Engineering chemical reactivity on cell surfaces through oligosaccharide biosynthesis Science 276, 1125-1128
12. Sampathkumar, S.-G., Li, A. V., Jones, M. B., Sun, Z., and Yarema, K. J. (2006) Metabolic installation of thiols into sialic acid modulates adhesion and stem cell biology Nat. Chem. Biol. 2, 149-152
13. Dondoni, A. (2008) The emergence of thiol-ene coupling as a click process for materials and bioorganic chemistry Angew. Chem., Int. Ed. 47, 8995-8997
14. Saxon, E. and Bertozzi, C. R. (2000) Cell surface engineering by a modified Staudinger reaction Science 287, 2007-2010
15. Best, M. D. (2009) Click chemistry and bioorthogonal reactions: unprecedented selectivity in the labeling of biological molecules Biochemistry 48, 6571-6584
16. Cravatt, B. F., Wright, A. T., and Kozarich, J. W. (2008) Activity-based protein profiling: from enzyme chemistry to proteomic chemistry Annu. Rev. Biochem. 77, 383-414
17. Salisbury, C. M. and Cravatt, B. F. (2007) Activity-based probes for proteomic profiling of histone deacetylase complexes Proc. Natl. Acad. Sci. U.S.A. 104, 1171-1176
18. Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M., and Cravatt, B. F. (2004) Activity-based probes for the proteomic profiling of metalloproteases Proc. Natl. Acad. Sci. U.S.A. 101, 10000-10005
19. Besanceney-Webler, C., Jiang, H., Zheng, T., Feng, L., Soriano Del Amo, D., Wang, W., Klivansky, L. M., Marlow, F. L., Liu, Y., and Wu, P. (2011) Increasing the efficacy of bioorthogonal click reactions for bioconjugation: a comparative study Angew. Chem., Int. Ed. 50, 8051-8056
20. Speers, A. E., Adam, G. C., and Cravatt, B. F. (2003) Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-Alkyne [3 + 2] cycloaddition J. Am. Chem. Soc. 125, 4686-4687
21. Praul, C. A., Brubaker, K. D., Leach, R. M., and Gay, C. V. (1998) Detection of endogenous biotin-containing proteins in bone and cartilage cells with streptavidin systems Biochem. Biophys. Res. Commun. 247, 312-314
22. Yang, Y.-Y., Grammel, M., Raghavan, A. S., Charron, G., and Hang, H. C. (2010) Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics Chem. Biol. 17, 1212-1222
23. Los, G. V., Encell, L. P., McDougall, M. G., Hartzell, D. D., Karassina, N., Zimprich, C., Wood, M. G., Learish, R., Ohana, R. F., Urh, M., Simpson, D., Mendez, J., Zimmerman, K., Otto, P., Vidugiris, G., Zhu, J., Darzins, A., Klaubert, D. H., Bulleit, R. F., and Wood, K. V. (2008) HaloTag: A novel protein labeling technology for cell imaging and protein analysis ACS Chem. Biol. 3, 373-382
24. Gronemeyer, T., Chidley, C., Juillerat, A., Heinis, C., and Johnsson, K. (2006) Directed evolution of O6-Alkylguanine-DNA alkyltransferase for applications in protein labeling Protein Eng. Des. Sel. 19, 309-316
25. Keppler, A., Kindermann, M., Gendreizig, S., Pick, H., Vogel, H., and Johnsson, K. (2004) Labeling of fusion proteins of O6-Alkylguanine-DNA alkyltransferase with small molecules in vivo and in vitro Methods 32, 437-444
26. Keppler, A., Gendreizig, S., Gronemeyer, T., Pick, H., Vogel, H., and Johnsson, K. (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo Nat. Biotechnol. 21, 86-89
27. Chidley, C., Mosiewicz, K., and Johnsson, K. (2008) A designed protein for the specific and covalent heteroconjugation of biomolecules Bioconjugate Chem. 19, 1753-1756
28. 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
29. Butt, T. R., Edavettal, S. C., Hall, J. P., and Mattern, M. R. (2005) SUMO fusion technology for difficult-to-express proteins Protein Expresssion Purif. 43, 1-9
30. Liu, L., Spurrier, J., Butt, T. R., and Strickler, J. E. (2008) Enhanced protein expression in the baculovirus/insect cell system using engineered SUMO fusions Protein Expresssion Purif. 62, 21-28
31. Marcotte, D. J., Liu, Y.-T., Arduini, R. M., Hession, C. A., Miatkowski, K., Wildes, C. P., Cullen, P. F., Hong, V., Hopkins, B. T., Mertsching, E., Jenkins, T. J., Romanowski, M. J., Baker, D. P., and Silvian, L. F. (2010) Structures of human Bruton's tyrosine kinase in active and inactive conformations suggest a mechanism of activation for TEC family kinases Protein Sci. 19, 429-439
32. Sicheri, F., Moarefi, I., and Kuriyan, J. (1997) Crystal structure of the Src family tyrosine kinase Hck Nature 385, 602-609
33. Xu, W., Harrison, S. C., and Eck, M. J. (1997) Three-dimensional structure of the tyrosine kinase c-Src Nature 385, 595-602
34. Pargellis, C., Tong, L., Churchill, L., Cirillo, P. F., Gilmore, T., Graham, A. G., Grob, P. M., Hickey, E. R., Moss, N., Pav, S., and Regan, J. (2002) Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site Nat. Struct. Biol. 9, 268-272
35. Liu, Y. and Gray, N. S. (2006) Rational design of inhibitors that bind to inactive kinase conformations Nat. Chem. Biol. 2, 358-364
36. Wan, P. T., Garnett, M. J., Roe, S. M., Lee, S., Niculescu-Duvaz, D., Good, V. M., Jones, C. M., Marshall, C. J., Springer, C. J., Barford, D., and Marais, R. (2004) Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF Cell 116, 855-867
37. Schindler, T., Bornmann, W., Pellicena, P., Miller, W. T., Clarkson, B., and Kuriyan, J. (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine kinase Science 289, 1938-1942
38. DiMauro, E. F., Newcomb, J., Nunes, J. J., Bemis, J. E., Boucher, C., Buchanan, J. L., Buckner, W. H., Cee, V. J., Chai, L., Deak, H. L., Epstein, L. F., Faust, T., Gallant, P., Geuns-Meyer, S. D., Gore, A., Gu, Y., Henkle, B., Hodous, B. L., Hsieh, F., Huang, X., Kim, J. L., Lee, J. H., Martin, M. W., Masse, C. E., McGowan, D. C., Metz, D., Mohn, D., Morgenstern, K. A., Oliveira-dos-Santos, A., Patel, V. F., Powers, D., Rose, P. E., Schneider, S., Tomlinson, S. A., Tudor, Y. Y., Turci, S. M., Welcher, A. A., White, R. D., Zhao, H., Zhu, L., and Zhu, X. (2006) Discovery of aminoquinazolines as potent, orally bioavailable inhibitors of Lck: synthesis, SAR, and in vivo anti-inflammatory activity J. Med. Chem. 49, 5671-5686
39. Ranjitkar, P., Brock, A. M., and Maly, D. J. (2010) Affinity reagents that target a specific inactive form of protein kinases Chem. Biol. 17, 195-206
40. Ranjitkar, P. and Maly, D. J. (2012) Affinity purification of protein kinases that adopt a specific inactive conformation Methods Mol. Biol. 928, 143-151
41. Seeliger, M. A., Ranjitkar, P., Kasap, C., Shan, Y., Shaw, D. E., Shah, N. P., Kuriyan, J., and Maly, D. J. (2009) Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations Cancer Res. 69, 2384-2392
42. Simard, J. R., Kluter, S., Grutter, C., Getlik, M., Rabiller, M., Rode, H. B., and Rauh, D. (2009) A new screening assay for allosteric inhibitors of cSrc Nat. Chem. Biol. 5, 394-396
43. Dar, A. C., Lopez, M. S., and Shokat, K. M. (2008) Small molecule recognition of c-Src via the Imatinib-binding conformation Chem. Biol. 15, 1015-1022
44. Choi, Y., Syeda, F., Walker, J. R., Finerty, P. J., Cuerrier, D., Wojciechowski, A., Liu, Q., Dhe-Paganon, S., and Gray, N. S. (2009) Discovery and structural analysis of Eph receptor tyrosine kinase inhibitors Bioorg. Med. Chem. Lett. 19, 4467-4470