Ribosome display and photo-cross-linking techniques for in vitro identification of target proteins of bioactive small molecules

Analytical Chemistry

Volumn 86, Issue 14, 2014, Pages 6768-6773

  Wada, Akira ^a,b,d   Hara, Shuta ^a,c   Osada, Hiroyuki ^a,c,d  

^a RIKEN   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^d Elements Chemistry Laboratory   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROPHORESIS; LAKES; MOLECULES; PROTEINS;

DETECTION AND IDENTIFICATIONS; EXPRESSION LEVELS; IDENTIFICATION OF UNKNOWNS; PHOTO-CROSS-LINKED; PHOTOCROSS-LINKING; RIBOSOME DISPLAY; SPECIFIC DETECTION; WESTERN-BLOT ANALYSIS;

BIOSYNTHESIS;

CROSS LINKING REAGENT; DIAZOMETHANE; FK 506 BINDING PROTEIN; HYBRID PROTEIN; MESSENGER RNA; PEPTIDE LIBRARY; PROTEIN; STOP CODON; TACROLIMUS;

CHEMISTRY; GENETICS; HUMAN; LUMINESCENCE; METABOLISM; PEPTIDE LIBRARY; PHOTOCHEMISTRY; POLYMERASE CHAIN REACTION; PROCEDURES; RIBOSOME; STOP CODON; X RAY CRYSTALLOGRAPHY;

CODON, TERMINATOR; CROSS-LINKING REAGENTS; CRYSTALLOGRAPHY, X-RAY; DIAZOMETHANE; HUMANS; LUMINESCENT MEASUREMENTS; PEPTIDE LIBRARY; PHOTOCHEMISTRY; POLYMERASE CHAIN REACTION; PROTEINS; RECOMBINANT FUSION PROTEINS; RIBOSOMES; RNA, MESSENGER; TACROLIMUS; TACROLIMUS BINDING PROTEIN 1A;

EID: 84904336883     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac4030208     Document Type: Article

References (44)

1. Huang, J.; Zhu, H.; Haggarty, S. J.; Spring, D. R.; Hwang, H.; Jin, F.; Snyder, M.; Schreiber, S. L. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 16594-16599
2. Bradner, J. E.; McPherson, O. M.; Koehler, A. N. Nat. Protoc. 2006, 1, 2344-2352
3. Palchaudhuri, R.; Hergenrother, P. J. ACS Chem. Biol. 2011, 6, 21-33
4. Kato, N.; Takahashi, S.; Nogawa, T.; Saito, T.; Osada, H. Curr. Opin. Chem. Biol. 2012, 16, 101-108
5. Stockwell, B. R. Nature 2004, 432, 846-854
6. Bradner, J. E.; McPherson, O. M.; Mazitschek, R.; Barnes-Seeman, D.; Shen, J. P.; Dhaliwal, J.; Stevenson, K. E.; Duffner, J. L.; Park, S. B.; Neuberg, D. S.; Nghiem, P.; Schreiber, S. L.; Koehler, A. N. Chem. Biol. 2006, 13, 493-504
7. Miyazaki, I.; Simizu, S.; Okumura, H.; Takagi, S.; Osada, H. Nat. Chem. Biol. 2010, 6, 667-673
8. Vrijens, K.; Lin, W.; Cui, J.; Farmer, D.; Low, J.; Pronier, E.; Zeng, F. Y.; Shelat, A. A.; Guy, K.; Taylor, M. R.; Chen, T.; Roussel, M. F. PLoS One 2013, 8, e59045
9. Herrero Martín, D.; Boro, A.; Schäfer, B. W. PLoS One 2013, 8, e55072
10. Zimmermann, T. J.; Bürger, M.; Tashiro, E.; Kondoh, Y.; Martinez, N. E.; Görmer, K.; Rosin-Steiner, S.; Shimizu, T.; Ozaki, S.; Mikoshiba, K.; Watanabe, N.; Hall, D.; Vetter, I. R.; Osada, H.; Hedberg, C.; Waldmann, H. ChemBioChem. 2013, 14, 115-122
11. Lamb, J.; Crawford, E. D.; Peck, D.; Modell, J. W.; Blat, I. C.; Wrobel, M. J.; Lerner, J.; Brunet, J. P.; Subramanian, A.; Ross, K. N.; Reich, M.; Hieronymus, H.; Wei, G.; Armstrong, S. A.; Haggarty, S. J.; Clemons, P. A.; Wei, R.; Carr, S. A.; Lander, E. S.; Golub, T. R. Science 2006, 313, 1929-1935
12. Young, D. W.; Bender, A.; Hoyt, J.; McWhinnie, E.; Chirn, G. W.; Tao, C. Y.; Tallarico, J. A.; Labow, M.; Jenkins, J. L.; Mitchison, T. J.; Feng, Y. Nat. Chem. Biol. 2008, 4, 59-68
13. Campillos, M.; Kuhn, M.; Gavin, A. C.; Jensen, L. J.; Bork, P. Science 2008, 321, 263-266
14. Lomenick, B.; Olsen, R. W.; Huang, J. ACS Chem. Biol. 2011, 21, 34-46
15. Ziegler, S.; Pries, V.; Hedberg, C.; Waldmann, H. Angew. Chem., Int. Ed. 2013, 52, 2744-2792
16. Chidley, C.; Haruki, H.; Pedersen, M. G.; Muller, E.; Johnsson, K. Nat. Chem. Biol. 2011, 7, 375-383
17. Hoess, R. H. Chem. Rev. 2001, 101, 3205-3218
18. Eisenhardt, S. U.; Schwarz, M.; Bassler, N.; Peter, K. Nat. Protoc. 2007, 2, 3063-3073
19. Heinis, C.; Rutherford, T.; Freund, S.; Winter, G. Nat. Chem. Biol. 2009, 5, 502-507
20. Sche, P. P.; McKenzie, K. M.; White, J. D.; Austin, D. J. Chem. Biol. 1999, 6, 707-716
21. Jin, Y.; Yu, J.; Yu, Y. G. Chem. Biol. 2002, 9, 157-162
22. Shim, J. S.; Lee, J.; Park, H.-J.; Park, S.-J.; Kwon, H. J. Chem. Biol. 2004, 11, 1455-1463
23. Kuroiwa, Y.; Takakusagi, Y.; Kusayanagi, T.; Kuramochi, K.; Imai, T.; Hirayama, T.; Ito, I.; Yoshida, M.; Sakaguchi, K.; Sugawara, F. PLoS One 2013, 8, e63073
24. Li, S.; Roberts, R. W. Chem. Biol. 2003, 10, 233-239
25. Horisawa, K.; Tateyama, S.; Ishizaka, M.; Matsumura, N.; Takashima, H.; Miyamoto-Sato, E.; Doi, N.; Yanagawa, H. Nucleic Acids Res. 2004, 32, e169
26. Cotton, S. W.; Zou, J.; Valencia, C. A.; Liu, R. Nat. Protoc. 2011, 6, 1163-1182
27. Schlippe, Y. V.; Hartman, M. C.; Josephson, K.; Szostak, J. W. J. Am. Chem. Soc. 2012, 134, 10469-10477
28. Hipolito, C. J.; Suga, H. Curr. Opin. Chem. Biol. 2012, 16, 196-203
29. Ueno, S.; Yoshida, S.; Mondal, A.; Nishina, K.; Koyama, M.; Sakata, I.; Miura, K.; Hayashi, Y.; Nemoto, N.; Nishigaki, K.; Sakai, T. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 11121-11126
30. McPherson, M.; Yang, Y.; Hammond, P. W.; Kreider, B. L. Chem. Biol. 2002, 9, 691-698
31. Shiheido, H.; Terada, F.; Tabata, N.; Hayakawa, I.; Matsumura, N.; Takashima, H.; Ogawa, Y.; Du, W.; Yamada, T.; Shoji, M.; Sugai, T.; Doi, N.; Iijima, S.; Hattori, Y.; Yanagawa, H. PLoS One 2012, 7, e38878
32. Mattheakis, L. C.; Bhatt, R. R.; Dower, W. J. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 9022-9026
33. Lamla, T.; Erdmann, V. A. J. Mol. Biol. 2003, 329, 381-388
34. Zahnd, C.; Amstutz, P.; Plückthun, A. Nat. Methods 2007, 4, 269-279
35. He, M.; Taussig, M. J. Nat. Methods 2007, 4, 281-288
36. Wada, A.; Sawata, S. Y.; Ito, Y. Biotechnol. Bioeng. 2008, 101, 1102-1107
37. Mie, M.; Shimizu, S.; Takahashi, F.; Kobatake, E. Biochem. Biophys. Res. Commun. 2008, 373, 48-52
38. Douthwaite, J. A. Methods Mol. Biol. 2012, 805, 45-57
39. Ohashi, H.; Kanamori, T.; Osada, E.; Akbar, B. K.; Ueda, T. Methods Mol. Biol. 2012, 805, 251-259
40. Wada, A. Front. Immunol. 2013, 4, 224
41. Shimizu, Y.; Inoue, A.; Tomari, Y.; Suzuki, T.; Yokogawa, T.; Nishikawa, K.; Ueda, T. Nat. Biotechnol. 2001, 19, 751-755
42. Bayley, H. In Photogenerated Reagents in Biochemistry and Molecular Biology; Work, T.; Burdon, R., Eds. Amsterdam: Elsevier, 1983; Vol. 12, p 187.
43. Brunner, J. Annu. Rev. Biochem. 1993, 62, 483-514
44. Kanoh, N.; Honda, K.; Simizu, S.; Muroi, M.; Osada, H. Angew. Chem., Int. Ed. 2005, 44, 3559-3562