The Use of the Escherichia coli Cell-Free Protein Synthesis for Structural Biology and Structural Proteomics

Cell-Free Protein Synthesis: Methods and Protocols

Volumn , Issue , 2008, Pages 99-109

  Kigawa, Takanori ^a   Inoue, Makoto ^a   Aoki, Masaaki ^a   Matsuda, Takayoshi ^a   Yabuki, Takashi ^a   Seki, Eiko ^a   Harada, Takushi ^a   Watanabe, Satoru ^a   Yokoyama, Shigeyuki ^a  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

Cell free protein synthesis; Escherichia coli; High throughput expression; Large scale protein production; Middle scale cell free protein synthesis; NMR screening; PCR based; Small scale; Structural biology; Structural proteomics; Structure determination

Indexed keywords

EID: 63549115383     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527622702.ch6     Document Type: Chapter

References (22)

1. Mittl, P. R., Grutter, M. G. (2001). Structural genomics: opportunities and challenges. Curr. Opin. Chem. Biol. 5: 402-408.
2. Chen, L., Oughtred, R., Berman, H. M., Westbrook, J. (2004). TargetDB: a target registration database for structural genomics projects. Bioinformatics 20: 2860-2862.
3. Christendat, D., Yee, A., Dharamsi, A., Kluger, Y., Gerstein, M., Arrowsmith, C. H., Edwards, A. M. (2000). Structural proteomics: prospects for high throughput sample preparation. Prog. Biophys. Mol. Biol. 73: 339-345.
4. Knaust, R. K., Nordlund, P. (2001). Screening for soluble expression of recombinant proteins in a 96-well format. Anal. Biochem. 297: 79-85.
5. Dieckman, L., Gu, M., Stols, L., Donnelly, M. I., Collart, F. R. (2002). High throughput methods for gene cloning and expression. Protein Expr. Purif. 25: 1-7.
6. Gilbert, M., Albala, J. S. (2002). Accelerating code to function: sizing up the protein production line. Curr. Opin. Chem. Biol. 6: 102-105.
7. Spirin, A. S., Baranov, V. I., Ryabova, L. A., Ovodov, S. Y., Alakhov, Y. B. (1988). A continuous cell-free translation system capable of producing polypeptides in high yield. Science 242: 1162-1164.
8. Kigawa, T., Yabuki, T., Yoshida, Y., Tsutsui, M., Ito, Y., Shibata, T., Yokoyama, S. (1999). Cell-free production and stableisotope labeling of milligram quantities of proteins. FEBS Lett. 442: 15-19.
9. Kigawa, T., Muto, Y., Yokoyama, S. (1995). Cell-free synthesis and amino acidselective stable isotope labeling of proteins for NMR analysis. J. Biomol. NMR 6: 129-134.
10. Yabuki, T., Kigawa, T., Dohmae, N., Takio, K., Terada, T., Ito, Y., Laue, E. D., Cooper, J. A., Kainosho, M., Yokoyama, S. (1998). Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis. J. Biomol. NMR 11: 295-306.
11. Kigawa, T., Yamaguchi-Nunokawa, E., Kodama, K., Matsuda, T., Yabuki, T., Matsuda, N., Ishitani, R., Nureki, O., Yokoyama, S. (2002). Selenomethionine incorporation into a protein by cell-free synthesis. J. Struct. Funct. Genomics 2: 29-35.
12. Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura, Y., Kyogoku, Y., Miki, K., Masui, R., Kuramitsu, S. (2000). Structural genomics projects in Japan. Nat. Struct. Biol. 7(Suppl.): 943-945.
13. Sawasaki, T., Ogasawara, T., Morishita, R., Endo, Y. (2002). A cell-free protein synthesis system for high-throughput proteomics. Proc. Natl. Acad. Sci. U.S.A. 99: 14652-14657.
14. Busso, D., Kim, R., Kim, S. H. (2003). Expression of soluble recombinant proteins in a cell-free system using a 96-well format. J. Biochem. Biophys. Methods 55: 233-240.
15. Vinarov, D. A., Lytle, B. L., Peterson, F. C., Tyler, E. M., Volkman, B. F., Markley, J. L. (2004). Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nat Methods 1: 149-153.
16. Waldo, G. S., Standish, B. M., Berendzen, J., Terwilliger, T. C. (1999). Rapid protein-folding assay using green fluorescent protein. Nat. Biotechnol. 17: 691-695.
17. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L., Studholme, D. J., Yeats, C., Eddy, S. R. (2004). The Pfam protein families database. Nucleic Acids Res. 32: D138-141.
18. Matsuda, T., Koshiba, S., Tochio, N., Seki, E., Iwasaki, N., Yabuki, T., Inoue, M., Yokoyama, S., Kigawa, T. (2007) Improving cell-free protein synthesis for stable-isotope labeling. J. Biomol. NMR 37: 225-229.
19. Hendrickson, W. A., Horton, J. R., LeMaster, D. M. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of threedimensional structure. EMBO J. 9: 1665-1672.
20. Kabayashi, N., Iwahara, J., Koshiba, S., Tomizawa, T., Tochio, N., Güntert, P., Kigawa, T., Yokoyama, S. (in press, 2007). KWIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J. Biomol. NMR.
21. Herrmann, T., Guntert, P., Wuthrich, K. (2002). Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319: 209-227.
22. Vinarov, D. A., Markley, J. L. (2005). High-throughput automated platform for nuclear magnetic resonance-based structural proteomics. Expert Rev. Proteomics 2: 49-55.