Cell-free protein production and labeling protocol for NMR-based structural proteomics

Nature Methods

Volumn 1, Issue 2, 2004, Pages 149-153

  Vinarov, Dmitriy A ^a   Lytle, Betsy L ^a,b   Peterson, Francis C ^a,b   Tyler, Ejan M ^a   Volkman, Brian F ^a,b   Markley, John L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; CARBON; NITROGEN; PROTEOME;

ARTICLE; CELL FREE SYSTEM; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; EVALUATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; ISOTOPE LABELING; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHYSIOLOGY; PROTEIN CONFORMATION; PROTEOMICS; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; VALIDATION STUDY;

ARABIDOPSIS PROTEINS; CARBON ISOTOPES; CELL-FREE SYSTEM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; ISOTOPE LABELING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; NITROGEN ISOTOPES; PROTEIN CONFORMATION; PROTEOME; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 14344256801     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth716     Document Type: Article

References (41)

1. Kramer, G., Kudlicki, W. & Hardesty, B. Cell-free coupled transcription-translation systems from Escherichia coli. in Protein Expression. A Practical Approach (eds. Higgens, S.J. & Hames, B.D.) 201-223 (Oxford Univ. Press, Oxford, UK, 1999).
2. Clemens, M.M. & Prujin, G.J. Protein synthesis in eukaryotic cell-free systems, in Protein Expression. A Practical Approach (eds. Higgens, SJ. & Hames, B.D.) 129-165 (Oxford Univ. Press, Oxford, UK, 1999).
3. Cubeddu, L. et al. Dictyostelium discoideum as expression host: isotopic labeling of a recombinant glycoprotein for NMR studies. Protein Expr. Purif. 19, 335-342 (2000).
4. Strauss, A. et al. Ami no-acid-type selective isotope labeling of proteins expressed in Baculovirus-infected insect cells useful for NMR studies. J. Biomol. NMR 26, 367-372 (2003).
5. 15N-amino acids in Spodoptera frugiperda (Sf9) insect cells. J. Biomol. NMR 25, 335-348 (2003).
6. Goff, S.A. & Goldberg, A.L. An increased content of protease LA, the Lon gene product, increases protein degradation and blocks growth in Escherichia coli. J. Biol. Chem. 262, 4508-4515 (1987).
7. Maurizi, M.R. Degradation in vitro of bacteriophage X N protein by Lon protease from Escherichia cob'. J. Biol. Chem. 262, 2696-2703 (1987).
8. Chrunyk, B.A., Evans, J., Lillquist, J., Young, P. & Wetzel, R. Inclusion-body formation and protein stability in sequence variants of interleukin-li. J. BioL Chem. 268, 18053-18061 (1993).
9. Shi, J., Pelton, J.G., Cho, H.S. & Wemmer, D.E. Protein signal assignments using specific labeling and cell-free synthesis. J. Biomol. NMR 28, 235-247 (2004).
10. Torizawa, T., Terauchi, T. & Kainosho, M. [Recent developments in NMR methods for structural biology]. Seikagaku 74, 1279-1284 (2002).
11. Kigawa, T., Muto, Y. & Yokoyama, S. Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis. J. Biomol. NMR 6, 129-134 (1995).
12. Yabuki, T. et al 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 (1998).
13. Klammt, C. et al. High level cell-free expression and specific labeling of integral membrane proteins. Eur. J. Biochem. 271, 568-580 (2004).
14. Henrich, B., Lubitz, W. & Plapp, R. Lysis of Escherichia coli by induction of cloned 4>X174 genes. Mol. Gen. Genet. 185, 493-497 (1982).
15. Guignard, L., Ozawa, K., Pursglove, S.E., Otting, G. & Dixon, N.E. NMR analysis of in v/tro-synthesized proteins without purification: a high-throughput approach. FEBS Lett. 524, 159-162 (2002).
16. Kigawa, T. & Yokoyama, S. [High-throughput cell-free protein expression system for structural genomics and proteomics studies]. Tanpakushitsu Kakusan Koso 47, 1014-1019 (2002).
17. Kigawa, T. et al. Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Lett. 442, 15-19 (1999).
18. Kim, D.M., Kigawa, T., Choi, C.Y. & Yokoyama, S. A highly efficient cell-free protein synthesis system from Escherichia cob'. Eur. J. Biochem. 239, 881-886 (1996).
19. Yokoyama, S. Protein expression systems for structural genomics and proteomics. Curr. Opin. Chem. BioL 7, 39-43 (2003).
20. Yokoyama, S. et al. Structural genomics projects in Japan. Nat. Struct. BioL 7, 943-945 (2000).
21. Kim, D.M. & Swartz, J.R. Prolonging cell-free protein synthesis by selective reagent additions. Biotechnol. Prog. 16, 385-390 (2000).
22. Yin, G. & Swartz, J.R. Enhancing multiple disulfide bonded protein folding in a cell-free system. Biotechnol. Bioeng. 86, 188-195 (2004).
23. Chumpolkulwong, N. et aL Effects of Escherichia cob ribosomal protein S12 mutations on cell-free protein synthesis. Eur. J. Biochem. 271, 1127-1134(2004).
24. Kawasaki, T., Gouda, M.D., Sawasaki, T., Takai, K. & Endo, Y. Efficient synthesis of a disulfide-containing protein through a batch cell-free system from wheat germ. Eur. J. Biochem. 270, 4780-4786 (2003).
25. Madin, K., Sawasaki, T., Ogasawara, T. & Endo, Y. A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proc. NatL Acad. Sci. USA 97, 559-564 (2000).
26. Morita, E.H., Sawasaki, T., Tanaka, R., Endo, Y. & Kohno, T. A wheat germ cell-free system is a novel way to screen protein folding and function. Protein Sci. 12, 1216-1221 (2003).
27. Sawasaki, T. et al. A bi layer cell-free protein synthesis system for high-throughput screening of gene products. FEBS Lett. 514, 102-105 (2002).
28. Sawasaki, T., Ogasawara, T., Morishita, R. & Endo, Y. A cell-free protein synthesis system for high-throughput proteomics. Proc. NatL Acad. Sci. USA 99, 14652- 14657 (2002).
29. Betton, J.M. Rapid translation system (RTS): a promising alternative for recombinant protein production. Curr. Protein Pept. Sci. 4, 73-80 (2003).
30. Altieri, A.S., Hinton, D.P. & Byrd, R.A. Association of biomolecular systems via pulsed field gradient NMR self-diffusion measurements. J. Am. Chem. Soc. 117, 7566-7567 (1995).
31. Bartels, C., Billeter, M., Guntert, P. & Wuthrich, K. Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J. Biomol. NMR 7, 207-213 (1996).
32. Herrmann, T., Guntert, P. & Wuthrich, K. 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(2002).
33. Linge, J.P., Williams, M.A., Spronk, C.A., Bonvin, A.M. & Nilges, M. Refinement of protein structures in explicit solvent. Proteins 50, 496-506 (2003).
34. Palmer III, A.G. NMR probes of molecular dynamics: overview and comparison with other techniques. Annu. Rev. Biophys. Biomol. Struct. 30, 129-155 (2001).
35. Terauchi, T., Ohki, S.Y. & Kainosho, M. [Developing a new approach for high-throughput, high-accuracy NMR structural analyses of genomic proteins]. Tanpakushitsu Kakusan Koso 47, 1045-1051 (2002).
36. Larsen, C.N. & Wang, H. The ubiquitin superfamily: members, features, and phylogenies. J. Proteome Res. 1, 411-419 (2002).
37. Giynberg, M., Jaroszewski, L. & Godzik, A. Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinformatics 4, 46 (2003).
38. Delaglio, F. et aL NMRPIPE—a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).
39. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289-302 (1999).
40. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PR0CHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).
41. Hooft, R.W.W., Vriend, G., Sander, C. & Abola, E.E. Errors in protein structures. Nature 381, 272 (1996).