Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro

Nature Methods

Volumn 2, Issue 10, 2005, Pages 757-762

  Evans, Michael S ^a   Ugrinov, Krastyu G ^a   Frese, Marc André ^a,b   Clark, Patricia L ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; MESSENGER RNA; SECM PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; CONCENTRATION RESPONSE; CONTROLLED STUDY; ESCHERICHIA COLI; FLUORESCENCE ANALYSIS; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; RIBOSOME; RNA TRANSLATION; SEQUENCE ANALYSIS;

BASE SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER; TRANSCRIPTION FACTORS;

ESCHERICHIA COLI;

EID: 27144451454     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth790     Document Type: Article

References (32)

1. Nissen, P., Hansen, J., Ban, N., Moore, P.B. & Steitz, T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930 (2000).
2. Berisio, R.et al. Structural insight into the role of the ribosomal tunnel in cellular regulation. Nat. Struct. Biol. 10 366-370 (2003).
3. Malkin, L.I. & Rich, A. Partial resistance of nascent polypeptide chains to proteolytic digestion due to ribosomal shielding. J. Mol. Biol. 26, 329-346 (1967).
4. Woolhead, C.A., McCormick, P.J. & Johnson, A.E. Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 116 725-736 (2004).
5. Komar, A.A., Kommer, A., Krasheninnikov, I.A. & Spirin, A.S. Cotranslational folding of globin. J. Biol. Chem. 272, 10646-10651 (1997).
6. Frydman, J., Erdjument-Bromage, H., Tempst, P. & Hartl, F.U. Cotranslational domain folding as the structural basis for the rapid de novo folding of firefly luciferase. Nat. Struct. Biol. 6 697-705 (1999).
7. Nicola, A.V., Chen, W. & Helenius, A. Cotranslational folding of an alphavirus capsid protein in the cytosol of Living cells. Nat. Cell Biol. 1, 341-345 (1999).
8. Clark P.L. & King, J. A newly synthesized, ribosome-bound polypeptide chain adopts conformations dissimilar from early in vitro refolding intermediates. J. Biol. Chem. 276, 25411-25420 (2001).
9. Fedorov, A.N. & Baldwin, T.O. Process of biosynthetic protein folding determines the rapid formation of native structure. J. Mol. Biol. 294, 579-586 (1999).
10. Clark, P.L. Protein folding in the cell: Reshaping the folding funnel. Trends Biochem. Sci. 29, 527-534 (2004).
11. Ghaemmaghami, S. & Oas, T.G. Quantitative protein stability measurement in vivo. Nat. Struct. Biol. 8, 879-882 (2001).
12. Dedmon, M.M., Patel, C.N., Young, G.B. & Pielak, G.J. FlgM gains structure in living cells. Proc Natl. Acad. Sci. USA 99, 12681-12684 (2002).
13. Ignatova, Z. & Gierasch, L.M. Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling. Proc. Natl. Acad. Sci. USA 101, 523-528 (2004).
14. Nakatogawa, H. & Ito, K. The ribosomal exit tunnel functions as a discriminating gate. Cell 108, 629-636 (2002).
15. Friguet, B., Djavadi-Ohaniance, L., King, J. & Goldberg, M.E. In vitro and ribosome-bound folding intermediates of P22 tailspike protein detected with monoclonal antibodies. J. Biol. Chem. 269 15945-15949 (1994).
16. Friguet, B., Djavadi-Ohaniance, L., Haase-Pettingell, C.A., King, J. & Goldberg, M.E. Properties of monoclonal antibodies selected for probing the conformation of wild-type and mutant forms of the P22 tailspike endorhamnosidase. J. Biol. Chem. 265, 10347-10351 (1990).
17. Jain, M., Evans, M.S., King, J. & Clark, P.L. Monoclonal antibody epitope mapping describes tailspike β-helix folding and aggregation intermediates. J. Biol. Chem. 280, 23032-23040 (2005).
18. Hanes, J. & Pluckthun, A. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. USA 94, 4937-4942 (1997).
19. Crameri, A., Whitehorn, E.A., Tate, E. & Stemmer, W.P. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14, 315-319 (1996).
20. Adams, S.R. et al. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: Synthesis and biological applications. J. Am. Chem. Soc. 124, 6063-6076 (2002).
21. Griffin, B.A., Adams, S.R. & Tsien, R.Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281 269-272 (1998).
22. Spedding, G. Isolation and analysis of ribosomes from prokaryotes, eukaryotes and organelles. in Ribosomes and Protein Synthesis (ed. Spedding, G.) 1-27 (Oxford University Press, New York, 1990).
23. Steinbacher, S. et al. Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer. Science 265 383-386 (1994).
24. Friguet, B., Chaffotte, A.F., Djavadi-Ohaniance, L. & Goldberg, M.E. Measurements of the true affinity constant in solution of antigen-antibody complexes by enzyme-linked immunosorbent assay. J. Immunol. Methods 77, 305-319 (1985).
25. Friguet, B., Djavadi-Ohaniance, L. & Goldberg, M.E. Polypeptide-antibody binding mechanism: Conformational adaptation investigated by equilibrium and kinetic analysis. Res. Immunol. 140, 355-376 (1989).
26. Sunohara, T., Jojima, K., Tagami, H., Inada, T. & Aiba, H. Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli. J. Biol. Chem. 279, 15368-15375 (2004).
27. Fuchs, A., Seiderer, C. & Seckler, R. In vitro folding pathway of phage P22 tailspike protein. Biochemistry 30, 6598-6604 (1991).
28. Mitraki, A., Fane, B., Haase-Pettingell, C., Sturtevant, J. & King J. Global suppression of protein folding defects and inclusion body formation. Science 253, 54-58 (1991).
29. King, J., Haase-Pettingell, C., Robinson, A.S., Speed M. & Mitraki A. Thermolabile folding intermediates: Inclusion body precursors and chaperonin substrates. FASEB J. 10, 57-66 (1996).
30. Speed, M.A., Morshead, T., Wang, D.I. & King, J. Conformation of P22 tailspike folding and aggregation intermediates probed by monoclonal antibodies. Protein Sci. 6, 99-108 (1997).
31. Laemmli, U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685 (1970).
32. Steinbacher, S. et al. Phage P22 tailspike protein: Crystal structure of the head-binding domain at 2.3 Å, fully refined structure of the endorhamnosidase at 1.56 Å resolution, and the molecular basis of O-antigen recognition and cleavage. J. Mol. Biol. 267, 865-880 (1997).