Identification of in vivo substrates of the chaperonin GroEL (original) (raw)

References

  1. Georgopoulos,C. & Welch,W. J. Role of the major heat shock proteins as molecular chaperones. Annu. Rev. Cell Biol. 9, 601–634 (1993).
    Article CAS Google Scholar
  2. Ellis,R. J. Roles of molecular chaperones in protein folding. Curr. Opin. Struct. Biol. 4, 117–122 (1994).
    Article CAS Google Scholar
  3. Hartl,F. U. Molecular chaperones in cellular protein folding. Nature 381, 571–580 (1996).
    Article ADS CAS Google Scholar
  4. Fayet,O., Ziegelhoffer,T. & Georgopoulos,C. The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures. J. Bacteriol. 171, 1379–1385 (1989).
    Article CAS Google Scholar
  5. Horwich,A. L., Low,K. B., Fenton,W. A., Hirshfield,I. N. & Furtak,K. Folding in vivo of bacterial cytoplasmic proteins: role of GroEL. Cell 74, 909–917 (1993).
    Article CAS Google Scholar
  6. Fenton,W. A., Kashi,Y., Furtak,K. & Horwich,A. L. Residues in chaperonin GroEL required for polypeptide binding and release. Nature 371, 614–619 (1994).
    Article ADS CAS Google Scholar
  7. Coyle,J. E., Jaeger,J., Gross,M., Robinson,C. V. & Radford,S. E. Structural and mechanistic consequences of polypeptide binding by GroEL. Fold. Design 2, R93–R104 (1997).
    Article CAS Google Scholar
  8. Sigler,P. B. et al. Structure and function in GroEL-mediated protein folding. Annu., Rev. Biochem. 67, 581–608 (1998).
    Article CAS Google Scholar
  9. Ranson,N. A., White,H. E. & Saibil,H. R. Chaperonins. Biochem. J. 333, 233–242 (1998).
    Article CAS Google Scholar
  10. Ewalt,K. L., Hendrick,J. P., Houry,W. A. & Hartl,F. U. In vivo observation of polypeptide flux through the bacterial chaperonin system. Cell 90, 491–500 (1997).
    Article CAS Google Scholar
  11. Pedersen,S. Escherichia coli ribosomes translate in vivo with variable rate. EMBO J. 3, 2895–2898 (1984).
    Article CAS Google Scholar
  12. Xu,D. & Nussinov,R. Favorable domain size in proteins. Fold. Design 3, 11–17 (1998).
    Article CAS Google Scholar
  13. Xu,Z. H., Horwich,A. L. & Sigler,P. B. The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex. Nature 388, 741–750 (1997).
    Article ADS CAS Google Scholar
  14. Ellis,R. J. & Hartl,F. U. Protein folding in the cell: Competing models of chaperonin function. FASEB J. 10, 20–26 (1996).
    Article CAS Google Scholar
  15. Rye,H. S. et al. GroEL–GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. Cell 97, 325–338 (1999).
    Article CAS Google Scholar
  16. Ellis,R. J. Molecular chaperones: avoiding the crowd. Curr. Biol. 7, R531–R533 (1997).
    Article CAS Google Scholar
  17. Gentry,D. R. & Burgess,R. R. The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase. Gene 48, 33–40 (1986).
    Article CAS Google Scholar
  18. Wada,M., Fujita,H. & Itikawa,H. Genetic suppression of a temperature-sensitive groES mutation by an altered subunit of RNA polymerase of Escherichia coli K-12. J. Bacteriol. 169, 1102–1106 (1987).
    Article CAS Google Scholar
  19. Ziemienowicz,A. et al. Both the Escherichia coli chaperone systems, GroEL/GroES and DnaK/DnaJ/GrpE, can reactivate heat-treated RNA polymerase. Different mechanisms for the same activity. J. Biol. Chem. 268, 25425–25431 (1993).
    CAS PubMed Google Scholar
  20. VanBogelen,R. A., Sankar,P., Clark,R. L., Bogan,J. A. & Neidhardt,F. C. The gene–protein database of Escherichia coli: edition 5. Electrophoresis 13, 1014–1054 (1992).
    Article CAS Google Scholar
  21. Hubbard,T. J. P., Ailey,B., Brenner,S. E., Murzin,A. G. & Chothia,C. SCOP: a structural classification of proteins database. Nucleic Acids Res. 27, 254–256 (1999).
    Article CAS Google Scholar
  22. Orengo,C. A. et al. The CATH database provides insights into protein structure/function relationships. Nucleic Acids Res. 27, 275–279 (1999).
    Article CAS Google Scholar
  23. Eisenberg,D., Wilcox,W. & McLachlan,A. D. Hydrophobicity and amphiphilicity in protein structure. J. Cell. Biochem. 31, 11–17 (1986).
    Article CAS Google Scholar
  24. Cheng,M. Y. et al. Mitochondrial heat-shock protien hsp60 is essential for assembly of proteins imported into yeast mitochondria. Nature 337, 620–625 (1989).
    Article ADS CAS Google Scholar
  25. Rye,H. S. et al. Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL. Nature 388, 792–798 (1997).
    Article ADS CAS Google Scholar
  26. Viitanen,P. V. et al. Chaperonin-facilitated refolding of the ribulsebisphosphate carboxylase and ATP hydrolysis by chaperonin 60 (GroEL) are K+ dependent. Biochemistry 29, 5665–5671 (1990).
    Article CAS Google Scholar
  27. Plaxco,K. W., Simons,K. T. & Baker,D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985–994 (1998).
    Article CAS Google Scholar
  28. Schlunegger,M. P., Bennett,M. J. & Eisenberg,D. Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Adv. Protein Chem. 50, 61–122 (1997).
    Article CAS Google Scholar
  29. Landry,S. J., Jordan,R., McMacken,R. & Gierasch,L. M. Different conformations for the same polypeptide bound to chaperones DnaK and GroEL. Nature 355, 455–457 (1992).
    Article ADS CAS Google Scholar
  30. Laminet,A. A., Ziegelhoffer,T., Georgopoulos,C. & Pluckthun,A. The Escherichia coli heat shock proteins GroEL and GroES modulate the folding of the beta-lactamase precursor. EMBO J. 9, 2315–2319 (1990).
    Article CAS Google Scholar
  31. Vitanen,P. V., Donaldson,G. K., Lorimer,G. H., Lubben,T. H. & Gatenby,A. A. Complex interactions between the chaperonin 60 molecular chaperone and dihydrofolate reductase. Biochemistry 30, 9716–9723 (1991).
    Article Google Scholar
  32. Smith,K. E., Voziyan,P. A. & Fisher,M. T. Partitioning of rhodanese onto GroEL–chaperonin binds a reversibly oxidized form derived from the native protein. J. Biol. Chem. 273, 28677–28681 (1998).
    Article CAS Google Scholar
  33. Hayer-Hartl,M. K., Weber,F. & Hartl,F. U. Mechanism of chaperonin action: GroES binding and release can drive GroEL-mediated protein folding in the absence of ATP hydrolysis. EMBO J. 15, 6111–6121 (1996).
    Article CAS Google Scholar
  34. Bjellqvist,B., Pasquali,C., Ravier,F., Sanchez,J. C. & Hochstrasser,D. A nonlinear wide-range immobilized pH gradient for two-dimensional electrophoresis and its definition in a relevant pH scale. Electrophoresis 14, 1357–1365 (1993).
    Article CAS Google Scholar
  35. Gorg,A., Postel,W. & Gunther,S. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9, 531–546 (1988).
    Article CAS Google Scholar
  36. Fountoulakis,M. & Langen,H. Identification of proteins by matrix-assisted laser desorption ionization-mass spectrometry following in-gel digestion in low-salt, nonvolatile buffer and simplified peptide recovery. Anal. Biochem. 250, 153–156 (1997).
    Article CAS Google Scholar
  37. Altschul,S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
    Article CAS Google Scholar
  38. Wootton,J. & Federhen,S. Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17, 149–163 (1993).
    Article CAS Google Scholar
  39. Labedan,B. & Riley,M. Gene products of Escherichia coli: sequence comparisons and common ancestries. Mol. Biol. Evol. 12, 980–987 (1995).
    CAS PubMed Google Scholar
  40. Klein,P., Kanehisa,M. & DeLisi,C. The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta 815, 468–476 (1985).
    Article CAS Google Scholar
  41. Frishman,D. & Argos,P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 27, 329–335 (1997).
    Article CAS Google Scholar
  42. Nakashima,H., Nishikawa,K. & Ooi,T. The folding type of a protein is relevant to the amino acid composition. J. Biochem. 99, 153–162 (1986).
    Article CAS Google Scholar
  43. Huynen,M. et al. Homology-based fold predictions for Mycoplasma genitalium proteins. J. Mol. Biol. 280, 323–326 (1998).
    Article CAS Google Scholar
  44. Frishman,D. & Mewes,H. W. Pedantic genome analysis. Trends Genet. 13, 415–416 (1997).
    Article CAS Google Scholar
  45. Bairoch,A. & Apweiler,R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 26, 38–42 (1998).
    Article CAS Google Scholar
  46. Karp,P. D., Riley,M., Paley,S. M., Pellegrini-Toole,A. & Krummenacker,M. EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 26, 50–53 (1998).
    Article CAS Google Scholar
  47. Meyer,S. L. Data Analysis for Scientists and Engineers. (Wiley, New York, 1975).
  48. Zhang,G. & Darst,S. A. Structure of the Escherichia coli RNA polymerase alpha subunit amino terminal domain. Science 281, 262–266 (1998).
    Article ADS CAS Google Scholar
  49. Nicholls,A., Sharp,K. A. & Honig,B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991).
    Article CAS Google Scholar

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