A simple model of chaperonin-mediated protein folding

Proteins: Structure, Function and Genetics

Volumn 24, Issue 3, 1996, Pages 345-351

  Chan, Hue Sun ^a   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

chaperone action; energy landscape; hydrophobic interaction; kinetic traps; lattice models; multiple folding pathways

Indexed keywords

CHAPERONIN;

ARTICLE; CALCULATION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CATALYSIS; CHAPERONINS; KINETICS; MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 0002617993     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199603)24:3<345::AID-PROT7>3.0.CO;2-F     Document Type: Article

References (37)

1. Pelham, H.R.B. Speculations on the functions of the major heat shock and glucose-regulated proteins. Cell 46:959-961, 1986.
2. Ellis, R.J., Laskey, H.A., Lorimer, G.H. (eds.). "Molecular Chaperones." London: The Royal Society and Chapman & Hall, 1993; and references therein.
3. Landry, S.J., Gierasch, L.M. Polypeptide interactions with molecular chaperones and their relationship to in vivo protein folding. Annu. Rev. Biophys. Biomol. Struct. 23:645-669, 1994; and references therein.
4. Hlodan, R., Hartl, F.U. How the protein folds in the cell. In: "Mechanisms of Protein Folding." Pain, R.H. (ed.). New York: Oxford University Press, 1994:194-228; and references therein.
5. Thirumalai, D. Theoretical perspectives on in vitro and in vivo protein folding. In: "Statistical Mechanics, Protein Structure, and Protein-Substrate Interactions." Doniach, S. (ed.). New York: Plenum, 1994:115-134.
6. Burston, S.G., Sleigh, R., Halsall, D.J., Smith, C.J., Holbrook, J.J., Clarke, A.R. The influence of chaperonins on protein folding. A mechanism for increasing the yield of the native form. Ann N.Y. Acad. Sci. 672:1-9, 1992.
7. Jackson, G.S., Staniforth, R.A., Halsall, D.J., Atkinson, T., Holbrook, J.J., Clarke, A.R., Burston, S.G. Binding and hydrolysis of nucleotides in the chaperonin catalytic cycle: Implications for the mechanism of assisted protein folding. Biochemistry 32:2554-2563, 1993.
8. Staniforth, R.A., Burston, S.G., Atkinson, T., Clarke, A.R. Affinity of chaperonin-60 for a protein substrate and its modulation by nucleotides and chaperonin-10. Biochem. J. 300:651-658, 1994.
9. Todd, M.J., Viitanen, P.V., Lorimer, G.H. Dynamics of the chaperonin ATPase cycle: Implications for facilitated protein folding. Science 265:659-666, 1994.
10. Weissman, J.S., Kashi, Y., Fenton, W.A., Horwich, A.L. GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms. Cell 78: 693-702, 1994.
11. Peralta, D., Hartman, D.J., Hoogenraad, N.J., Høj, P.B. Generation of a stable folding intermediate which can be rescued by the chaperonins GroEL and GroES. FEBS Lett. 339:45-49, 1994.
12. Chen, S., Roseman, A.M., Hunter, A.S., Wood, S.P., Burston, S.G., Ranson, N.A., Clarke, A.R., Saibil, H.R. Location of a folding protein and shape changes in GroEL-GroES complexes imaged by cryo-electron microscopy. Nature 371:261-264, 1994.
13. Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D.C., Joachimiak, A., Horwich, A.L., Sigler, P.B. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371:578-586, 1994.
14. Martin, J., Langer, T., Boteva, R., Schramel, A., Horwich, A.L , Hartl, F.-U. Chaperonin-mediated protein folding at the surface of GroEL through a 'molten globule'-like intermediate. Nature 352:36-42, 1991.
15. Saibil, H.R., Zheng, D., Roseman, A.M., Hunter, A.S., Watson, G.M.F., Chen, S., auf der Mauer, A., O'Hara, B.P., Wood, S.P., Mann, W.H., Barnett, L.K., Ellis, R.J. ATP induces large quaternary rearrangements in a cage-like chaperonin structure. Curr. Biol. 3:265-273, 1993.
16. Creighton, T.E. Unfolding protein folding. Nature 352:17-18, 1991.
17. Agard, D.A. To fold or not to fold. . . . Science 260:1903-1904, 1993.
18. Chan, H.S., Dill, K.A. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238-9257, 1994.
19. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., Chan, H.S. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:561-602, 1995.
20. Chan, H.S., Dill, K.A. Energy landscape and the collapse dynamics of homopolymers. J. Chem. Phys. 99:2116-2127, 1993.
21. Camacho, C.J., Thirumalai, D. Kinetics and thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. USA 90:6369-6372, 1993.
22. Chan, H.S., Dill, K.A. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20:447-490, 1991.
23. Socci, N.D., Onuchic, J.N. Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101:1519-1528, 1994.
24. Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I. Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052-6062, 1994.
25. Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes, P.G. Funnels, pathways and the energy landscape of protein folding: A synthesis. Proteins 21:167-195, 1995.
26. Karplus, M , Šali, A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73, 1995.
27. Todd, M.J., Lorimer, G.H., Thirumalai, D. Chaperonin facilitated protein folding: Optimization of rate and yield by an iterative annealing mechanism. Proc. Natl. Acad. Sci. USA, in press.
28. Gulukota, K., Wolynes, P.G. Statistical mechanics of kinetic proofreading in protein folding in vivo. Proc. Natl. Acad. Sci. USA 91:9292-9296, 1994.
29. Sfatos, C.D., Gutin, A.M., Abkevich, V.I., Shakhnovich, E.I. Simulations of chaperone assisted folding. Biochemistry, in press.
30. Tian, G., Vainberg, I.E., Tap, W.D., Lewis, S.A., Cowan, N.J. Specificity in chaperonin-mediated protein folding. Nature 375:250-253, 1995.
31. Gray, T.E., Fersht, A.R. Refolding of barnase in the presence of GroE. J. Mol. Biol. 232:1197-1207, 1993.
32. Laminet, A.A., Ziegelhoffer, T., Georgopoulos, C., Plückthun, A. The Escherichia coli heat shock proteins GroEL and GroES modulate the folding of β-lactamase precursor. EMBO J. 9:2315-2319, 1990.
33. Goloubinoff, P., Christeller, J.T., Gatenby, A.A., Lorimer, G.H. Reconstitution of active dimeric ribulose bisphosphate carboxylase from an unfolded state depends on two chaperonin proteins and Mg-ATP. Nature 342:884-889, 1989.
34. Hemmingsen, S.M., Woolford, C., van der Vies, S.M., Tilly, K., Dennis, D.T., Georgopoulos, C.P., Hendrix, R.W., Ellis, R.J. Homologous plant and bacterial proteins chaperone oligomeric protein assembly. Nature 333:330-334, 1988.
35. Braig, K., Simon, M., Furuya, F., Hainfeld, J.F., Horwich, A.L. A polypeptide bound by the chaperonin GroEL is localized within a central cavity. Proc. Natl. Acad. Sci. USA 90:3978-3982, 1993.
36. Zahn, R., Spitzfaden, C., Ottiger, M., Wüthrich, K., Plückthun, A. Destabilization of the complete protein secondary structure on binding to the chaperone GroEL. Nature 368: 261-265, 1994.
37. Chan, H.S., Dill, K.A. "Sequence space soup" of proteins and copolymers. J. Chem. Phys. 95:3775-3787, 1991.