Protein folding in the cell: Reshaping the folding funnel

Trends in Biochemical Sciences

Volumn 29, Issue 10, 2004, Pages 527-534

  Clark, Patricia L ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; CHAPERONE; HEAT SHOCK PROTEIN 60; POLYPEPTIDE;

CELL ACTIVITY; CONFORMATION; DILUTION; ENERGY; IN VITRO STUDY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; REVIEW; RIBOSOME;

EID: 4644285228     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2004.08.008     Document Type: Article

References (55)

1. A. Mitraki Quasi-irreversibility in the unfolding-refolding transition of phosphoglycerate kinase induced by guanidine hydrochloride Eur. J. Biochem. 163 1987 29 34
2. W. Harrington, and N.V. Rao Collagen structure in solution. I. Kinetics of helix regeneration in single chain gelatins Biochemistry 9 1970 3714 3724
3. A. Mitraki, and J. King Protein folding intermediates and inclusion body formation Biotechnology 7 1989 690 697
4. R. Wetzel For protein misassembly, it's the 'I' decade Cell 86 1996 699 702
5. C.B. Anfinsen, and E. Haber Studies on the reduction and re-formation of protein disulphide bonds J. Biol. Chem. 236 1961 1361 1363
6. R.F. Goldberger Acceleration of reactivation of reduced bovine pancreatic ribonuclease by a microsomal system from rat liver J. Biol. Chem. 238 1963 628 635
7. F.U. Hartl Molecular chaperones in protein folding: the art of avoiding sticky situations Trends Biochem. Sci. 19 1994 20 25
8. J. King Thermolabile folding intermediates: inclusion body precursors and chaperonin substrates FASEB J. 10 1996 57 66
9. S.W. Raso, and J. King Protein folding and human disease R.H. Pain Mechanisms of Protein Folding 2000 Oxford University Press 406 422
10. J. London Renaturation of Escherichia coli tryptophanase after exposure to 8 M urea. Evidence for the existence of nucleation centers Eur. J. Biochem. 47 1974 409 415
11. M.A. Speed Multimeric intermediates in the pathway to the aggregated inclusion body state for P22 tailspike polypeptide chains Protein Sci. 4 1995 900 908
12. D.J. Hulmes Building collagen molecules, fibrils, and suprafibrillar structures J. Struct. Biol. 137 2002 2 10
13. 1-antitrypsin Biochemistry 32 1993 500 508
14. C.M. Dobson The structural basis of protein folding and its links with human disease Philos. Trans. R. Soc. Lond. B. Biol. Sci. 356 2001 133 145
15. R. Tycko Progress towards a molecular-level structural understanding of amyloid fibrils Curr. Opin. Struct. Biol. 14 2004 96 103
16. H.A. Lashuel α-Synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils J. Mol. Biol. 322 2002 1089 1102
17. K.A. Dill Theory for the folding and stability of globular proteins Biochemistry 24 1985 1501 1509
18. J.D. Bryngelson, and P.G. Wolynes Spin glasses and the statistical mechanics of protein folding Proc. Natl. Acad. Sci. U. S. A. 84 1987 7524 7528
19. S.D. Betts Mutational effects on inclusion body formation Adv. Protein Chem. 50 1997 243 264
20. F.A.O. Marston The purification of eukaryotic polypeptides synthesized in Escherichia coli Biochem. J. 240 1986 1 12
21. S. Istrail Lattice simulations of aggregation funnels for protein folding J. Comput. Biol. 6 1999 143 162
22. R.I. Dima, and D. Thirumalai Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics Protein Sci. 11 2002 1036 1049
23. A.V. Smith, and C.K. Hall Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model J. Mol. Biol. 312 2001 187 202
24. Y. Liu, and D. Eisenberg 3D domain swapping: as domains continue to swap Protein Sci. 11 2002 1285 1299
25. K.A. Dill, and H.S. Chan From Levinthal to pathways to funnels Nat. Struct. Biol. 4 1997 10 19
26. C.R. Locker, and R. Hernandez A minimalist model protein with multiple folding funnels Proc. Natl. Acad. Sci. U. S. A. 98 2001 9074 9079
27. F. Massi, and J.E. Straub Energy landscape theory for Alzheimer's amyloid β-peptide fibril elongation Proteins Struct. Funct. Genet. 42 2001 217 229
28. A. Mitraki Global suppression of protein folding defects and inclusion body formation Science 253 1991 54 58
29. W.C. Wigley A protein sequence that can encode native structure by disfavoring alternate conformations Nat. Struct. Biol. 9 2002 381 388
30. J.S. Richardson, and D.C. Richardson Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation Proc. Natl. Acad. Sci. U. S. A. 99 2002 2754 2759
31. S.M. van der Vies Conformational states of ribulose-bisphosphate carboxylase and their interaction with chaperonin 60 Biochemistry 31 1992 3635 3644
32. R.J. Ellis, and F.U. Hartl Protein folding in the cell: competing models of chaperonin function FASEB J. 10 1996 20 26
33. A. Baumketner Effects of confinement in chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape J. Mol. Biol. 332 2003 701 713
34. R.J. Ellis Macromolecular crowding: obvious but underappreciated Trends Biochem. Sci. 26 2001 597 604
35. S.S. Jaswal Energetic landscape of α-lytic protease optimizes longevity through kinetic stability Nature 415 2002 343 346
36. F.U. Hartl, and M. Hayer-Hartl Molecular chaperones in the cytosol: from nascent chain to folded protein Science 295 2002 1852 1858
37. B. Bukau Getting newly synthesized proteins into shape Cell 101 2000 119 122
38. J. Frydman Folding of newly translated proteins in vivo: the role of molecular chaperones Annu. Rev. Biochem. 70 2001 603 647
39. A.N. Fedorov, and T.O. Baldwin Process of biosynthetic protein folding determines the rapid formation of native structure J. Mol. Biol. 294 1999 579 586
40. R. Seckler Reconstitution of the thermostable trimeric phage P22 tailspike protein from denatured chains in vitro J. Biol. Chem. 264 1989 11750 11753
41. A.A. Komar Cotranslational folding of globin J. Biol. Chem. 272 1997 10646 10651
42. A.V. Nicola Co-translational folding of an alphavirus capsid protein in the cytosol of living cells Nat. Cell Biol. 1 1999 341 345
43. L.I. Malkin, and A. Rich Partial resistance of nascent polypeptide chains to proteolytic digestion due to ribosomal shielding J. Mol. Biol. 26 1967 329 346
44. C.A. Woolhead Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins Cell 116 2004 725 736
45. C. Bernabeu, and J.A. Lake Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: immune mapping of the nascent chain Proc. Natl. Acad. Sci. U. S. A. 79 1982 3111 3115
46. P.L. Clark, and J. King A newly synthesized, ribosome-bound polypeptide chain adopts conformations dissimilar from early in vitro refolding intermediates J. Biol. Chem. 276 2001 25411 25420
47. J. Frydman Co-translational domain folding as the structural basis for the rapid de novo folding of firefly luciferase Nat. Struct. Biol. 6 1999 697 705
48. C.C. Chow Chain length dependence of apomyoglobin folding: structural evolution from misfolded sheets to native helices Biochemistry 42 2003 7090 7099
49. S.E. Jackson, and A.R. Fersht Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition Biochemistry 30 1991 10428 10433
50. T. Schindler Extremely rapid protein folding in the absence of intermediates Nat. Struct. Biol. 2 1995 663 673
51. T.R. Sosnick Molecular collapse: the rate-limiting step in two-state cytochrome c folding Proteins Struct. Funct. Genet. 24 1996 413 426
52. R. Schwartz Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues Protein Sci. 10 2001 1023 1031
53. F. Chiti Kinetic partitioning of protein folding and aggregation Nat. Struct. Biol. 9 2002 137 143
54. J. Klein-Seetharaman Long-range interactions within a nonnative protein Science 295 2002 1719 1722
55. J.N. Onuchic Theory of protein folding: the energy landscape perspective Annu. Rev. Phys. Chem. 48 1997 545 600