Nucleation mechanisms in protein folding

Current Opinion in Structural Biology

Volumn 7, Issue 1, 1997, Pages 3-9

  Fersht, Alan R ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN INHIBITOR; MUTANT PROTEIN;

AMINO TERMINAL SEQUENCE; CELL NUCLEUS; GENETIC ENGINEERING; KINETICS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; REVIEW; THEORY;

EID: 0031043161     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80002-4     Document Type: Article

References (73)

1. Bryngelson JD, Wolynes PG. Spin-glasses and the statistical-mechanics of protein folding. Proc Natl Acad Sci USA. 84:1987;7524-7528.
2. Shakhnovich EI, Farztdinov G, Gutin AM, Karplus M. Protein folding bottlenecks - a lattice Monte-Carlo simulation. Phys Rev Lett. 67:1991;1665-1668.
3. Skolnick J, Kolinski A. Dynamic Monte-Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J Mol Biol. 221:1991;499-531.
4. Miller R, Danko CA, Fasolka MJ, Balazs AC, Chan H, Dill KA. Folding kinetics of proteins and copolymers. J Chem Phys. 96:1992;768-780.
5. Camacho CJ, Thirumalai D. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA. 90:1993;6369-6372.
6. Abkevich VI, Gutin AM, Shakhnovich EI. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33:1994;10026-10036.
7. Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 369:1994;248-251.
8. Abkevich VI, Gutin AM, Shakhnovich EI. Domains in folding of model proteins. Protein Sci. 4:1995;1167-1177.
9. Dill KA, Bromberg S, Yue KZ, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:1995;561-602.
10. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci USA. 92:1995;3626-3630.
11. Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. A test of lattice protein folding algorithms. Proc Natl Acad Sci USA. 92:1995;325-329.
12. Karplus M, Sali A. Theoretical-studies of protein-folding and unfolding. Curr Opin Struct Biol. 5:1995;58-73.
13. Caflisch A, Karplus M. Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. J Mol Biol. 252:1995;672-708.
14. Li AJ, Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol. 257:1996;412-429.
15. Daggett V, Li AJ, Itzhaki LS, Otzen DE, Fersht AR. Structure of the transition-state for folding of a protein-derived from experiment and simulation. J Mol Biol. 257:1996;430-440.
16. Levinthal C. Are there pathways for protein folding? J Chem Phys. 85:1968;44-45.
17. Tsong TY, Baldwin RL, Elson EL. Properties of the refolding and unfolding reactions of ribonuclease A. Proc Natl Acad Sci USA. 69:1972;1809-1812.
18. Ptitsyn OB. Stage mechanism of the self-organization of protein molecules. Dokl Acad Nauk. 210:1973;1213-1215.
19. Ptitsyn OB. Kinetic and equilibrium intermediates in protein folding. Protein Eng. 7:1994;593-596.
20. Kim PS, Baldwin RL. Intermediates in the folding reactions of small proteins. Annu Rev Biochem. 59:1990;631-660.
21. Karplus M, Weaver DL. Protein folding dynamics - the diffusion-collision model and experimental data. Protein Sci. 3:1994;650-668.
22. Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA. 70:1973;697-701.
23. Wetlaufer DB. Nucleation in protein folding - confusion of structure and process. Trends Biochem Sci. 15:1990;414-415.
24. Ptitsyn O. How molten is the molten globule? Nat Struct Biol. 3:1996;488-490.
25. Brandts JF, Halvorson HR, Brennan M. Consideration of the possibility that the slow step in protein denaturation reactions is due to Cis - Trans isomerism of proline residues. Biochemistry. 14:1975;4953-4963.
26. Kim PS, Baldwin RL. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem. 51:1982;459-489.
27. Jackson SE, Fersht AR. Folding of chymotrypsin inhibitor-2.1. evidence for a two-state transition. Biochemistry. 30:1991;10428-10435.
28. Jackson SE, Fersht AR. Folding of chymotrypsin inhibitor-2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding. Biochemistry. 30:1991;10436-10443.
29. Alexander P, Orban J, Bryan P. Kinetic analysis of folding and unfolding the 56-amino acid IgG-binding domain of streptococcal protein-G. Biochemistry. 31:1992;7243-7248.
30. Viguera AR, Martinez JC, Filimonov VV, Mateo PL, Serrano L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry. 33:1994;2142-2150.
31. Sosnick TR, Mayne L, Hiller R, Englander SW. The barriers in protein folding. Nat Struct Biol. 1:1994;149-156.
32. Kuszewski J, Clore GM, Gronenborn AM. Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G. Protein Sci. 3:1994;1945-1952.
33. Kragelund BB, Robinson CV, Knudsen J, Dobson CM, Poulsen FM. Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein. Biochemistry. 34:1995;7217-7224.
34. Schindler TS, Herrier M, Marahiel MA, Schmid FX. Extremely rapid folding in the absence of intermediates. Nat Struct Biol. 2:1995;663-673.
35. Huang GS, Oas TG. Submillisecond folding of monomeric lambda repressor. Proc Natl Acad Sci USA. 92:1995;6878-6882.
36. Villegas V, Azuaga A, Catasus LI, Reverter D, Mateo PL, Avilés FX, Serrano L. Evidence for a two-state transition in the folding process of the activation domain of human procarboxypeptidase A2. Biochemistry. 34:1995;15105-15110.
37. Panchenko AR, Lutheyschulten Z, Wolynes PG. Foldons, protein structural modules, and exons. Proc Natl Acad Sci USA. 93:1996;2008-2013.
38. Fersht AR. Characterizing transition states in protein folding: an essential step in the puzzle. Curr Opin Struct Biol. 5:1995;79-84.
39. Matthews JM, Fersht AR. Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: observation of Hammond behavior for the gross structure of the transition state and anti-Hammond behavior for structural elements for unfolding folding of barnase. Biochemistry. 34:1995;6805-6814.
40. Itzhaki LS, Otzen DE, Fersht AR. The structure of the transition-state for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods - evidence for a nucleation-condensation mechanism for protein-folding. J Mol Biol. 254:1995;260-288.
41. Fersht AR. Protein folding and stability - the pathway of folding of barnase. FEBS Lett. 325:1993;5-16.
42. Lopez-Hernandes I, Serrano L. Structure of the transition state for folding of the 129-amino acid protein CheY resembles that of the smaller protein, C12. Fold Des. 2:1996;43-55.
43. Viguera AR, Serrano L, Wilmanns M. Different folding transition-states may result in the same native structure. Nat Struct Biol. 3:1996;874-880.
44. Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding - a lattice model study of the requirements for folding to the native state. J Mol Biol. 235:1994;1614-1636.
45. Guo Z, Thirumalai D. Kinetics and thermodynamics of folding of a de-novo designed 4- helix bundle protein. J Mol Biol. 263:1996;323-343.
46. Wolynes PG, Lutheyschulten Z, Onuchic JN. Fast folding experiments and the topography of protein folding energy landscapes. Chem Biol. 3:1996;425-432.
47. Otzen DE, Itzhaki LS, Elmasry NF, Jackson SE, Fersht AR. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci USA. 91:1994;10422-10425.
48. Gay GD, Ruiz-Sanz J, Neira JL, Itzhaki LS, Fersht AR. Folding of a nascent polypeptide chain in vitro: cooperative formation of structure in a protein module. Proc Natl Acad Sci USA. 92:1995;3683-3686.
49. Itzhaki LS, Neira JL, Ruizsanz J, Gay GD, Fersht AR. Search for nucleation sites in smaller fragments of chymotrypsin inhibitor-2. J Mol Biol. 254:1995;289-304.
50. Bryngelson JD, Wolynes PG. A simple statistical field-theory of heteropolymer collapse with application to protein folding. Biopolymers. 30:1990;1-2.
51. Shakhnovich E, Abkevich V, Ptitsyn O. Conserved residues and the mechanism of protein folding. Nature. 379:1996;96-98.
52. Guo ZY, Thirumalai D. Kinetics of protein folding: nucleation mechanism, time scales, and pathways. Biopolymers. 36:1995;83-102.
53. Gutin AM, Abkevich VI, Shakhnovich EI. Is burst hydrophobic collapse necessary for protein folding? Biochemistry. 34:1995;3066-3076.
54. Thirumalai D, Guo ZY. Nucleation mechanism for protein folding and theoretical predictions for hydrogen-exchange labeling experiments. Biopolymers. 35:1995;137-140.
55. Thirumalai D. From minimal models to real proteins - time scales for protein-folding kinetics. J Phys I. 5:1995;1457-1467.
56. Thirumalai D, Guo ZY. Nucleation mechanism for protein-folding and theoretical predictions for hydrogen-exchange labeling experiments. Biopolymers. 35:1995;137-140.
57. Fersht AR. Dissection of the structure and activity of the tyrosyl-tRNA Synthetase by Site-Directed Mutagenesis. Biochemistry. 26:1987;8031-8037.
58. Neira JL, Davis B, Prat Gay GD, Ladurner AG, Buckle AM, Fersht A. Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary fragments of cleaved chymotrypsin inhibitor 2. Direct evidence for a nucleation mechanism. Fold Des. 1:1996;189-208.
59. Go N. Theoretical studies of protein folding. Annu Rev Biophys Bioeng. 12:1983;183-210.
60. Govindarajan S, Goldstein RA. Optimal local propensities for model proteins. Proteins. 22:1995;413-418.
61. Muñoz V, Cronet P, López-Hernández E, Serrano L. Analysis of the effect of local interactions in protein stability. Fold Des. 1:1996;167-178.
62. Viguera AR, Villegas V, Avilés FX, Serrano L. Favourable, native-like helical local interactions can accelerate protein folding. Fold Des. 1:1996;23-33.
63. Creighton TE. Protein folding: an unfolding story. Curr Biol. 5:1995;353-356.
64. Fersht AR. Optimization of rates of protein-folding - the nucleation- condensation mechanism and its implications. Proc Natl Acad Sci USA. 92:1995;10869-10873.
65. Fersht AR. Catalysis, binding and enzyme-substrate complementarity. Proc R Soc London B. 365:1974;397-407.
66. Bryngelson JD, Wolynes PG. Intermediates and barrier crossing in a random energy-model (with applications to protein folding). J Phys Chem. 93:1989;6902-6915.
67. Kippen AD, Fersht AR. Analysis of the mechanism of assembly of cleaved barnase from two peptide fragments and its relevance to the folding pathway of uncleaved barnase. Biochemistry. 34:1995;1464-1468.
68. Gay GD, Ruiz-Sanz J, Davis B, Fersht AR. The structure of the transition-state for the association of 2 fragments of the barley chymotrypsin inhibitor-2 to generate native-like protein - implications for mechanisms of protein-folding. Proc Natl Acad Sci USA. 91:1994;10943-10946.
69. Finkelstein AV, Galzitskaya OV, Badretdinov AY. A folding pathway solving Levinthal's paradox. Progr Biophys Mol Biol Suppl. 65:1996;53-53.
70. Arcus VL, Vuilleumier S, Freund SMV, Bycroft M, Fersht AR. Toward solving the folding pathway of barnase; The complete backbone C-13, N-15, and H-1 NMR assignments of its pH-denatured state. Proc Natl Acad Sci USA. 91:1994;9412-9416.
71. Freund S, Wong KB, Fersht AR. Initiation sites of protein-folding by NMR analysis. Proc Natl Acad Sci USA. 93:1996;10600-10603.
72. Wong KB, Freund S, Fersht AR. Cold denaturation of barstar - H-1, N-15 and C-13 NMR assignment and characterization of residual structure. J Mol Biol. 259:1996;805-818.
73. Dinner AR, Sali A, Karplus M. The folding mechanism of larger model proteins - role of native structure. Proc Natl Acad Sci USA. 93:1996;8356-8361.