Early events in protein folding

Current Opinion in Structural Biology

Volumn 13, Issue 1, 2003, Pages 75-81

  Ferguson, Neil ^a   Fersht, Alan R ^a  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; PROTEIN;

MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; SIMULATION; SPECTROSCOPY;

EID: 0037308894     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00009-X     Document Type: Review

References (67)

1. Baldwin R.L. Protein chemistry - Pieces of the folding puzzle. Nature. 346:1990;409-410.
2. Jackson S.E. How do small single-domain proteins fold? Fold Des. 3:1998;R81-R91.
3. Nolting B., Golbik R., Fersht A.R. Submillisecond events in protein-folding. Proc. Natl. Acad. Sci. U.S.A. 92:1995;10668-10672.
4. Huang G.S., Oas T.G. Submillisecond folding of monomeric lambda-repressor. Proc. Natl. Acad. Sci. U.S.A. 92:1995;6878-6882.
5. Myers J.K., Oas T.G. Preorganized secondary structure as an important determinant of fast protein folding. Nat. Struct. Biol. 8:2001;552-558.
6. Spector S., Raleigh D.P. Submillisecond folding of the peripheral subunit-binding domain. J. Mol. Biol. 293:1999;763-768.
7. Fersht A: Structure And Mechanism In Protein Science: A Guide To Enzyme Catalysis And Folding. New York: Freeman; 1999.
8. Fersht A.R., Matouschek A., Serrano L. The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224:1992;771-782.
9. Burton R.E., Huang G.S., Daugherty M.A., Fullbright P.W., Oas T.G. Microsecond protein folding through a compact transition state. J. Mol. Biol. 263:1996;311-322.
10. Jager M., Nguyen H., Crane J.C., Kelly J.W., Gruebele M. The folding mechanism of a β-sheet: the WW domain. J. Mol. Biol. 311:2001;373-393.
11. Ferguson N., Johnson C.M., Macias M., Oschkinat H., Fersht A.R. Ultrafast folding of WW domains without structured aromatic clusters in the denatured state. Proc. Natl. Acad. Sci. U.S.A. 98:2001;13002-13007.
12. Mayor U., Johnson C.M., Daggett V., Fersht A.R. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. U.S.A. 97:2000;13518-13522.
13. Kuhlman B., Evans P.A., Raleigh D.P. Submillisecond folding of the N-terminal domain of the ribosomal protein L9. Biophys. J. 74:1998;A128.
14. Hagen S.J., Hofrichter J., Eaton W.A. Rate of intrachain diffusion of unfolded cytochrome c. J. Phys. Chem. B. 101:1997;2352-2365.
15. Kramers H.A. Physica. 4:1940;283-304.
16. Jacob M., Schmid F.X. Protein folding as a diffusional process. Biochemistry. 38:1999;13773-13779.
17. Hagen S.J., Eaton W.A. Two-state expansion and collapse of a polypeptide. J. Mol. Biol. 301:2000;1019-1027.
18. Qi P.X., Sosnick T.R., Englander S.W. The burst phase in ribonuclease A folding and solvent dependence of the unfolded state. Nat. Struct. Biol. 5:1998;882-884.
19. Sosnick T.R., Shtilerman M.D., Mayne L., Englander S.W. Ultrafast signals in protein folding and the polypeptide contracted state. Proc. Natl. Acad. Sci. U.S.A. 94:1997;8545-8550.
20. Chan H.S., Dill K.A. Polymer principles in protein-structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20:1991;447-490.
21. Bieri O., Wirz J., Hellrung B., Schutkowski M., Drewello M., Kiefhaber T. The speed limit for protein folding measured by triplet-triplet energy transfer. Proc. Natl. Acad. Sci. U.S.A. 96:1999;9597-9601.
22. Lapidus L.J., Eaton W.A., Hofrichter J. Measuring the rate of intramolecular contact formation in polypeptides. Biophys. J. 80:2001;721.
23. Szabo A., Schulten K., Schulten Z. First passage time approach to diffusion controlled reactions. J. Chem. Phys. 72:1980;4350-4357.
24. Lapidus L.J., Eaton W.A., Hofrichter J. Measuring dynamic flexibility of the coil state of a helix-forming peptide. J. Mol. Biol. 319:2002;19-25.
25. Huang C.Y., Klemke J.W., Getahun Z., DeGrado W.F., Gai F. Temperature-dependent helix-coil transition of an alanine based peptide. J. Am. Chem. Soc. 123:2001;9235-9238.
26. Lednev I.K., Karnoup A.S., Sparrow M.C., Asher S.A. Alpha-helix peptide folding and unfolding activation barriers: a nanosecond UV resonance Raman study. J. Am. Chem. Soc. 121:1999;8074-8086.
27. Lednev I.K., Karnoup A.S., Sparrow M.C., Asher S.A. Transient UV Raman spectroscopy finds no crossing barrier between the peptide alpha-helix and fully random coil conformation. J. Am. Chem. Soc. 123:2001;2388-2392.
28. Jas G.S., Eaton W.A., Hofrichter J. Effect of viscosity on the kinetics of alpha-helix and beta-hairpin formation. J. Phys. Chem. B. 105:2001;261-272.
29. Plaxco K.W., Millett I.S., Segel D.J., Doniach S., Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat. Struct. Biol. 6:1999;554-556.
30. Pollack L., Tate M.W., Darnton N.C., Knight J.B., Gruner S.M., Eaton W.A., Austin R.H. Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering. Proc. Natl. Acad. Sci. U.S.A. 96:1999;10115-10117.
31. Woenckhaus J., Kohling R., Thiyagarajan P., Littrell K.C., Seifert S., Royer C.A., Winter R. Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding. Biophys. J. 80:2001;1518-1523.
32. Chen H.M., Markin V.S., Tsong T.Y. pH-induced folding/unfolding of staphylococcal nuclease - determination of kinetic-parameters by the sequential-jump method. Biochemistry. 31:1992;1483-1491.
33. Wallenhorst W.F., Green S.M., Roder H. Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease. Biochemistry. 36:1997;5795-5805.
34. Panick G., Malessa R., Winter R., Rapp G., Frye K.J., Royer C.A. Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle X-ray scattering and Fourier-transform infrared spectroscopy. J. Mol. Biol. 275:1998;389-402.
35. Perl D., Holtermann G., Schmid F.X. Role of the chain termini for the folding transition state of the cold shock protein. Biochemistry. 40:2001;15501-15511.
36. Lapidus L.J., Eaton W.A., Hofrichter J. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl. Acad. Sci. U.S.A. 97:2000;7220-7225.
37. Hagen S.J., Carswell C.W., Sjolander E.M. Rate of intrachain contact formation in an unfolded protein: temperature and denaturant effects. J. Mol. Biol. 305:2001;1161-1171.
38. Thompson P.A., Munoz V., Jas G.S., Henry E.R., Eaton W.A., Hofrichter J. The helix-coil kinetics of a heteropeptide. J. Phys. Chem. B. 104:2000;378-389.
39. Thompson P.A., Eaton W.A., Hofrichter J. Laser temperature jump study of the helix⇔coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. Biochemistry. 36:1997;9200-9210.
40. Huang C.Y., Getahun Z., Wang T., DeGrado W.F., Gai F. Time-resolved infrared study of the helix-coil transition using C-13-labeled helical peptides. J. Am. Chem. Soc. 123:2001;12111-12112.
41. Huang C.Y., Getahun Z., Zhu Y.J., Klemke J.W., DeGrado W.F., Gai F. Helix formation via conformation diffusion search. J. Am. Chem. Soc. 99:2002;2788-2793.
42. Bryngelson J.D., Onuchic J.N., Socci N.D., Wolynes P.G. Funnels, pathways, and the energy landscape of protein-folding - a synthesis. Proteins. 21:1995;167-195.
43. Hummer G., Garcia A.E., Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins. 42:2001;77-84.
44. Hummer G., Garcia A.E., Garde S. Conformational diffusion and helix formation kinetics. Phys. Rev. Lett. 85:2000;2637-2640.
45. Leeson D.T., Gai F., Rodriguez H.M., Gregoret L.M., Dyer R.B. Protein folding and unfolding on a complex energy landscape. Proc. Natl. Acad. Sci. U.S.A. 97:2000;2527-2532.
46. Sabelko J., Ervin J., Gruebele M. Observation of strange kinetics in protein folding. Proc. Natl. Acad. Sci. U.S.A. 96:1999;6031-6036.
47. Clarke D.T., Doig A.J., Stapley B.J., Jones G.R. The alpha-helix folds on the millisecond time scale. Proc. Natl. Acad. Sci. U.S.A. 96:1999;7232-7237.
48. Kuwajima K., Yamaya H., Sugai S. The burst-phase intermediate in the refolding of β-lactoglobulin studied by stopped-flow circular dichroism and absorption spectroscopy. J. Mol. Biol. 264:1996;806-822.
49. Forge V., Hoshino M., Kuwata K., Arai M., Kuwajima K., Batt C.A., Goto Y. Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like β-sheet and non-native alpha-helix. J. Mol. Biol. 296:2000;1039-1051.
50. Kuwata K., Shastry R., Cheng H., Hoshino M., Batt C.A., Goto Y., Roder H. Structural and kinetic characterization of early folding events in beta-lactoglobulin. Nat. Struct. Biol. 8:2001;151-155.
51. Shastry R.M.C., Roder H., Kuwata K., Goto Y. Kinetic evidence for non-native A-helix at the N-terminus of β-lactoglobulin. Biophys. J. 80:2001;722.
52. Gulotta M., Gilmanshin R., Buscher T.C., Callender R.H., Dyer R.B. Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape. Biochemistry. 40:2001;5137-5143.
53. Colley C.S., Clark I.P., Griffiths-Jones S.R., George M.W., Searle M.S. Steady state and time-resolved IR spectroscopy of the native and unfolded states of bovine ubiquitin: protein stability and temperature-jump kinetic measurements of protein folding at low pH. Chem. Commun. 16:2000;1493-1494.
54. Munoz V., Thompson P.A., Hofrichter J., Eaton W.A. Folding dynamics and mechanism of β-hairpin formation. Nature. 390:1997;196-199.
55. Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998;985-994.
56. Ferguson N., Pires J.R., Toepert F., Johnson C.M., Pan Y.P., Daggett V., Oschkinat H., Fersht A.R. Using flexible loop mimetics to extend Phi-value analysis to secondary structure interactions. Proc. Natl. Acad. Sci. U.S.A. 98:2001;13008-13013.
57. Martinez J.C., Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat. Struct. Biol. 6:1999;1010-1016.
58. Riddle D.S., Grantcharova V.P., Santiago J.V., Alm E., Ruczinski I., Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 6:1999;1016-1024.
59. Lee J.C., Gray H.B., Winkler J.R. Cytochrome c′ folding triggered by electron transfer: fast and slow formation of four-helix bundles. Proc. Natl. Acad. Sci. U.S.A. 98:2001;7760-7764.
60. Burton R.S., Myers J.K., Oas T.G. Ultrafast folding of monomeric λ-repressor: experimental characterization and accurate theoretical prediction of folding rates. Biophys. J. 74:1998;A24.
61. Roder H., Colon W. Kinetic role of early intermediates in protein folding. Curr. Opin. Struct. Biol. 7:1997;15-28.
62. Ferguson N., Capaldi A.P., James R., Kleanthous C., Radford S.E. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J. Mol. Biol. 286:1999;1597-1608.
63. Capaldi A.P., Shastry M.C.R., Kleanthous C., Roder H., Radford S.E. Ultrarapid mixing experiments reveal that Im7 folds via an on-pathway intermediate. Nat. Struct. Biol. 8:2001;68-72.
64. Capaldi A.P., Kleanthous C., Radford S.E. Im7 folding mechanism: misfolding on a path to the native state. Nat. Struct. Biol. 9:2002;209-216.
65. Otzen D.E., Oliveberg M. Salt-induced detour through compact regions of the protein folding landscape. Proc. Natl. Acad. Sci. U.S.A. 96:1999;11746-11751.
66. Arcovito A., Gianni S., Brunori M., Travaglini-Allocatelli C., Bellelli A. Fast coordination changes in cytochrome c do not necessarily imply folding. J. Biol. Chem. 276:2001;41073-41078.
67. Jones C.M., Henry E.R., Hu Y., Chan C.K., Luck S.D., Bhuyan A., Roder H., Hofrichter J., Eaton W.A. Fast events in protein-folding initiated by nanosecond laser photolysis. Proc. Natl. Acad. Sci. U.S.A. 90:1993;11860-11864.