Direct observation of ultrafast folding and denatured state dynamics in single protein molecules

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 44, 2009, Pages 18569-18574

  Neuweiler, Hannes ^a   Johnson, Christopher M ^a   Fersht, Alan R ^a,b  

^a MRC CENTRE FOR PROTEIN ENGINEERING   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Fluorescence correlation spectroscopy; Intrachain diffusion; Photoinduced electron transfer; Protein folding; Speed limit

Indexed keywords

ARTICLE; ELECTRON TRANSPORT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN INTERACTION; TEMPERATURE MEASUREMENT;

ELECTRONS; KINETICS; LIGHT; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOLVENTS; SPECTROMETRY, FLUORESCENCE;

EID: 73249133356     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0910860106     Document Type: Article

References (33)

1. Kapanidis AN, Strick T (2009) Biology, one molecule at a time. Trends Biochem Sci 34:234-243.
2. Schuler B, Eaton WA (2008) Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 18:16-26.
3. Fersht AR, Daggett V (2002) Protein folding and unfolding at atomic resolution. Cell 108:573-582.
4. Magde D, Webb WW, Elson E (1972) Thermodynamic fluctuations in a reacting system: Measurement by fluorescence correlation spectroscopy. Phys Rev Lett 29:705-708.
5. Eigen M, Rigler R (1994) Sorting single molecules: Application to diagnostics and evolutionary biotechnology. Proc Natl Acad Sci USA 91:5740-5747.
6. Hess ST, Huang S, Heikal AA, Webb WW (2002) Biological and chemical applications of fluorescence correlation spectroscopy: A review. Biochemistry 41:697-705.
7. Neuweiler H, et al. (2002) Detection of individual p53-autoantibodies by using quenched peptide-based molecular probes. Angew Chem Int Ed Engl 41:4769-4773.
8. Doose S, Neuweiler H, Sauer M (2009) Fluorescence quenching by photoinduced electron transfer: A reporter for conformational dynamics of macromolecules. Chemphyschem 10:1389-1398.
9. Neuweiler H, Doose S, Sauer M (2005) A microscopic view of miniprotein folding: Enhanced folding efficiency through formation of an intermediate. Proc Natl Acad Sci USA 102:16650-16655.
10. Neuweiler H, et al. (2009) Downhill versus barrier-limited folding of BBL 2: Mechanistic insights from kinetics of folding monitored by independent tryptophan probes. J Mol Biol 387:975-985.
11. Ferguson N, et al. (2005) Ultra-fast barrier-limited folding in the peripheral subunitbinding domain family. J Mol Biol 353:427-446.
12. Neuweiler H, et al. (2009) The folding mechanism of BBL: Plasticity of transition state structure observed within an ultrafast folding protein family. J Mol Biol 390:1060-1073.
13. Ansari A, Jones CM, Henry ER, Hofrichter J, Eaton WA (1992) The role of solvent viscosity in the dynamics of protein conformational changes. Science 256:1796-1798.
14. Hagen SJ, Qiu L, Pabit SA (2005) Diffusional limits to the speed limit of protein folding: Fact or friction? J Phys: Condens Matter 17:S1503-S1514.
15. Neuweiler H, Löllmann M, Doose S, Sauer M (2007) Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy. J Mol Biol 365:856-869.
16. Ferguson N, et al. (2005) Simulation and experiment at high temperatures: Ultrafast folding of a thermophilic protein by nucleation-condensation. JMol Biol 347:855-870.
17. Sharpe TD, Ferguson N, Johnson CM, Fersht AR (2008) Conservation of transition state structure in fast folding peripheral subunit-binding domains. J Mol Biol 383:224-237.
18. Mayor U, Grossmann JG, Foster NW, Freund SM, Fersht AR (2003) The denatured state of Engrailed Homeodomain under denaturing and native conditions. J Mol Biol 333:977-991.
19. Religa TL, Markson JS, Mayor U, Freund SM, Fersht AR (2005) Solution structure of a protein denatured state and folding intermediate. Nature 437:1053-1056.
20. Kohn JE, et al. (2004) Random-coil behavior and the dimensions of chemically unfolded proteins. Proc Natl Acad Sci USA 101:12491-12496.
21. Deniz AA, et al. (2000) Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc Natl Acad Sci USA 97:5179-5184.
22. Nettels D, Gopich IV, Hoffmann A, Schuler B (2007) Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc Natl Acad Sci USA 104:2655-2660.
23. Krieger F, Fierz B, Bieri O, Drewello M, Kiefhaber T (2003) Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J Mol Biol 332:265-274.
24. Huang F, Nau WM (2003) A conformational flexibility scale for amino acids in peptides. Angew Chem Int Ed Engl 42:2269-2272.
25. Szabo A, Schulten K, Schulten Z (1980) First passage time approach to diffusion controlled reactions. J Chem Phys 72:4350-4357.
26. Fierz B, Kiefhaber T (2007) End-to-end vs interior loop formation kinetics in unfolded polypeptide chains. J Am Chem Soc 129:672-679.
27. Lide DR (1994) CRC Handbook of Chemistry and Physics (CRC Press, Boca Raton, FL).
28. Bieri O, et al. (1999) The speed limit for protein folding measured by triplet-triplet energy transfer. Proc Natl Acad Sci USA 96:9597-9601.
29. Kubelka J, Hofrichter J, Eaton WA (2004) The protein folding 'speed limit.' Curr Opin Struct Biol 14:76-88.
30. Ferguson N, Schartau PJ, Sharpe TD, Sato S, Fersht AR (2004) One-state downhill versus conventional protein folding. J Mol Biol 344:295-301.
31. Huang F, Ying L, Fersht AR (2009) Direct observation of barrier limited folding of BBL by single-molecule fluorescence resonance energy transfer. Proc Natl Acad Sci USA 106:16239-16244.
32. Krichevsky O, Bonnet G (2002) Fluorescence correlation spectroscopy: The technique and its applications. Rep Prog Phys 65:251-297.
33. Vaiana AC, et al. (2003) Fluorescence quenching of dyes by tryptophan: Interactions at atomic detail from combination of experiment and computer simulation. J Am Chem Soc 125:14564-14572.