Probing the kinetics of single molecule protein folding

Biophysical Journal

Volumn 87, Issue 6, 2004, Pages 3633-3641

  Leite, Vitor B P ^a   Onuchic, José N ^b   Stell, George ^c   Wang, Jin ^c,d  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c STONY BROOK UNIVERSITY   (United States)

^d CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; DYNAMICS; ENERGY; FLUORESCENCE; KINETICS; MEASUREMENT; PROTEIN FOLDING; SIMULATION; TEMPERATURE DEPENDENCE; THEORY;

EID: 10044255342     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.046243     Document Type: Article

References (65)

1. Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052-6062.
2. Baldwin, R. L. 1995. The nature of protein-folding pathways-the classical versus the new view. J. Biomol. NMR. 5:103-109.
3. Berezhkovskii, A. M., A. Szabo, and G. H. Weiss. 1999. Theory of single-molecule fluorescence spectroscopy of two-state systems. Chem. Phys. 110:9145-9150.
4. Boczko, E. M., and C. L. Brooks. 1995. First-principles calculation of the folding free-energy of a 3-helix bundle protein. Science. 269:393-396.
5. Bryngelson, J. D., J. O. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein folding-a synthesis. Proteins Struct. Funct. Genet. 21:167-195.
6. Bryngelson, J. D., and P. G. Wolynes. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:6902-6915.
7. Chahine, J., H. Nymeyer, V. B. P. Leite, N. D. Socci, and J. N. Onuchic. 2002. Specific and nonspecific collapse in protein folding funnels. Phys. Rev. Lett. 88:168101.
8. Chan, H. S., and K.A. Dill. 1994. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238-9257.
9. Chan, H. S., S. Shimizu, and H. Kaya. 2004. Cooperativity principles in protein folding. Methods Enzymol. 380:350-379.
10. Cieplak, M., T. X. Hoang, and M. S. Li. 1999. Scaling of folding properties in simple models of proteins. Phys. Rev. Lett. 83:1684-1687.
11. Deniz, A. A., T. A. Laurence, G. S. Beligere, M. Dahan, A. B. Martin, D. S. Chemla, P. E. Dawson, P. G. Schultz, and S. Weiss. 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.
12. Eaton, W. A., V. Muñoz, P. A. Thompson, C.-K. Chan, and J. Hofrichter. 1997. Submillisecond kinetics of protein folding. Curr. Opin. Struct. Biol. 7:10-14.
13. Eaton, W. A., V. Muñoz, S. J. Hagen, G. S. Jas, L. J. Lapidus, E. R. Henry, and J. Hofrichter. 2000. Fast kinetics and mechanisms in protein folding. Annu. Rev. Biophys. Biomol. Struct. 29:327-359.
14. Frauenfelder, H., F. Parak, and R. D. Young. 1988. Conformational substrates in proteins. Annu. Rev. Biophys. Biophys. Chem. 17:451-479.
15. Frauenfelder, H., S. G. Sligar, and P. G. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598-1603.
16. Garcia-Mira, M. M., M. Sadqi, N. Fischer, J. M. Sanchez-Ruiz, and V. Muñoz. 2002. Experimental identification of downhill protein folding. Science. 298:2191-2195.
17. Goldstein, R. A., Z. A. Luthey-Schulten, and P. G. Wolynes. 1992. Optimal protein-folding codes from spin-glass theory. Proc. Natl. Acad. Sci. USA. 89:4918-4922.
18. Gopich, I., G. Hummer, and A. Szabo. 2003a. Theory and single molecule experiments. ACS Abst. Phys. 226:112-112.
19. Gopich, I. G., and A. Szabo. 2003b. Statistics of transitions in single molecule kinetics. J. Chem. Phys. 118:454-455.
20. Gutin, A. M., V. I. Abkevich, and E. I. Shakhnovich. 1996. Chain length scaling of protein folding time. Phys. Rev. Lett. 77:5433-5436.
21. Huang, G. S., and T. G. Oas. 1995. Submillisecond folding of monomeric λ-repressor. Proc. Natl. Acad. Sci. USA. 92:6878-6882.
22. Itzhaki, L. S., D. E. Otzen, and A. R. Fersht. 1995. 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. 254:260-288.
23. Jia, Y. W., D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser. 1999. Folding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem. Phys. 247:69-83.
24. Kaya, H., and H. S. Chan. 2000. Energetic components of cooperative protein folding. Phys. Rev. Lett. 85:4823-4826.
25. Kaya, H., and H. S. Chan. 2002. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding? J. Mol. Biol 315:899-909.
26. Kaya, H., and H. S. Chan. 2003a. Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins. 52:524-533.
27. Kaya, H., and H. S. Chan. 2003b. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? J. Mol. Biol. 326:91-931.
28. Kaya, H., and H. S. Chan. 2003c. Origins of chevron rollovers in non-two-state protein folding kinetics. Phys. Rev.Lett. 90:258104.
29. Kirkpatrick, T. R., D. Thirumalai, and P. G. Wolynes. 1989. Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. Phys. Rev. A. 40:1045-1054.
30. Klimov, D. K., and D. Thirumalai. 1998. Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics. J. Chem. Phys. 109:4119-4125.
31. Kuhlman, B., D. L. Luisi, P. A. Evans, and D. P. Raleigh. 1998. Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L91. J. Mol. Biol. 284:1661-1670.
32. Laurents, D. V., and R. L. Baldwin. 1998. Protein folding: matching theory and experiment. Biophys. J. 75:428-434.
33. Lee, C. L., C. T. Lin, G. Stell, and J. Wang. 2003. Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules. Phys. Rev. E. 67:041905.
34. Levinthal, C. 1969. Proceedings in Mossbauer Spectroscopy in Biological Systems. P. Debrunner, J. Tsubris, and E. Munck, editors. University of Illinois Press, Urbana, IL. 22.
35. Lipman, E. A., B. Schuler, O. Bakajin, and W. A. Eaton. 2003. Single-molecule measurement of protein folding kinetics. Science. 301:1233-1235.
36. Lu, H. P., L. Y. Xun, and X. S. Xie. 1998. Single-molecule enzymatic dynamics. Science. 282:1877-1882.
37. Moerner, W. E. 1996. High-resolution optical spectroscopy of single molecules in solids. Acc. Chem. Res. 29:563-571.
38. Nguyen, H., M. Jäger, A. Moretto, M. Gruebele, and J. W. Kelly. 2003. Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc. Natl. Acad. Sci. USA. 100:3948-3953.
39. Onuchic, J. N., J. Wang, and P. G. Wolynes. 1999. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions. Chem. Phys. 247:175-184.
40. Sabelko, J., J. Ervin, and M. Gruebele. 1999. Stretching lattice models of protein folding. Proc. Natl. Acad. Sci. USA. 96:6031-6036.
41. Sadqi, M., L. J. Lapidus, and V. Munoz. 2003. How fast is protein hydrophobic collapse? Proc. Natl. Acad. Sci. USA. 100:12117-12122.
42. Saven, J. G., J. Wang, and P. G. Wolynes. 1994. Kinetics of protein folding: the dynamics of globally connected rough energy landscapes with biases. J. Chem. Phys. 101:11037-11043.
43. Schenter, G. K., H. P. Lu, and X. S. Xie. 1999. Statistical analyses and theoretical models of single-molecule enzymatic dynamics. J. Phys. Chem. A. 103:10477-10488.
44. Schuler, B., E. A. Lipman, and W. A. Eaton. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:743-747.
45. Seno, F., C. Micheletti, A. Maritan, and J. R. Banavar. 1998. Variational approach to protein design and extraction of interaction potentials. Phys. Rev. Lett. 81:2172-2175.
46. Shakhnovich, E. I., and A. M. Gutin. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA. 90:7195-7199.
47. Shakhnovich, E. I., and A. M. Gutin. 1989. Relaxation to equilibrium in the random energy model. Europhys. Lett. 9:569-572.
48. Socci, N. D., and J. N. Onuchic. 1994. Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101:1519-1528.
49. Socci, N. D., and J. N. Onuchic. 1995. Kinetic and thermodynamic analysis of protein-like heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:4732-4744.
50. Socci, N. D., J. N. Onuchic, and P. G. Wolynes. 1996. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104:5860-5868.
51. Wang, J. 2003a. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys. Rev. Lett. 90:188101-1-188101- 4.
52. Wang, J. 2003b. Statistics, pathways and dynamics of single molecule protein folding. J. Chem. Phys. 118:952-958.
53. Wang, J., and P. G. Wolynes. 1995. Intermittency of single molecule reaction dynamics in fluctuating environments. Phys. Rev. Lett. 74:4317-4320.
54. Wang, J., J. G. Saven, and P. G. Wolynes. 1996. Kinetics in a globally connected, correlated random energy model. J. Chem. Phys. 105:11276-11284.
55. Wang, J., and P. G. Wolynes. 1999. Intermittency of activated events in single molecules: the reaction diffusion description. J. Chem. Phys. 110:4812-4819.
56. Wang, J. 2004a. The complex kinetics of protein folding in wide temperature ranges. Biophys. J. 87:2164-2171.
57. Wang, J., W. M. Huang, H. Y. Lu, and E. K. Wang. 2004b. Downhill kinetics of biomolecular interface binding: global connected scenario. Biophys. J. 87:2187-2194.
58. Wolynes, P. G., J. N. Onuchic, and D. Thirumalai. 1995. Navigating the folding routes. Science. 267:1619-1620.
59. Xia, X., and P. G. Wolynes. 2001. Microscopic theory of heterogeneity and nonexponential relaxations in supercooled liquids. Phys. Rev. Lett. 86:5526-5529.
60. Yang, H., and X. S. Xie. 2002a. Statistical approaches for probing single-molecule dynamics photon-by-photon. Chem. Phys. 284:423-437.
61. Yang, H., and X. S. Xie. 2002b. Probing single-molecule dynamics photon by photon. J. Chem. Phys. 117:10965-10979.
62. Yang, H., G. B. Luo, P. Karnchanaphanurach, T. M. Louie, I. Rech, S. Cova, L. Xun, and X. S. Xie. 2003. Protein conformational dynamics probed by single-molecule electron transfer. Science. 302:262-266.
63. Zhou, Y., C. Zhang, G. Stell, and J. Wang. 2003. Temperature dependence of the distribution of the first-passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second-hairpin fragment of protein G. J. Am. Chem. Soc. 125:6300-6305.
64. Zhuang, X. W., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
65. Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.