Single-molecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin

Nature Physics

Volumn 2, Issue 4, 2006, Pages 282-286

  Brujić, Jasna ^a   Hermans, Rodolfo I Z ^a,b   Walther, Kirstin A ^a,b   Fernandez, Julio M ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLASS; GLASS TRANSITION; MOLECULES; PROTEINS;

CONFORMATIONAL ENERGIES; EXPONENTIAL DISTRIBUTIONS; FOLDED CONFORMATION; MULTIPLE TIMESCALES; OUT OF EQUILIBRIUM; SINGLE MOLECULE FORCE SPECTROSCOPY; STATISTICAL ENERGY; STRUCTURAL FLUCTUATIONS;

CONFORMATIONS;

EID: 33645765218     PISSN: 17452473     EISSN: 17452481     Source Type: Journal    
DOI: 10.1038/nphys269     Document Type: Article

References (35)

1. Ansari, A. et al. Protein states and proteinquakes. Proc. Natl Acad. Sci. USA 82, 5000-5004 (1985).
2. Frauenfelder, H., Sligar, S. G. & Wolynes, P. The energy landscapes and motions of proteins. Science 254, 1598-1603(1991).
3. Karplus, M., Gao, Y. Q., Ma, J., van der Vaart, A. & Yang, W. Protein structural transitions and their functional role. Phil. Trans. A 363, 331-356 (2005).
4. 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, 167195 (1995).
5. Dill, K. A. et at Principles of protein folding - a perspective from simple exact models. Protein Sci. 4, 561-602(1995).
6. Lazaridis, T.& Karplus, M. 'New view' of protein folding reconciled with the old through multiple unfolding simulations. Science 278, 1928-1931 (1997).
7. Hyeon, C. & Thirumalai, D. Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc. Natl Acad. Sci. USA 100, 10249-10253 (2003).
8. Kneller, G. R. Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models. Phys. Chem. Chem. Phys. 7, 2641-2655 (2005).
9. Lindorff-Larsen, K., Best, R. B., DePristo, M. A., Dobson, C. M. & Vendruscolo, M. Simultaneous determination of protein structure and dynamics. Nature 433, 128-132 (2005).
10. Xue, Q. & Yeung, E. S. Differences in the chemical reactivity of individual molecules of an enzyme. Nature 373, 681-683 (1995).
11. van Oijen, A. M. et al. Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder. Science 301, 1235-1238 (2003).
12. Itoh, K. & Sasai, M. Dynamical transition and proteinquake in photoactive yellow protein. Proc. Natl Acad. Sci. USA 101, 14736-14741 (2004).
13. Yang, H. et al. Protein conformational dynamics probed by single-molecule electron transfer. Science 302, 262-266 (2003).
14. Min, W., Luo, G., Cherayil, B. J., Kou, S. C. & Xie, X. S. Observation of a power-law memory kernel for fluctuations within a single protein molecule. Phys. Rev. Lett. 94, 198302 (2005).
15. Fersht, A.R. Structure and Mechanism in Protein Science (Freeman, New York, 1992).
16. Carrion-Vazquez, M. et al. Protein nanomechanics -as studied by single-molecule force spectroscopy AFM. Biophys. J. 75, 662-671 (1998).
17. Li, H. B., Carrion-Vazquez, M., Oberhauser, A. F., Marszalek, P. E. & Fernandez, J. M. Point mutations alter the mechanical stability of immunoglobulin modules. Nature Struct. Biol. 7, 1117-1120 (2000).
18. Schlierf, M., Li, H. & Fernandez, J. M. The unfolding kinetics of ubiquitin captured with single-molecule force-damp techniques. Proc. NatlAcad. Sci. USA 101, 7299-7304 (2004).
19. Ross, S. Stochastic Processes (Wiley, New York, 1996).
20. Johnston, D. & Wu, S. M. Foundations of Cellular Neurophysiokgy (MIT Press, Cambridge, Massachusetts, 1995).
21. Colquhoun, D., Hatton, C. J. & Hawkes, A G. The quality of maximum likelihood estimates of ion channel rate constants. J. Physiol. 547, 699-728 (2003).
22. Chekmarev, S. F., Krivov, S. V. & Karplus, M. Folding time distributions as an approach to protein folding kinetics. J. Phys. Chem. B 109, 5312-5330 (2005).
23. Lee, C., Stell, G. & Wang, J. First passage time distribution and non-markovian diffusion dynamics of protein folding. J. Chem. Phys. 118, 959-968 (2003).
24. Angell, C. A. Perspective on the glass-transition. J. Phys. Chem. Solids 49, 863-871 (1988).
25. Lubchenko, V & Wolynes, P. G. Theory of aging in structural glasses. J. Chem. Phys. 121, 2852-2865(2004).
26. Marques, M. I. & Stanley, H. E. Relationship between fragility, diffusive directions and energy barriers in a supercooled liquid. Physica A 345, 395-403 (2005).
27. Derrida, B. Random-energy model -limit of a family of disordered models. Proc. Natl Acad. Sci. USA 45, 79-82 (1980).
28. Pande, V., Grosberg, A. & Tanaka, T. Statistical mechanics of simple models of protein folding and design. Biofhys. J. 73, 3192-3210 (1997).
29. Bereu, V., Martinelli, M., Massa, C., Pardi, L. & Leporini, D. A study of the deep structure of the energy landscape of glassy polystyrene: the exponential distribution of the energy barriers revealed by high-field electron spin resonance spectroscopy. Biophys. J. 16, L479-L488 (2004).
30. Monthus, C. & Bouchaud, J. Models of traps and glass phenomenology. J. Phys. A 29, 3847-3869(1996).
31. Lee, A. L & Wand, A J. Microscopic origins of entropy, heat capacity and the glass transition in proteins. Nature 411, 501-504(2004).
32. Nevo, R., Brumfeld, V., Kapon, R., Hinterdorfer, P. & Reich, Z. Direct measurement of protein energy landscape roughness. EMBO Rep. 6, 482-486 (2005).
33. Rao, F. & Caflisch, A The protein folding network J. Mol. Biol. 342, 299-306 (2004).
34. Barabási, A.-L & Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nature 5, 101-113(2004).
35. Song, C., Havlin, S. & Makse, H. A. Self-similarity of complex networks. Nature 433, 392-395 (2005).