Simulation of the mechanical unfolding of ubiquitin: Probing different unfolding reaction coordinates by changing the pulling geometry

Journal of Chemical Physics

Volumn 121, Issue 10, 2004, Pages 4826-4832

  Li, Pai Chi ^a   Makarov, Dmitrii E ^a  

^a The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MECHANICAL UNFOLDING; MULTIDIMENSIONAL ENERGY LANDSCAPE; QUASISTATIC PROCESS; THERMAL DENATURATION;

ATOMIC FORCE MICROSCOPY; COMPUTATIONAL METHODS; ELECTRON TRANSITIONS; ERROR CORRECTION; FREE ENERGY; HYDROGEN BONDS; MATHEMATICAL MODELS; POTENTIAL ENERGY; PROTEINS; RATE CONSTANTS; REACTION KINETICS;

MOLECULAR DYNAMICS;

UBIQUITIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELASTICITY; GENETIC PROCEDURES; MECHANICAL STRESS; MECHANICS; MOTION; PROTEIN DENATURATION; PROTEIN FOLDING; STRUCTURE ACTIVITY RELATION; ULTRASTRUCTURE;

COMPUTER SIMULATION; ELASTICITY; MECHANICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR PROBE TECHNIQUES; MOTION; PROTEIN DENATURATION; PROTEIN FOLDING; STRESS, MECHANICAL; STRUCTURE-ACTIVITY RELATIONSHIP; UBIQUITIN;

EID: 4544284283     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1778152     Document Type: Article

References (49)

1. N.-L. Chan and C. P. Hill, Nat. Struct. Biol. 8, 650 (2001).
2. J. Peng, D. Schwartz, J. E. Elias et al., Nat. Biotechnol. 21, 921 (2003).
3. C. M. Pickart, Trends Biochem. Sci. 25, 544 (2000).
4. C. M. Pickart, Annu. Rev. Biochem. 70, 503 (2001).
5. V. Chau, J. W. Tobias, A. Bachmair, D. Marriott, D. J. Ecker, D. K. Gonda, and A. Varshavsky, Science 243, 1576 (1989).
6. R. M. Hofmann and C. M. Pickart, Cell 96, 645 (1999).
7. J. Spenee, R. R. Gali, G. Dittmar, F. Sherman, M. Karin, and D. Finley, Cell 102, 67 (2000).
8. J.-M. Galan and R. Haguenauer-Tsapis, EMBO J. 16, 5847 (1997).
9. M. Carrion-Vazquez, H. Li, H. Lu, P. E. Marszalek, A. F. Oberhauser, and J. M. Fernandez, Nat. Struct. Biol. 10, 738 (2003).
10. H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten, Biophys. J. 75, 662 (1998).
11. H. Lu and K. Schulten, Chem. Phys. 247, 141 (1999).
12. B. Isralewitz, M. Gao, and K. Schulten, Curr. Opin. Struct. Biol. 11, 224 (2001).
13. P. E. Marsalek, H. Lu, H. Li, M. Carrion-Vazquez, A. F. Oberhauser, K. Schulten, and J. Fernandez, Nature (London) 402, 100 (1999).
14. D. J. Brockwell, G. S. Beddard, J. Clarkson et al., Biophys. J. 83, 458 (2002).
15. P.-C. Li and D. E. Makarov, I. Phys. Chem. B 108, 745 (2004).
16. D. J. Brockwell, E. Paci, R. C. Zinober, G. S. Beddard, P. D. Olmsted, D. A. Smith, R. N. Perham, and S. E. Radford, Nat. Struct. Biol. 10, 731 (2003).
17. M. Baisera, S. Stepaniants, S. Izrailev, Y. Oono, and K. Schulten, Biophys. J. 73, 1281 (1997).
18. S. Izrailev, S. Stepaniants, M. Baisera, Y. Oono, and K. Schulten, Biophys. J. 72, 1568 (1997).
19. E. Galugan, C. J. Roberts, M. C. Davies, S. J. B. Tendler, and P. M. Williams, J. Chem. Phys. 114, 3208 (2001).
20. B. Heymann and H. Grubmuller, Biophys. J. 81, 1295 (2001).
21. B. Heymann and H. Grubmuller, Chem. Phys. Lett. 303, 1 (1999).
22. P.-C. Li and D. E. Makarov, J. Chem. Phys. 119, 9260 (2003).
23. H. Grubmuller, B. Heymann, and P. Tavan, Science 271, 997 (1996).
24. P. M. Williams, S. B. Fowler, R. B. Best, J. L. Toca-Herrera, K. A. Scott, A. Steward, and J. Clarke, Nature (London) 422, 446 (2003).
25. M. Carrion-Vazquez, A. F. Oberhauser, S. B. Fowler, P. E. Marsalek, S. E. Broedel, J. Clarke, and J. M. Fernandez, Proc. Natl. Acad. Sci. U.S.A. 96, 3694 (1999).
26. J. A. McCammon and S. C. Harvey, Dynamics of Proteins and Nucleic Acids (Canbridge University Press, Cambridge, 1987).
27. D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic, San Diego, 2002).
28. D. Qiu, P. S. Shenkin, F. P. Hollinger, and W. C. Still, J. Phys. Chem. A 101, 3005 (1997).
29. A. D. MacKerell, D. Bashford, M. Bellott et al., J. Phys. Chem. B 102, 3586 (1998).
30. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
31. G. I. Bell, Science 200, 618 (1978).
32. P. Hanggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990).
33. C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science 265, 1599 (1994).
34. M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub, Science 276, 1109 (1997).
35. M. Rief, J. M. Fernandez, and H. E. Gaub, Phys. Rev. Lett. 81, 4764 (1998).
36. M. Fixman and J. Kovac, J. Chem. Phys. 58, 1564 (1973).
37. O. Kratky and G. Porod, Recl. Trav. Chim. Pays-Bas 68, 1106 (1949).
38. D. E. Makarov, P. K. Hansma, and H. Metiu, J. Chem. Phys. 114, 9663 (2001).
39. M. B. Viani, T. E. Schaffer, G. T. Paloczi et al., Rev. Sci. Instrum. 70, 4300 (1999).
40. M. B. Viani, T. E. Schaffer, A. Chand, M. Rief, H. E. Gaub, and P. K. Hansma, J. Appl. Phys. 86, 2258 (1999).
41. R. C. Zinober, D. J. Brockwell, G. S. Beddard, A. W. Blake, P. D. Olmsted, S. E. Radford, and D. A. Smith, Protein Sci. 11, 2759 (2002).
42. A. F. Oberhauser, C. Badilla-Fernandez, M. Carrion-Vazquez, and J. M. Fernandez, J. Mol. Biol. 319, 433 (2002).
43. G. Hummer and A. Szabo, Biophys. J. 85, 5 (2003).
44. M. Schlierf, H. Li, and J. M. Fernandez, Proc. Natl. Acad. Sci. U.S.A. 101, 7299 (2004).
45. R. Rohs, C. Etchebest, and R. Lavery, Biophys. J. 76, 2760 (1999).
46. K. Eom, P.-C. Li, D. E. Makarov, and G. J. Rodin, J. Phys. Chem. B 107, 8730 (2003).
47. I. Schwaiger, C. Sattler, D. R. Hostetter, and M. Rief, Nat. Mater, 1, 232 (2002).
48. S. Khorasanizadeh, I. D. Peters, T. R. Butt, and H. Roder, Biochemistry 32, 7054 (1993).
49. R. Koradi, M. Billeter, and K. Wüthrich, J. Mol. Graphics 14, 51 (1996).