Free-energy landscape of mechanically unfolded model proteins: Extended Jarzinsky versus inherent structure reconstruction

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 78, Issue 3, 2008, Pages

  Luccioli, Stefano ^a,b   Imparato, Alberto ^c   Torcini, Alessandro ^a,b,d  

^a ISTITUTO DEI SISTEMI COMPLESSI   (Italy)

^b INFN SEZIONE DI FIRENZE   (Italy)

^c ISI FOUNDATION   (Italy)

^d CENTRE DE PHYSIQUE THÉORIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS; ESTIMATION; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY;

END-TO-END DISTANCE; FOLDABILITY; FOLDING TRANSITION; FREE-ENERGY LANDSCAPES; HETEROPOLYMERS; JARZYNSKI EQUALITY; LATTICE MODELING; MODEL PROTEINS; NATIVE CONFIGURATION; QUANTITATIVE AGREEMENT; RANDOM SEQUENCING; STEERED MOLECULAR DYNAMICS; STRUCTURAL TRANSITIONS; STRUCTURE RECONSTRUCTION; UMBRELLA SAMPLING;

FREE ENERGY;

EID: 51849113213     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.78.031907     Document Type: Article

References (69)

1. D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
2. F. H. Stillinger and T. A. Weber, Science SCIEAS 0036-8075 10.1126/science.225.4666.983 225, 983 (1984).
3. S. Sastry, P. G. Debenedetti, and F. H. Stillinger, Nature (London) NATUAS 0028-0836 10.1038/31146 393, 554 (1998).
4. L. Angelani, R. Di Leonardo, G. Ruocco, A. Scala, and F. Sciortino, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.5356 85, 5356 (2000).
5. T. S. Grigera, A. Cavagna, I. Giardina, and G. Parisi, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.88.055502 88, 055502 (2002).
6. Z. Guo and D. Thirumalai, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1996.0578 263, 323 (1996).
7. M. A. Miller and D. J. Wales, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.480011 111, 6610 (1999);
8. P. N. Mortenson and D. J. Wales, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1343486 114, 6443 (2001);
9. P. N. Mortenson, D. A. Evans, and D. J. Wales, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1484389 117, 1363 (2002).
10. S. V. Krivov and M. Karplus, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1517606 117, 10894 (2002).
11. D. A. Evans and D. J. Wales, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1540099 118, 3891 (2003).
12. N. Nakagawa and M. Peyrard, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0600102103 103, 5279 (2006);
13. N. Nakagawa and M. Peyrard, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.74.041916 74, 041916 (2006).
14. J. Kim and T. Keyes, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0665776 111, 2647 (2007).
15. A. Baumketner, J.-E. Shea, and Y. Hiwatari, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.67.011912 67, 011912 (2003).
16. D. A. Evans and D. J. Wales, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1759317 121, 1080 (2004).
17. P. E. Leopold, M. Montal, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.89.18.8721 89, 8721 (1992).
18. M. Carrion-Vazquez, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.7.3694 96, 3694 (1999);
19. B. Onoa, Science SCIEAS 0036-8075 10.1126/science.1081338 299 1892 (2003).
20. M. Carrion-Vazquez, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/nsb965 10, 738 (2003).
21. A. Irbäck, S. Mitternacht, and S. Mohanty, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0501581102 102, 13427 (2005).
22. D. J. Brockwell, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/nsb968 10, 731 (2003).
23. A. Imparato and L. Peliti, Eur. Phys. J. B EPJBFY 1434-6028 10.1140/epjb/e2004-00201-3 39, 357 (2004).
24. C. Jarzynski, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78. 2690 78, 2690 (1997);
25. G. E. Crooks, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.60.2721 60 2721 (1999).
26. D. Collin, Nature (London) NATUAS 0028-0836 10.1038/nature04061 437, 231 (2005).
27. D. K. West, P. O. Olmsted, and E. Paci, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2393232 125, 204910 (2006).
28. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.071034098 98, 3658 (2001).
29. T. Speck and U. Seifert, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.70.066112 70, 066112 (2004).
30. A. Imparato and L. Peliti, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2005-10067-5 70, 740 (2005).
31. A. Imparato and L. Peliti, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.72.046114 72, 046114 (2005).
32. N. C. Harris, Y. Song, and C.-H. Kiang, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.99.068101 99, 068101 (2007).
33. A. Imparato, F. Sbrana, and M. Vassalli, Europhys. Lett. EULEEJ 0295-5075 82, 58006 (2008).
34. A. Imparato, S. Luccioli, and A. Torcini, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.99.168101 99, 168101 (2007).
35. Z. Guo and D. Thirumalai, Biopolymers BIPMAA 0006-3525 10.1002/bip.360360108 36, 83 (1995).
36. Z. Guo and C. L. Brooks III, Biopolymers BIPMAA 0006-3525 10.1002/(SICI)1097-0282(199712)42:7<745::AID-BIP1>3.0.CO;2-T 42, 745 (1997).
37. S. Fowler, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(02)00805-7 322, 841 (2002).
38. E. Paci and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.100124597 97, 6521 (2000).
39. D. K. West, P. O. Olmsted, and E. Paci, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2186637 124, 144909 (2004).
40. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(74)80109-0 28, 578 (1974).
41. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.63.1195 63, 1195 (1989);
42. S. Kumar, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540130812 13, 1011 (1992);
43. B. Roux, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/0010-4655(95) 00053-I 91, 275 (1995).
44. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.87.9.3526 87, 3526 (1990).
45. R. S. Berry, N. Elmaci, J. P. Rose, and B. Vekhter, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.18.9520 94, 9520 (1997).
46. T. Veitshans, D. Klimov, and D. Thirumalai, Folding Des. FODEFH 1359-0278 10.1016/S1359-0278(97)00002-3 2, 1 (1997).
47. J. G. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.97.050601 97, 050601 (2006).
48. D. J. Lacks, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.051953 88, 3494 (2005).
49. F.-Y. Li, J.-M. Yuan, and C.-Y. Mou, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.63.021905 63, 021905 (2001).
50. A. Blondel and M. Karplus, J. Comput. Chem. JCCHDD 0192-8651 10.1002/(SICI)1096-987X(19960715)17:9<1132::AID-JCC5>3.0.CO;2-T 17, 1132 (1996).
51. A. Rampioni, Ph.D. thesis, Firenze, 2005.
52. W. Kabsch, Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. ACACBN 0567-7394 10.1107/S0567739476001873 A32, 922 (1976).
53. W. H. Press, Numerical Recipes (Cambridge University Press, New York, 1994).
54. A. Imparato and L. Peliti, J. Stat. Mech.: Theory Exp. ZZZZZZ 1742-5468 (2006) P03005.
55. O. Braun, A. Hanke, and U. Seifert, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.158105 93, 158105 (2004).
56. A. Torcini, R. Livi, and A. Politi, J. Biol. Phys. JBPHBZ 0092-0606 10.1023/A:1013104123892 27, 181 (2001).
57. L. Bongini, R. Livi, A. Politi, and A. Torcini, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.061111 68, 061111 (2003);
58. L. Bongini, R. Livi, A. Politi, and A. Torcini, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.72.051929 72, 051929 (2005).
59. P-G De Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, New York, 1979).
60. D. K. West, E. Paci, and P. D. Olmsted, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.74.061912 74, 061912 (2006).
61. A. Imparato, A. Pelizzola, and M. Zamparo, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.148102 98, 148102 (2007).
62. J. S. Langer, Ann. Phys. ANPYA2 0003-3804 54, 258 (1969).
63. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. RMPHAT 0034-6861 10.1103/RevModPhys.62.251 62, 251 (1990).
64. R. Zwanzig, Nonequilibrium Statistical Mechanics, (Oxford University Press, Oxford, 2001).
65. R. Chelli, S. Marsili, and P. Procacci, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.77.031104 77, 031104 (2008).
66. D. D. L. Minh and A. B. Adib, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.180602 100, 180602 (2008).
67. R. Chelli, A. Imparato, S. Luccioli, P. Procacci, and A. Torcini (unpublished).
68. G. Biroli and R. Monasson, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2000-00248-2 50, 155 (2000).
69. S. Mitternacht, S. Luccioli, A. Torcini, A. Imparato, and A. Irbäck (unpublished).