Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins

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

Volumn 89, Issue 3, 2014, Pages

  Mey, Antonia S J S ^a   Geissler, Phillip L ^b,c   Garrahan, Juan P ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; PROTEINS; TRAJECTORIES;

AMINO ACID SEQUENCE; DYNAMIC TRANSITIONS; DYNAMICAL PHASE TRANSITION; DYNAMICAL PROPERTIES; DYNAMICAL TRANSITION; HETEROGENEOUS INTERACTIONS; INTERACTION ENERGIES; INTERACTION POTENTIALS;

METASTABLE PHASES;

PROTEIN;

AMINO ACID SEQUENCE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN DENATURATION; STATISTICAL MODEL; ULTRASTRUCTURE;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEINS;

EID: 84898944059     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.89.032109     Document Type: Article

References (33)

1. D. Chandler, Introduction to Modern Statistical Mechanics (Oxford University Press, New York, 1987).
2. N. Goldenfeld, Lectures on Phase Transitions and the Renormalization Group (Addison-Wesley, Reading, MA, 1992).
3. P. M. Chaikin and T. C. Lubensky, Principles of Condensed Matter Physics (Cambridge University Press, Cambridge, 2000).
4. L. Peliti, Statistical Mechanics in a Nutshell (Princeton University Press, Princeton, NJ, 2011).
5. E. I. Shakhnovich and A. M. Gutin, Nature 346, 773 (1990). NATUAS 0028-0836 10.1038/346773a0 (Pubitemid 20251095)
6. E. I. Shakhnovich, Chem. Rev. 106, 1559 (2006). CHREAY 0009-2665 10.1021/cr040425u (Pubitemid 43792772)
7. G. D. Rose, P. J. Fleming, J. R. Banavar, and A. Maritan, Proc. Natl. Acad. Sci. USA 103, 16623 (2006). PNASA6 0027-8424 10.1073/pnas.0606843103 (Pubitemid 44737304)
8. H. Abe and N. Go, Biopolymers 20, 1013 (1981). BIPMAA 0006-3525 10.1002/bip.1981.360200512
9. N. Gō, Annu. Rev. Biophys. Bioeng. 12, 183 (1983). ABPBBK 0084-6589 10.1146/annurev.bb.12.060183.001151
10. N. D. Socci and J. N. Onuchic, J. Chem. Phys. 101, 1519 (1994). JCPSA6 0021-9606 10.1063/1.467775
11. E. Paci, M. Vendruscolo, and M. Karplus, Proteins 47, 379 (2002). 18PLAF 0887-3585 10.1002/prot.10089 (Pubitemid 34438687)
12. J. K. Weber, R. L. Jack, and V. S. Pande, J. Am. Chem. Soc. 135, 5501 (2013). JACSAT 0002-7863 10.1021/ja4002663
13. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and P. G. Wolynes, Proteins 21, 167 (1995). 18PLAF 0887-3585 10.1002/prot.340210302
14. I. E. T. Iben, D. Braunstein, W. Doster, H. Frauenfelder, M. K. Hong, J. B. Johnson, S. Luck, P. Ormos, A. Schulte, P. J. Steinbach, A. H. Xie, and R. D. Young, Phys. Rev. Lett. 62, 1916 (1989). PRLTAO 0031-9007 10.1103/PhysRevLett. 62.1916
15. J. Chahine, H. Nymeyer, V. B. P. Leite, N. D. Socci, and J. N. Onuchic, Phys. Rev. Lett. 88, 168101 (2002). PRLTAO 0031-9007 10.1103/PhysRevLett.88. 168101
16. A. Gutin, A. Sali, V. Abkevich, M. Karplus, and E. I. Shakhnovich, J. Chem. Phys. 108, 6466 (1998). JCPSA6 0021-9606 10.1063/1.476053
17. M. Merolle, J. P. Garrahan, and D. Chandler, Proc. Natl. Acad. Sci. USA 102, 10837 (2005). PNASA6 0027-8424 10.1073/pnas.0504820102 (Pubitemid 41105953)
18. J. P. Garrahan, R. L. Jack, V. Lecomte, E. Pitard, K. van Duijvendijk, and F. van Wijland, Phys. Rev. Lett. 98, 195702 (2007). PRLTAO 0031-9007 10.1103/PhysRevLett.98.195702 (Pubitemid 47139480)
19. V. Lecomte, C. Appert-Rolland, and F. van Wijland, J. Stat. Phys. 127, 51 (2007). JSTPBS 0022-4715 10.1007/s10955-006-9254-0
20. L. O. Hedges, R. L. Jack, J. P. Garrahan, and D. Chandler, Science 323, 1309 (2009). SCIEAS 0036-8075 10.1126/science.1166665
21. R. L. Jack, L. O. Hedges, J. P. Garrahan, and D. Chandler, Phys. Rev. Lett. 107, 275702 (2011). PRLTAO 0031-9007 10.1103/PhysRevLett.107.275702
22. B. Gin, J. P. Garrahan, and P. L. Geissler, J. Mol. Biol. 392, 1303 (2009). JMOBAK 0022-2836 10.1016/j.jmb.2009.06.058
23. A. Sali, E. Shakhnovich, and M. Karplus, J. Mol. Biol. 235, 1614 (1994). JMOBAK 0022-2836 10.1006/jmbi.1994.1110 (Pubitemid 24150408)
24. L. G. Garcia and A. F. Pereira de Araújo, Proteins 62, 46 (2006). 18PLAF 0887-3585 10.1002/prot.20711 (Pubitemid 43063004)
25. S. Miyazawa and R. L. Jernigan, Macromolecules 18, 534 (1985). MAMOBX 0024-9297 10.1021/ma00145a039
26. E. I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994). 10.1103/PhysRevLett. 72.3907
27. L. A. Mirny, V. I. Abkevich, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA 95, 4976 (1998). PNASA6 0027-8424 10.1073/pnas.95.9.4976 (Pubitemid 28208535)
28. M. Baiesi, C. Maes, and B. Wynants, Phys. Rev. Lett. 103, 010602 (2009). PRLTAO 0031-9007 10.1103/PhysRevLett.103.010602
29. H. Touchette, Phys. Rep. 478, 1 (2009). PRPLCM 0370-1573 10.1016/j.physrep.2009.05.002
30. E. S. Loscar, A. S. J. S. Mey, and J. P. Garrahan, J. Stat. Mech. (2011) P12011. 1742-5468 10.1088/1742-5468/2011/12/P12011
31. T. Speck, A. Malins, and C. P. Royall, Phys. Rev. Lett. 109, 195703 (2012). PRLTAO 0031-9007 10.1103/PhysRevLett.109.195703
32. F. Chiti and C. Dobson, Nat. Chem. Biol. 5, 15 (2009). 1552-4450 10.1038/nchembio.131
33. J. P. Garrahan, R. Jack, V. Lecomte, E. Pitard, K. van Duijvendijk, and F. van Wijland, J. Phys. A 42, 075007 (2009). 1751-8113 10.1088/1751-8113/42/7/ 075007