Extracting physically intuitive reaction coordinates from transition networks of a β-Sheet Miniprotein

Journal of Physical Chemistry B

Volumn 114, Issue 20, 2010, Pages 6979-6989

  Qi, Bo ^a,b   Muff, Stefanie ^c   Caflisch, Amedeo ^c   Dinner, Aaron R ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX NATURE; COMPLEX REACTIONS; FOLDING PROCESS; NATIVE STATE; NON-NATIVE STATE; NUMBER OF DEGREES OF FREEDOM; PHYSICAL VARIABLES; REACTION COORDINATES; STABLE STATE;

COMPUTER SIMULATION;

EID: 77952683491     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp101476g     Document Type: Article

References (29)

1. Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, E. S. J. Chem. Phys. 1998, 108, 334-350
2. Ma, A.; Dinner, A. R. J. Phys. Chem. B 2005, 109, 6769-6779
3. Best, R. B.; Hummer, G. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6732-6737
4. Peters, B.; Trout, B. L. J. Chem. Phys. 2006, 125 054108
5. Peters, B.; Beckham, G. T.; Trout, B. L. J. Chem. Phys. 2007, 127 034109
6. Antoniou, D.; Schwartz, S. D. J. Chem. Phys. 2009, 130, 151103
7. Rao, F.; Caflisch, A. J. Mol. Biol. 2004, 342, 299-306
8. Gfeller, D.; De Los Rios, P.; Caflisch, A.; Rao, F. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1817-1822
9. Singhal, N.; Snow, C. D.; Pande, V. S. J. Chem. Phys. 2004, 121, 415-425
10. Metzner, P.; Schutte, C.; Vanden-Eijnden, E. J. Chem. Phys. 2006, 125 084110
11. Hummer, G.; Kevrekidis, I. G. J. Chem. Phys. 2003, 118, 10762-10773
12. Krivov, S. V.; Karplus, M. J. Phys. Chem. B 2006, 110, 12689-12698
13. Krivov, S. V.; Muff, S.; Caflisch, A.; Karplus, M. J. Phys. Chem. B 2008, 112, 8701-8714
14. Ferrara, P.; Caflisch, A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10780-10785
15. Muff, S.; Caflisch, A. Proteins: Struct., Funct., Bioinf. 2008, 70, 1185-1195
16. Muff, S.; Caflisch, A. J. Phys. Chem. B 2009, 113, 3218-3226
17. Muff, S.; Caflisch, A. J. Chem. Phys. 2009, 130, 125104
18. Hu, J.; Ma, A.; Dinner, A. R. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 4615-4620
19. Lazaridis, T.; Karplus, M. Proteins: Struct., Funct., Genet. 1999, 35, 133-152
20. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614
21. Krivov, S. V.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14766-14770
22. So, S. S.; Karplus, M. J. Med. Chem. 1996, 39, 1521-1530
23. So, S. S.; Karplus, M. J. Med. Chem. 1996, 39, 5246-5256
24. Seeber, M.; Cecchini, M.; Rao, F.; Settanni, G.; Caflisch, A. Bioinformatics 2007, 23, 2625-2627
25. Im, W.; Roux, B. J. Mol. Biol. 2002, 319, 1177-1197
26. Ma, A.; Nag, A.; Dinner, A. R. J. Chem. Phys. 2006, 124, 144911
27. De Alba, E.; Santoro, J.; Rico, M.; Jimenez, M. A. Protein Sci. 1999, 8, 854-865
28. Krivov, S. V.; Karplus, M. J. Chem. Phys. 2002, 117, 10894-10903
29. Dellago, C.; Bolhuis, P. G.; Chandler, D. J. Chem. Phys. 1998, 108, 9236-9245