Robustness of atomistic Gō models in predicting native-like folding intermediates

Journal of Chemical Physics

Volumn 137, Issue 8, 2012, Pages

  Estacio S G ^a   Fernandes, C S ^a   Krobath, H ^a   Faisca P F N ^a   Shakhnovich, E I ^b  

^a Centro de Fisica da Materia Condensada   (Portugal)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; PROTEIN FOLDING; PROTEINS;

FOLDING BEHAVIOR; FOLDING INTERMEDIATES; INTERMEDIATE STATE; METHODOLOGICAL STRATEGIES; MOLECULAR DYNAMICS SIMULATIONS; NATIVE STRUCTURES; SIMULATIONS OF PROTEIN FOLDING; STRUCTURAL CLUSTERING;

PRINCIPAL COMPONENT ANALYSIS;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; MOLECULAR DYNAMICS; MUTATION; PROTEIN FOLDING; SRC HOMOLOGY DOMAIN; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN FOLDING; PROTEINS; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 84865722488     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4747492     Document Type: Article

References (55)

1. C. M. Dobson, Nature (London) 426, 884 (2003). 10.1038/nature02261 (Pubitemid 38056880)
2. F. Chiti and C. M. Dobson, Annu. Rev. Biochem. 75, 333 (2006). 10.1146/annurev.biochem.75.101304.123901 (Pubitemid 44118036)
3. A. I. Bartlett and S. E. Radford, Nat. Struct. Mol. Biol. 16, 582 (2009). 10.1038/nsmb.1592
4. P. Sherwood, B. R. Brooks, and M. S. P. Sansom, Curr. Opin. Struct. Biol. 18, 630 (2008). 10.1016/j.sbi.2008.07.003
5. V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. D. Snow, E. J. Sorin, and B. Zagrovic, Biopolymers 68, 91 (2003). 10.1002/bip.10219
6. G. R. Bowman, V. A. Voelz, and V. S. Pande, Curr. Opin. Struct. Biol. 21, 4 (2011). 10.1016/j.sbi.2010.10.006
7. C. D. Snow, N. Nguyen, V. S. Pande, and M. Gruebele, Nature (London) 420, 102 (2002). 10.1038/nature01160 (Pubitemid 35291448)
8. J. C. Faver, M. L. Benson, X. He, B. P. Roberts, B. Wang, M. S. Marshall, C. D. Sherrill, and K. M. Merz, PLoS One 6, e18868 (2011). 10.1371/journal. pone.0018868
9. K. A. Dill, Protein Sci. 8, 1166 (1999). 10.1110/ps.8.6.1166
10. H. Taketomi, Y. Ueda, and N. Go, Int. J. Pept. Protein Res. 7, 445 (1975). 10.1111/j.1399-3011.1975.tb02465.x
11. H. Kaya and H. S. Chan, J. Mol. Biol. 326, 911 (2003). 10.1016/S0022-2836(02)01434-1 (Pubitemid 36279329)
12. K. W. Plaxco, K. T. Simons, and D. Baker, J. Mol. Biol. 277, 985 (1998). 10.1006/jmbi.1998.1645 (Pubitemid 28195995)
13. I. A. Hubner, J. Shimada, and E. I. Shakhnovich, J. Mol. Biol. 336, 745 (2004). 10.1016/j.jmb.2003.12.032 (Pubitemid 38183026)
14. K. Lindorff-Larsen, M. Vendruscolo, E. Paci, and C. M. Dobson, Nat. Struct. Mol. Biol. 11, 443 (2004). 10.1038/nsmb765 (Pubitemid 38568948)
15. M. Vendruscolo, E. Paci, C. M. Dobson, and M. Karplus, Nature (London) 409, 641 (2001). 10.1038/35054591 (Pubitemid 32154819)
16. R. D. M. Travasso, P. F. N. Faisca, and A. Rey, J. Chem. Phys. 133, 125102 (2010). 10.1063/1.3485286
17. C. Clementi, A. E. Garcia, and J. N. Onuchic, J. Mol. Biol. 326, 933 (2003). 10.1016/S0022-2836(02)01379-7 (Pubitemid 36284722)
18. P. F. N. Faisca, R. D. M. Travasso, R. C. Ball, and E. I. Shakhnovich, J. Chem. Phys. 129, 095108 (2008). 10.1063/1.2973624
19. I. A. Hubner, M. Oliveberg, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. U.S.A. 101, 8354 (2004). 10.1073/pnas.0401672101 (Pubitemid 38736579)
20. I. A. Hubner, K. A. Edmonds, and E. I. Shakhnovich, J. Mol. Biol. 349, 424 (2005). 10.1016/j.jmb.2005.03.050 (Pubitemid 40693760)
21. H. S. Chan, Z. Q. Zhang, S. Wallin, and Z. R. Liu, Annu. Rev. Phys. Chem. 62, 301 (2011). 10.1146/annurev-physchem-032210-103405
22. A. I. Jewett, V. S. Pande, and K. W. Plaxco, J. Mol. Biol. 326, 247 (2003). 10.1016/S0022-2836(02)01356-6 (Pubitemid 36279372)
23. J. I. Sulkowska, P. Sulkowski, P. Szymczak, and M. Cieplak, Phys. Rev. Lett. 100, 058106 (2008). 10.1103/PhysRevLett.100.058106 (Pubitemid 351230709)
24. J. I. Sulkowska and M. Cieplak, Biophys. J. 95, 3174 (2008). 10.1529/biophysj.107.127233
25. P. F. N. Faisca, R. D. M. Travasso, T. Charters, A. Nunes, and M. Cieplak, Phys. Biol. 7, 016009 (2010). 10.1088/1478-3975/7/1/016009
26. S. Matysiak and C. Clementi, J. Mol. Biol. 363, 297 (2006). 10.1016/j.jmb.2006.07.088 (Pubitemid 44414843)
27. L. Prieto and A. Rey, J. Chem. Phys. 130, 115101 (2009). 10.1063/1.3089708
28. J. E. Ollerenshaw, H. Kaya, H. S. Chan, and L. E. Kay, Proc. Natl. Acad. Sci. U.S.A. 101, 14748 (2004). 10.1073/pnas.0404436101 (Pubitemid 39410746)
29. M. Larriva, L. Prieto, P. Bruscolini, and A. Rey, Proteins: Struct., Funct., Bioinf. 78, 73 (2010). 10.1002/prot.22521
30. H. Krobath, S. G. Estácio, P. F. N. Faísca, and E. I. Shakhnovich, Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants., J. Mol. Biol. (in press). 10.1016/j.jmb.2012.06.020
31. L. Prieto and A. Rey, J. Chem. Phys. 129, 115101 (2008). 10.1063/1.2977744
32. M. F. Rey-Stolle, M. Enciso, and A. Rey, J. Comput. Chem. 30, 1212 (2009). 10.1002/jcc.21149
33. E. Paci, M. Vendruscolo, and M. Karplus, Biophys. J. 83, 3032 (2002). 10.1016/S0006-3495(02)75308-3
34. C. Clementi, Curr. Opin. Struct. Biol. 18, 10 (2008). 10.1016/j.sbi.2007.10.005
35. J. Tsai, R. Taylor, C. Chothia, and M. Gerstein, J. Mol. Biol. 290, 253 (1999). 10.1006/jmbi.1999.2829 (Pubitemid 29308589)
36. N. Go and H. Abe, Biopolymers 20, 991 (1981). 10.1002/bip.1981.360200511
37. J. Shimada, E. L. Kussell, and E. I. Shakhnovich, J. Mol. Biol. 308, 79 (2001). 10.1006/jmbi.2001.4586 (Pubitemid 33027629)
38. N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, Folding Des. 3, 577 (1998). 10.1016/S1359-0278(98)00072-8 (Pubitemid 29023621)
39. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999). 10.1016/S0009-2614(99)01123-9
40. J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. 3, 26 (2007). 10.1021/ct0502864
41. D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P. A. Kollman, AMBER 11, University of California, San Francisco, 2010.
42. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995). 10.1063/1.470117
43. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23 (3), 327-341 (1977). 10.1016/0021-9991(77)90098-5
44. Molecular Operating Environment (MOE), 2009.10; Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite 910, Montreal, QC, Canada, H3A 2R7, 2009.
45. M. Feig, J. Karanicolas, and C. L. Brooks, J. Mol. Graphics 22, 377 (2004). 10.1016/j.jmgm.2003.12.005 (Pubitemid 38510304)
46. J. Y. Shao, S. W. Tanner, N. Thompson, and T. E. Cheatham, J. Chem. Theory Comput. 3, 2312 (2007). 10.1021/ct700119m
47. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993). 10.1002/prot.340170408 (Pubitemid 23358549)
48. A. Kitao and N. Go, Curr. Opin. Struct. Biol. 9, 164 (1999). 10.1016/S0959-440X(99)80023-2 (Pubitemid 29452893)
49. P. L. Privalov and N. N. Khechinashvili, J. Mol. Biol. 86, 665 (1974). 10.1016/0022-2836(74)90188-0
50. H. S. Chan, S. Shimizu, and H. Kaya, Methods Enzymol. 380, 350 (2004). 10.1016/S0076-6879(04)80016-8 (Pubitemid 38297503)
51. H. Kaya and H. S. Chan, Proteins 40, 637 (2000). 10.1002/1097- 0134(20000901)40:4637::AID-PROT80>3.0.CO;2-4
52. P. F. N. Faisca and K. W. Plaxco, Protein Sci. 15, 1608 (2006). 10.1110/ps.062180806
53. D. Narzi, I. Daidone, A. Amadei, and A. Di Nola, J. Chem. Theory Comput. 4, 1940 (2008). 10.1021/ct800157v
54. G. G. Maisuradze, A. Liwo, and H. A. Scheraga, J. Mol. Biol. 385, 312 (2009). 10.1016/j.jmb.2008.10.018
55. N. C. Benson and V. Daggett, Protein Sci. 17, 2038 (2008). 10.1110/ps.037473.108