What is the time scale for α-helix nucleation?

Journal of the American Chemical Society

Volumn 133, Issue 17, 2011, Pages 6809-6816

  De Sancho, David ^a   Best, Robert B ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARRHENIUS KINETICS; BEST FIT; ELEMENTARY PROCESS; FOLDING REACTIONS; FORCE FIELDS; HELICAL STATE; HELIX FORMATION; HELIX NUCLEATION; RATE COEFFICIENTS; RE-EQUILIBRATION; RELAXATION CURVES; RELAXATION MODES; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; SPECTROSCOPIC MEASUREMENTS; TEMPERATURE DEPENDENT; TEMPERATURE JUMP; TIME-SCALES; ULTRA-FAST; WATER MODELS;

EXPONENTIAL FUNCTIONS; MARKOV PROCESSES; MOLECULAR DYNAMICS; NUCLEATION; PEPTIDES; PROTEIN FOLDING; REACTION KINETICS; RELAXATION PROCESSES;

COMPUTER SIMULATION;

WATER;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; DIFFUSION COEFFICIENT; FLUORESCENCE ANALYSIS; FORCE; KINETICS; MICROSCOPY; MOLECULAR DYNAMICS; PROTEIN STRUCTURE; ROOM TEMPERATURE; TEMPERATURE DEPENDENCE; VISCOSITY;

FLUORESCENCE; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 79955395931     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja200834s     Document Type: Article

References (76)

1. Mohammed, O.; Jas, G.; Lin, M.; Zewail, A. Angew. Chem. Int. Ed. 2009, 48, 1521-3773
2. Eaton, W. A.; Muñoz, V.; Thompson, P. A.; Henry, E. R.; Hofrichter, J. Acc. Chem. Res. 1998, 31, 745-753
3. Eaton, W. A.; Muñoz, V.; Hagen, S. J.; Jas, G. S.; Lapidus, L. J.; Henry, E. R.; Hofrichter, J. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 327-359
4. Ferguson, N.; Fersht, A. R. Curr. Opin. Struct. Biol. 2003, 13, 75-81
5. Muñoz, V.; Thompson, P.; Hofrichter, J.; Eaton, W. Nature 1997, 390, 196-199
6. Dyer, R. B.; Gai, F.; Woodruff, W. H. Acc. Chem. Res. 1998, 31, 709-716
7. Thompson, P. A.; Muñoz, V.; Jas, G. S.; Henry, E. R.; Eaton, W. A.; Hofrichter, J. J. Phys. Chem. B 2000, 104, 378-389
8. Lapidus, L. J.; Eaton, W. A.; Hofrichter, J. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220-7225
9. Möglich, A.; Joder, K.; Kiefhaber, T. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 12394-12399
10. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr. Opin. Struct. Biol. 2004, 14, 76-88
11. Muñoz, V.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11311-11316
12. Alm, E.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11305-11310
13. Du, D.; Zhu, Y.; Huang, C.-Y.; Gai, F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15915-15920
14. Olsen, K. A.; Fesinmeyer, R. M.; Stewart, J. M.; Andersen, N. H. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 15483-15487
15. Fierz, B.; Satzger, H.; Root, C.; Gilch, P.; Zinth, W.; Kiefhaber, T. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2163-2168
16. Yeh, I.-C.; Hummer, G. J. Am. Chem. Soc. 2002, 124, 6563-6568
17. Clarke, D. T.; Doig, A. J.; Stapley, B. J.; Jones, G. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7232-7237
18. Williams, S.; Causgrove, T.; Gilmanshin, R.; Fang, K.; Callender, R.; Woodruff, W.; Dyer, R. Biochemistry 1996, 35, 691-697
19. Lednev, I.; Karnoup, A.; Sparrow, M.; Asher, S. J. Am. Chem. Soc. 1999, 121, 8074-8086
20. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 2000, 104, 9200-9210
21. Huang, C.-Y.; Klemke, J. W.; Getahun, Z.; DeGrado, W. F.; Gai, F. J. Am. Chem. Soc. 2001, 123, 9235-9238
22. Huang, C.-Y.; Getahun, Z.; Zhu, Y.; Klemke, J. W.; DeGrado, W. F.; Gai, F. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2788-2793
23. Werner, J. H.; Dyer, R. B.; Fesinmeyer, R. M.; Andersen, N. H. J. Phys. Chem. B 2002, 106, 487-494
24. Wang, T.; Zhu, Y.; Getahun, Z.; Du, D.; Huang, C.-Y.; DeGrado, W. F.; Gai, F. J. Phys. Chem. B 2004, 108, 15301-15310
25. Bredenbeck, J.; Helbing, J.; Kumita, J. R.; Woolley, G. A.; Hamm, P. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2379-2384
26. Fierz, B.; Reiner, A.; Kiefhaber, T. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 1057-1062
27. Brooks, C. L. J. Phys. Chem. 1996, 100, 2546-2549
28. Ferrara, P.; Apostolakis, J.; Caflisch, A. J. Phys. Chem. B 2000, 104, 5000-5010
29. Hiltpold, A.; Ferrara, P.; Gsponer, J.; Caflisch, A. J. Phys. Chem. B 2000, 104, 10080-10086
30. Hummer, G.; García, A. E.; Garde, S. Phys. Rev. Lett. 2000, 85, 2637-2640
31. Jun, B.; Weaver, D. L. J. Chem. Phys. 2000, 112, 4394-4401
32. Hummer, G.; Garcia, A. E.; Garde, S. Proteins 2001, 42, 77-84
33. Buchete, N.-V.; Straub, J. E. J. Phys. Chem. B 2001, 105, 6684-6697
34. Garcia, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782-2787
35. Doshi, U. R.; Muñoz, V. J. Phys. Chem. B 2004, 108, 8497-8506
36. Gnanakaran, S.; Garcia, A. E. Proteins 2005, 59, 773-782
37. Paschek, D.; Gnanakaran, S.; Garcia, A. E. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6765-6770
38. Sorin, E. J.; Pande, V. S. Biophys. J. 2005, 88, 2472-2493
39. Sorin, E. J.; Rhee, Y. M.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2006, 356, 248-256
40. Dzubiella, J. J. Am. Chem. Soc. 2008, 130, 14000-14007
41. Dzubiella, J. J. Phys. Chem. B 2009, 113, 16689-16694
42. Hegefeld, W. A.; Chen, S.-E.; DeLeon, K. Y.; Kuczera, K.; Jas, G. S. J. Phys. Chem. A 2010, 114, 12391-12402
43. Mukherjee, S.; Chowdhury, P.; Bunagan, M. R.; Gai, F. J. Phys. Chem. B 2008, 112, 9146-9150
44. Ma, H.; Wan, C.; Zewail, A. H. J. Am. Chem. Soc. 2006, 128, 6338-6340
45. Mackerell, A. D.; Feig, M.; Brooks, C. L. J. Am. Chem. Soc. 2004, 126, 698-699
46. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712-725
47. Best, R. B.; Buchete, N.-V.; Hummer, G. Biophys. J. 2008, 95, L7-L9
48. Best, R. B.; Hummer, G. J. Phys. Chem. B 2009, 113, 9004-9015
49. Best, R. B.; Mittal, J. J. Phys. Chem. B 2010, 114, 8790-8798
50. Mittal, J.; Best, R. B. Biophys. J. 2010, 99, L26-L28
51. Best, R. B.; Mittal, J. J. Phys. Chem. B 2010, 114, 14916-14923
52. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Proteins 2010, 78, 1950-1958
53. Freddolino, P. L.; Harrison, C. B.; Liu, Y.; Schulten, K. Nature Phys. 2010, 751, 751-758
54. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A. J. Comput. Chem. 2003, 24, 1999-2012
55. Abascal, J. L. F.; Vega, C. J. Chem. Phys. 2005, 123, 234505
56. Buchete, N.-V.; Hummer, G. J. Phys. Chem. B 2008, 112, 6057-6069
57. Buchete, N.-V.; Hummer, G. Phys. Rev. E 2008, 77, 030902
58. Swope, W. C.; Pitera, J. W.; Suits, F. J. Phys. Chem. B 2004, 108, 6571-6581
59. Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. J. Chem. Phys. 2007, 126, 155101
60. Noe, F.; Horenko, I.; Schutte, C.; Smith, J. C. J. Chem. Phys. 2007, 126, 155102
61. Voelz, V. A.; Singh, V. R.; Wedemeyer, W. J.; Lapidus, L. J.; Pande, V. S. J. Am. Chem. Soc. 2010, 132, 4702-4709
62. Bowman, G. R.; Beauchamp, K. A.; Boxer, G.; Pande, V. S. J. Chem. Phys. 2009, 131, 124101
63. Noe, F.; Schutte, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19011-19016
64. Voelz, V. A.; Bowman, G. R.; Beauchamp, K.; Pande, V. S. J. Am. Chem. Soc. 2010, 132, 1526-1528
65. Bowman, G. R.; Voelz, V. A.; Pande, V. S. J. Am. Chem. Soc. 2011, 133, 664-667
66. Noe, F.; Doose, S.; Daidone, I.; Lollmann, M.; Sauer, M.; Chodera, J. D.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A.
67. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
68. Gunsteren, W. F. V.; Berendsen, H. J. C. Mol. Simul. 1988, 1, 173-185
69. Lifson, S.; Roig, A. J. Chem. Phys. 1961, 34, 1963-1974
70. Sreerama, N.; Woody, R. W.; Methods Enzym., D. Numerical Computer Methods 2004, 383, 318-351
71. Bullheller, B. M.; Rodger, A.; Hirst, J. D. Phys. Chem. Chem. Phys. 2007, 9, 2020-2035
72. Northrup, S. H.; Hynes, J. T. J. Chem. Phys. 1978, 69, 5246-5260
73. Sriraman, S.; Kevrekidis, I. G.; Hummer, G. J. Phys. Chem. B 2005, 109, 6479-6484
74. Zimm, B. H.; Bragg, J. K. J. Chem. Phys. 1959, 31, 526-535
75. Schwarz, G. J. Mol. Biol. 1965, 11, 64-77
76. Steiner, R. F.; Kirby, E. P. J. Phys. Chem. 1969, 73, 4130-4135