Crowding alters the folding kinetics of a β-hairpin by modulating the stability of intermediates

Journal of the American Chemical Society

Volumn 134, Issue 24, 2012, Pages 10200-10208

  Kurniawan, Nicholas A ^a   Enemark, Søren ^a   Rajagopalan, Raj ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

COMPACT STRUCTURES; CONFIGURATION SPACE; CONFORMATIONAL SPACE; FOLDING DYNAMICS; FOLDING INTERMEDIATES; FOLDING KINETICS; HAIRPIN STRUCTURES; HYDROPHOBIC CONTACT; KINETIC TRAPS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR LEVELS; PROTEIN STRUCTURES; STRUCTURAL CHANGE; STRUCTURAL TRANSITIONS;

HYDROPHOBICITY; KINETIC ENERGY; MOLECULAR DYNAMICS; STABILITY;

KINETICS;

ARTICLE; ATOM; BETA HAIRPIN; CONFORMATION; HYDROPHOBICITY; KINETICS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN FOLDING; PROTEIN STABILITY; STRUCTURE ANALYSIS;

KINETICS; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY;

EID: 84862563574     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja302943m     Document Type: Article

References (45)

1. Perham, M.; Stagg, L.; Wittung-Stafshede, P. FEBS Lett. 2007, 581, 5065-5069
2. Homouz, D.; Stagg, L.; Wittung-Stafshede, P.; Cheung, M. S. Biophys. J. 2009, 96, 671-680
3. van den Berg, B.; Ellis, R. J.; Dobson, C. M. EMBO J. 1999, 18, 6927-6933
4. Ellis, R. J. Curr. Opin. Struct. Biol. 2001, 11, 114-119
5. Chebotareva, N. A.; Kurganov, B. I.; Livanova, N. B. Biochemistry (Moscow) 2004, 69, 1239-1251
6. Zhou, H. X.; Rivas, G. N.; Minton, A. P. Annu. Rev. Biophys. 2008, 37, 375-397
7. Zhou, H.-X. J. Mol. Recognit. 2004, 17, 368-375
8. Minton, A. P. Biophys. J. 2005, 88, 971-985
9. Tsao, D.; Dokholyan, N. V. Phys. Chem. Chem. Phys. 2010, 12, 3491-3500
10. van den Berg, B.; Wain, R.; Dobson, C. M.; Ellis, R. J. EMBO J. 2000, 19, 3870-3875
11. Cheung, M. S.; Klimov, D.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 4753-4758
12. Sasahara, K.; McPhie, P.; Minton, A. P. J. Mol. Biol. 2003, 326, 1227-1237
13. Tokuriki, N.; Kinjo, M.; Negi, S.; Hoshino, M.; Goto, Y.; Urabe, I.; Yomo, T. Protein Sci. 2004, 13, 125-133
14. Stagg, L.; Zhang, S. Q.; Cheung, M. S.; Wittung-Stafshede, P. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18976-18981
15. Hong, J. A.; Gierasch, L. M. J. Am. Chem. Soc. 2010, 132, 10445-10452
16. Christiansen, A.; Wang, Q.; Samiotakis, A.; Cheung, M. S.; Wittung-Stafshede, P. Biochemistry 2010, 49, 6519-6530
17. Qin, S.; Zhou, H.-X. Biophys. J. 2009, 97, 12-19
18. Schlesinger, A. P.; Wang, Y. Q.; Tadeo, X.; Millet, O.; Pielak, G. J. Am. Chem. Soc. 2011, 133, 8082-8085
19. Samiotakis, A.; Wittung-Stafshede, P.; Cheung, M. S. Int. J. Mol. Sci. 2009, 10, 572-588
20. Dhar, A.; Samiotakis, A.; Ebbinghaus, S.; Nienhaus, L.; Homouz, D.; Gruebele, M.; Cheung, M. S. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 17586-17591
21. Samiotakis, A.; Cheung, M. S. J. Chem. Phys. 2011, 135, 175101
22. Elcock, A. H. Curr. Opin. Struct. Biol. 2010, 20, 196-206
23. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. Science 2011, 334, 517-520
24. Snow, C. D.; Nguyen, N.; Pande, V. S.; Gruebele, M. Nature 2002, 420, 102-106
25. Honda, S.; Yamasaki, K.; Sawada, Y.; Morii, H. Structure 2004, 12, 1507-1518
26. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature 1997, 390, 196-199
27. Du, D. G.; Zhu, Y. J.; Huang, C. Y.; Gai, F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15915-15920
28. Ellis, R. J. Trends Biochem. Sci. 2001, 26, 597-604
29. Ellis, R. J.; Minton, A. P. Nature 2003, 425, 27-28
30. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
31. Matthes, D.; de Groot, B. L. Biophys. J. 2009, 97, 599-608
32. van der Spoel, D.; Seibert, M. M. Phys. Rev. Lett. 2006, 96, 238102
33. Enemark, S.; Rajagopalan, R. Phys. Chem. Chem. Phys. 2012, 10.1039/c2cp40285h
34. Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436
35. Hatfield, M. P.; Murphy, R. F.; Lovas, S. J. Phys. Chem. B 2010, 114, 3028-3037
36. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9068-9073
37. Thukral, L.; Smith, J. C.; Daidone, I. J. Am. Chem. Soc. 2009, 131, 18147-18152
38. Best, R. B.; Mittal, J. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 11087-11092
39. Stagg, L.; Christiansen, A.; Wittung-Stafshede, P. J. Am. Chem. Soc. 2011, 133, 646-648
40. Wagner, C.; Kiefhaber, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6716-6721
41. Mukherjee, S.; Waegele, M. M.; Chowshury, P.; Guo, L.; Gai, F. J. Mol. Biol. 2009, 393, 227-236
42. Jefferys, B. R.; Kelley, L. A.; Sternberg, M. J. E. J. Mol. Biol. 2010, 397, 1329-1338
43. McCallister, E. L.; Alm, E.; Baker, D. Nat. Struct. Biol. 2000, 7, 669-673
44. Dhar, A.; Girdhar, K.; Singh, D.; Gelman, H.; Ebbinghaus, S.; Gruebele, M. Biophys. J. 2011, 101, 421-430
45. Miklos, A. C.; Li, C. G.; Sharaf, N. G.; Pielak, G. J. Biochemistry 2010, 49, 6984-6991