A lattice protein with an amyloidogenic latent state: Stability and folding kinetics

Journal of Physical Chemistry B

Volumn 111, Issue 10, 2007, Pages 2675-2687

  Palyanov, Andrey Yu ^a   Krivov, Sergei V ^b   Karplus, Martin ^b,c   Chekmarev, Sergei F ^a  

^a KUTATELADZE INSTITUTE OF THERMOPHYSICS   (Russian Federation)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; MATHEMATICAL MODELS; RATE CONSTANTS;

AMYLOIDOGENIC PROTEINS; PRINCIPAL COORDINATE ANALYSIS;

PROTEIN FOLDING;

EID: 34047253345     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp067027a     Document Type: Article

References (35)

1. Dinner, A. R.; Šali, A.; Smith, L. J.; Dobson, C. M.; Karplus, M. Trends Biochem. Sci. 2000, 25, 331-339.
2. Wang, Z.; Mottonen, J.; Goldsmith, E. J. Biochemistry 1996, 35, 16443-16448.
3. Ye, S.; Goldsmith, E. J. Curr. Opin. Struct. Biol. 2001, 11, 740-745.
4. Sohl, J. L.; Jaswal, S. S.; Agard, D. A. Nature 1998, 395, 817-819.
5. Volkman, B. F.; Lipson, D.; Wemmer, D. E.; Kern, D. Science 2001, 291, 2429-2433.
6. Hu, X.; Wang, Y. J. Biomol. Struct. Dyn. 2006, 23, 509-517.
7. Dobson, C. M. Nature 2003, 426, 884-890.
8. Jiménez, J. L.; Guijarro, J. I.; Orlova, E.; Zurdo, J.; Dobson, C. M.; Sunde, M.; Saibil, H. R. EMBO J. 1999, 18, 815-821.
9. Guo, Z. Y.; Thirumalai, D. Biopolymers 1995, 36, 83-102.
10. Abkevich, V. I.; Gutin, A. M.; Shakhnovich, E. I. Proteins 1998, 31, 335-344.
11. Nakamura, N. K.; Sasai, M. Proteins 2001, 43, 280-291.
12. Abkevich, V. I.; Gutin, A. M.; Shakhnovich, E. I. J. Chem. Phys. 1994, 101, 6052-6062.
13. Dinner, A. R.; Karplus, M. J. Phys Chem. B 1999, 103, 7976-7994.
14. Chekmarev, S. F.; Krivov, S. V.; Karplus, M. J. Phys Chem. B 2005, 109, 5312-5330.
15. Šali, A.; Shakhnovich, E.; Karplus, M. Nature 1994, 369, 248-251.
16. Locker, C. R.; Hernandez, R. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 9074-9079.
17. Gō, N. Annu. Rev. Biophys. Bioeng. 1983, 12, 183-210.
18. Dill, K. A. Biochemistry 1985, 24, 1501-1509.
19. Leonhard, K.; Prausnitz, J. M.; Radke, C. J. Phys. Chem. Chem. Phys. 2003, 5, 5291-5299.
20. Gupta, P.; Hall, C. K.; Voegler, A. C. Protein Sci. 1998, 7, 2642-2652.
21. Harrison, P. M.; Chan, H. S.; Prusiner, S. B.; Cohen, F. E. J. Mol. Biol. 1999, 286, 593-606.
22. Dima, R. I.; Thirumalai, D. Protein Sci. 2002, 11, 1036-1049.
23. Fawzi, N. L.; Chubukov, V.; Clark, L. A.; Brown, S.; Head-Gordon, T. Protein Sci. 2005, 14, 993-1003.
24. Cellmer, T.; Bratko, D.; Prausnitz, J. M.; Blanch H. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 11692-11697.
25. Cellmer, T.; Bratko, D.; Prausnitz, J. M.; Blanch, H. Biotechnol. Bioeng. 2005, 89, 78-87.
26. Galzitskaya, O. V.; Finkelstein, A. V. Protein Eng. 1995, 8, 883-892.
27. Karplus, M. Fold. Des. 1997, 2, 569-576.
28. Krivov, S. V.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14766-14770.
29. Krivov, S. V.; Karplus, M. J. Phys. Chem. B 2006, 110, 12689-12698.
30. Krivov, S. V.; Karplus, M., to be submitted for publication.
31. Lay, D. Linear Algebra and Its Applications, 2nd ed.; Addison-Wesley: New York, 2000.
32. Rhee, Y.; Pande, V. J. Phys. Chem. B 2005, 109, 6780-6786.
33. Chekmarev, S. F.; Krivov, S. V.; Karplus, M. J. Phys. Chem. B 2006, 110, 8865-8869.
34. Okazaki, K.; Koga, N.; Takada, S.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11844-11849.
35. Dumoulin, M.; Kumita, J. R.; Dobson, C. M. Acc. Chem. Res. 2006, 39, 603-610.