The role of plastic β-hairpin and weak hydrophobic core in the stability and unfolding, of a full sequence design protein

Journal of Chemical Physics

Volumn 121, Issue 23, 2004, Pages 12104-12111

  Lei, Hongxing ^a   Duan, Yong ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HAIRPIN SEGMENT; HYDROPHOBIC CORE; PROTEIN STABILITY; STRUCTURAL HETEROGENEITY;

COMPUTER SIMULATION; HIGH TEMPERATURE EFFECTS; HYDROPHOBICITY; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE; PLASTICITY;

PROTEINS;

AMINO ACID; PROTEIN; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETICS; HYDROPHOBICITY; MUTATION; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

AMINO ACIDS; COMPUTER SIMULATION; HYDROPHOBICITY; MODELS, MOLECULAR; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOLVENTS; THERMODYNAMICS;

EID: 11044221141     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1822916     Document Type: Article

References (46)

1. R. L. Baldwin, Annu. Rev. Biochem. 44, 453 (1975).
2. G. Fischer and F. X. Schmid, Biochemistry 29, 2205 (1990).
3. A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 92, 10869 (1995).
4. B. Nolting and K. Andert, Proteins 41, 288 (2000).
5. A. R. Ortiz and J. Skolnick, Biophys. J. 79, 1787 (2000).
6. J. K. Myers and T. G. Oas, Annu. Rev. Biochem. 71, 783 (2002).
7. V. Daggett and A. Fersht, Nat. Rev. Mol. Cell Biol. 4, 497 (2003).
8. A. L. Horwich and J. S. Weissman, Cell 89, 499 (1997).
9. N. Gregersen, L. Bolund, and P. Bross, Methods Mol. Biol. 232, 3 (2003).
10. M. Sunde. Protein Sci. 13, 1704 (2004).
11. L. Pollack, M. W. Tate, A. C. Finnefrock et al., Phys. Rev. Lett. 86, 4962 (2001).
12. S. Doniach, Chem. Rev. (Washington, D.C.) 101, 1763 (2001).
13. R. M. Ballew, J. Sabelko, and M. Gruebele, Proc. Natl. Acad. Sci. U.S.A. 93, 5759 (1996).
14. W. A. Eaton, V. Munoz, S. J. Hagen, G. S. Jas, L. J. Lapidus, E. R. Henry, and J. Hofrichter, Annu. Rev. Biophys. Biomol. Struct. 29, 327 (2000).
15. R. Callender and R. B. Dyer, Curr. Opin. Struct. Biol. 12, 628 (2002).
16. Y. Duan, L. Wang, and P. A. Kollman, Proc. Natl. Acad. Sci. U.S.A. 95, 9897 (1998).
17. X. Daura, B. Jaun, D. Seebach, W. F. van Gunsteren, and A. E. Mark, J. Mol. Biol. 280, 925 (1998).
18. A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 99, 14122 (2002).
19. S. Y. Lee, Y. Fujitsuka, H. Kim do, and S. Takada, Proteins 55, 128 (2004).
20. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
21. V. Daggett and M. Levitt, J. Mol. Biol. 232, 600 (1993).
22. A. R. Fersht and V. Daggett, Cell 108, 573 (2002).
23. A. Li and V. Daggett, J. Mol. Biol. 275, 677 (1998).
24. A. Li and V. Daggett, J. Mol. Biol. 257, 412 (1996).
25. Y. Pan and V. Daggett, Biochemistry 40, 2723 (2001).
26. V. Daggett, Adv. Perit Dial 68, 83 (2001).
27. J. E. Shea and C. L. Brooks III, Annu. Rev. Phys. Chem, 52, 499 (2001).
28. J. Kleinjung, F. Fraternali, S. R. Martin, and P. M. Bayley, Proteins 50, 648 (2003).
29. Y. Y. Sham, B. Ma, C. J. Tsai, and R. Nussinov, Proteins 46, 308 (2002).
30. N. Rathore, Q. Yan, and J. J. De Pablo, J. Chem. Phys. 120, 5781 (2004).
31. H. S. Choi, J. Huh, and W. H. Jo, Biophys. J. 85, 1492 (2003).
32. B. I. Dahiyat and S. L. Mayo, Science 278, 82 (1997).
33. L. Wang, Y. Duan, R. Shortle, B. Imperiali, and P. A. Kollman, Protein Sci. 8, 1292 (1999).
34. E. Z. Wen and R. Luo, J. Chem. Phys. 121, 2412 (2004).
35. W. D. Cornell, P. Cieplak, C. I. Bayly et al., J. Am. Chem. Soc. 117, 5179 (1995).
36. Y. Duan, C. Wu, S. Chowdhury et al., J. Comput. Chem. 24, 1999 (2003).
37. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
38. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Chem. 23, 327 (1977).
39. W. Kabsch and C. Sander, Biopolymers 22, 2577 (1983).
40. A. R. Viguera, C. Vega, and L. Serrano, Proc. Natl. Acad. Sci. U.S.A. 99, 5349 (2002).
41. J. N. Onuchic, N. D. Socci, Z. Luthey-Schulten, and P. G. Wolynes, Folding Des. 1, 441 (1996).
42. J. E. Shea, J. N. Onuchic, and C. L. Brooks III, Proc. Natl. Acad. Sci. U.S.A. 99, 16064 (2002).
43. R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003).
44. C. A. Sarisky and S. L. Mayo, J. Mol. Biol. 307, 1411 (2001).
45. S. R. Griffiths-Jones, A. J. Maynard, and M. S. Searle, J. Mol. Biol. 292, 1051 (1999).
46. H. Hu, M. Elstner, and J. Hermans, Proteins 50, 451 (2003).