Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

Journal of Chemical Physics

Volumn 128, Issue 20, 2008, Pages

  Tripathi, Swarnendu ^a   Portman, John J ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CONFORMATIONS; MOLECULAR DYNAMICS; MOLECULAR MODELING; MOLECULAR STRUCTURE;

BINDING LOOP; CALMODULIN; CONFORMATIONAL TRANSITION;

PROTEINS;

CALCIUM; CALMODULIN; METHIONINE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; KINETICS; METABOLISM; MICROCOMPUTER; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS; TIME;

BINDING SITES; CALCIUM; CALMODULIN; KINETICS; METHIONINE; MICROCOMPUTERS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS; TIME FACTORS;

EID: 44449109605     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2928634     Document Type: Article

References (53)

1. H. Frauenfelder, S. G. Sligar, and P. G. Wolynes, Science 254, 1598 (1991).
2. M. Gerstein, A. M. Lesk, and C. Chothia, Biochemistry 33, 6739 (1994).
3. M. R. Nelson and W. J. Chazin, Protein Sci. 7, 270 (1998).
4. R. D. Brokx, M. M. Lopez, H. J. Vogel, and G. Makhatadze, J. Biol. Chem. 276, 14083 (2001).
5. J. J. Chou, S. Li, C. B. Klee, and A. Bax, Nat. Struct. Biol. 8, 990 (2001).
6. T. N. Tsalkova and P. L. Privalov, J. Mol. Biol. 181, 533 (1985).
7. S. Linse, A. Helmersson, and S. Forsen, J. Biol. Chem. 266, 8050 (1991).
8. J. L. Baber, A. Szabo, and N. Tjandra, J. Am. Chem. Soc. 123, 3953 (2001).
9. A. Malmendal, J. Evenas, S. Forsen, and M. Akke, J. Mol. Biol. 293, 883 (1999).
10. R. Ishima and D. A. Torchia, Nat. Struct. Biol. 7, 740 (2000).
11. J. Evenas, S. Forsen, A. Malmendal, and M. Akke, J. Mol. Biol. 289, 603 (1999).
12. Z. Grabarek, J. Mol. Biol. 346, 1351 (2005).
13. Z. Grabarek, J. Mol. Biol. 359, 509 (2006).
14. H. Kuboniwa, N. Tjandra, S. Grzesiek, H. Ren, C. B. Klee, and A. Bax, Nat. Struct. Biol. 2, 768 (1995).
15. M. Zhang, T. Tanaka, and M. Ikura, Nat. Struct. Biol. 2, 758 (1995).
16. J. J. Portman, S. Takada, and P. G. Wolynes, Phys. Rev. Lett. 81, 5237 (1998).
17. J. J. Portman, S. Takada, and P. G. Wolynes, J. Chem. Phys. 114, 5069 (2001).
18. J. J. Portman, S. Takada, and P. G. Wolynes, J. Chem. Phys. 114, 5082 (2001).
19. W. Wriggers, E. Mehler, F. Pitici, H. Weinstein, and K. Schulten, Biophys. J. 74, 1622 (1998).
20. D. Vigil, S. C. Gallagher, J. Trewhella, and A. E. Garcia, Biophys. J. 80, 2082 (2001).
21. D. M. Zuckerman, J. Phys. Chem. B 108, 5127 (2004).
22. Y.-G. Chen and G. Hummer, J. Am. Chem. Soc. 129, 2414 (2007).
23. M. Bixon and R. Zwanzig, J. Chem. Phys. 68, 1896 (1978).
24. K. Okazaki, N. Koga, S. Takada, J. N. Onuchic, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 103, 11844 (2006).
25. R. B. Best, Y. G. Chen, and G. Hummer, Structure (London) 13, 1755 (2005).
26. P. Maragakis and M. Karplus, J. Mol. Biol. 352, 807 (2005).
27. S. Miyazawa and R. L. Jernigan, J. Mol. Biol. 256, 623 (1996).
28. M. K. Kim, R. L. Jernigan, and G. S. Chirikjian, Biophys. J. 83, 1620 (2002).
29. R. B. Russell and G. J. Barton, Proteins: Struct., Funct., Genet. 14, 309 (1992).
30. V. A. Likic, E. E. Strehler, and P. R. Gooley, Protein Sci. 12, 2215 (2003).
31. N. C. J. Strynadka and M. N. James, Annu. Rev. Biochem. 58, 951 (1989).
32. K. Siivari, M. Zhang, I. A. G. Palmer, and H. J. Vogel, FEBS Lett. 366, 104 (1995).
33. B. A. Shoemaker, J. J. Portman, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 97, 8868 (2000).
34. N. Sinha, S. Kumar, and R. Nussinov, Structure (London) 9, 1165 (2001).
35. A. Lewit-Bentley and S. Rety, Curr. Opin. Struct. Biol. 10, 637 (2000).
36. P. Lundstrom, F. A. A. Mulder, and M. Akke, Proc. Natl. Acad. Sci. U.S.A. 102, 16984 (2005).
37. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and P. G. Wolynes, Proteins: Struct., Funct., Genet. 21, 167 (1995).
38. G. M. Verkhivker, D. Bouzida, D. K. Gehlhaar, P. A. Rejto, S. T. Freer, and P. W. Rose, Curr. Opin. Struct. Biol. 12, 197 (2002).
39. J. Wang, K. Zhang, H. Y. Lu, and E. K. Wang, Phys. Rev. Lett. 96, 168101 (2006).
40. G. A. Papoian and P. Wolynes, Biopolymers 63, 333 (2003).
41. G. M. Verkhivker, D. Bouzida, D. K. Gellhaar, P. A. Tejto, S. T. Freer, and P. W. Rose, Proc. Natl. Acad. Sci. U.S.A. 100, 5148 (2003).
42. O. Miyashita, J. N. Onuchic, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 100, 12570 (2003).
43. Y. Levy, P. G. Wolynes, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 101, 511 (2004).
44. S. Yang, S. S. Cho, Y. Levy, M. S. Cheung, H. Levine, P. G. Wolynes, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 101, 13786 (2004).
45. Y. Levy, S. S. Cho, J. N. Onuchic, and P. G. Wolynes, J. Mol. Biol. 346, 1121 (2005).
46. Y. J. Huang and G. T. Montelione, Nature (London) 438, 36 (2005).
47. V. Tozzini, Curr. Opin. Struct. Biol. 15, 144 (2005).
48. M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996).
49. I. Bahar, A. R. Atilgan, M. C. Demirel, and B. Erman, Phys. Rev. Lett. 80, 2733 (1998).
50. F. Tama and C. L. Brooks, J. Mol. Biol. 318, 733 (2002).
51. O. Miyashita, P. G. Wolynes, and J. N. Onuchic, J. Phys. Chem. B 109, 1959 (2004).
52. C. Zong, C. J. Wilson, T. Shen, P. Wittung-Stafshede, S. L. Mayo, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 104, 3159 (2007).
53. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14, 33 (1996).