Inherent flexibility of calmodulin domains: A normal-mode analysis study

Journal of Physical Chemistry B

Volumn 106, Issue 42, 2002, Pages 11036-11040

  Barton, N P ^a   Verma, C S ^a   Caves, L S D ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CALMODULIN; NORMAL MODE ANALYSIS;

CALCIUM; COMPUTER SIMULATION; CONFORMATIONS; NUMERICAL METHODS; PROTEINS;

MOLECULAR DYNAMICS;

EID: 0037168294     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp026692q     Document Type: Article

References (34)

1. Vogel, H. J. Biochem. Cell Biol. 1994, 72, 357-76.
2. Yap, K. L.; Kim, J.; Truong, K.; Sherman, M.; Yuan, T.; Ikura, M. J. Struct. Funct. Genomics 2001, 1, 8-14.
3. Babu, Y. S.; Bugg, C. E.; Cook, W. J. J. Mol. Biol. 1988, 204, 191-204.
4. Meador, W. E.; Means, A. R.; Quiocho, F. A. Science (Washington, D.C.) 1992, 257, 1251-1254.
5. Ikura, M.; Clore, G. M.; Gronenborn, A. M.; Zhu, G.; Klee, C. B.; Bax, A. Science (Washington, D.C.) 1992, 256, 632-638.
6. Bayley, P. M.; Findlay, W. A.; Martin, S. R. Protein Sci. 1996, 5, 1215-1228.
7. Zhang, M.; Yuan, T. Biochem. Cell Biol. 1998, 76, 313-23.
8. Dunker, K. A.; Brown, C. J.; Lawson, J. D.; Iakoucheva, L. M.; Obradovic, Z. Biochemistry 2002, 41, 6573-6582.
9. Wilson, M. A.; Brunger, A. T. J. Mol. Biol. 2000, 301, 1237.
10. Chou, J. J.; Li, S.; Klee, C. B.; Bax, A. Nat. Struct. Biol. 2001, 8, 990-997.
11. Wrigger, W.; Mehler, E.; Pitici, F.; Weinstein, H.; Schulten, K. Biophys. J. 1998, 74, 1622-1639.
12. Vigil, D.; Gallagher, S. C.; Trewhella, J.; Garcia, A. E. Biophys. J. 2001, 80, 2082-2092.
13. Barton, N. P. Conformational Flexibility of Calmodulin; Caves, L. S. D. Ed.; University of York: York, U.K., 2002 (in preparation).
14. Barth, A.; Martin, S. R.; Bayley, P. M. J. Biol. Chem. 1998, 273, 2174-2183.
15. Wall, M. E.; Clarage, J. B.; Phillips, G. N. Structure 1997, 5, 1599-1612.
16. Brooks, B. R.; Bruccoleri, R. B.; Olafson, B. D.; State, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
17. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. J. Phys. Chem. B 1998, 102, 3586-3616.
18. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
19. Brunger, A. T.; Karplus, M. Proteins 1988, 4, 148-156.
20. Grubmueller, H. Solvate 1.0, version 1.0; 1996.
21. Marchand, S.; Roux, B. Proteins 1998, 33, 265-284.
22. Berendsen, H.; Postma, J.; Van Gunsteren, W.; Dinola, A.; Haak, J. J. Chem. Phys. 1984, 81, 3684-3690.
23. Kabsch, W. Acta Crystallogr., Sect. A 1976, 32. 922-923.
24. Elber, R.; Karplus, M. Science (Washington, D.C.) 1987, 235, 318-321.
25. Gentleman, R.; Ihaka, R. R Statistical Language, version 1.1.1.; Auckland, New Zealand, 2000.
26. Brooks, B. R.; Janezic, D.; Karplus, M. J. Comput. Chem. 1995, 16, 1522-1542.
27. Fisher, S.; Smith, J. C.; Verma, C. S. J. Phys. Chem. B 2001, 105, 8050-8055.
28. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Proteins 1993, 17, 412.
29. Caves, L. S.; Evanseck, J. D.; Karplus, M. Protein Sci. 1998, 7, 649-666.
30. Zhang, M.; Tanaka, T.; Ikura, M. Nat. Struct. Biol. 1995, 2, 758-767.
31. van Vlijmen, H. W. T.; Karplus, M. J. Phys. Chem. B 1999, 103, 3009-3021.
32. Afshar, M.; Caves, L. S. D.; Hubbard, R. E.; Grassy, G.; Calas, B. A Unified Structural Model of Target Recognition in Calmodulin and Myosin Light Chains. Unpublished work, 1997.
33. Schumacher, M. A.; Rivard, A. F.; Bachinger, H. P.; Adelman, J. P. Nature (London) 2001, 410, 1120-1124.
34. Drum, C. L.; Yan, S. Z.; Bard, J.; Shen, Y. Q.; Lu, D.; Soelaiman, S. Grabarek, Z.; Bohm, A.; Tang, W. J. Nature (London) 2002, 415, 396-402.