Molecular dynamics simulations of calcium-free calmodulin in solution

Journal of Biomolecular Structure and Dynamics

Volumn 19, Issue 5, 2002, Pages 801-819

  Yang, Cheng ^a   Kuczera, Krzysztof ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; CALCIUM BINDING PROTEIN; CALMODULIN; LINK PROTEIN; SOLVENT;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CALCIUM BINDING; CARBOXY TERMINAL SEQUENCE; CHEMICAL INTERACTION; CONFORMATIONAL TRANSITION; DIFFUSION COEFFICIENT; ELECTRIC POTENTIAL; FLUORESCENCE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; RADIATION SCATTERING; SIMULATION;

EID: 0036250080     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2002.10506786     Document Type: Article

References (51)

1. Crivici, A., and Ikura, M., 1995. Annu Rev. Biophys. Biomol. Struct, 24:85–116.
2. Eldik, L. J.V., and Watterson, D. M., 1998. Calmodulin and Calcium Signal Transduction. San Diego, CA:Academic Press.
3. Zhang, M., Tanaka, M., and Ikura, T., 1995. Nature Struct. Biol, 2:758–767.
4. Kuboniwa, H., Tjandra, N., Grzesiek, S., Ren, H., Klee, C. B., and Bax, A., 1995. Nature Struct Biol, 2:768–776.
5. Babu, Y. S., Bugg, C. E., and Cook, W. J., 1988. J. Mol. Biol, 204:191–204.
6. Taylor, D. A., Sack, J. S., Maune, J. F., Beckingham, K., and Quiocho, F. A., 1991. J. Biol. Chem, 266:21375–21380.
7. Chattopdhyaya, R., Meador, W. E., Means, A. R., and Quiocho, F. A., 1992. J. Mol. Biol, 228:1177–1192.
8. Rao, S. T., Wu, S., Satyshur, K. A., Ling, K.-Y., Kung, C., and Sundaralingam, M., 1993. Protein Sci, 2:436–447.
9. Ikura, M., Clore, M., Gronenborn, A. M., Zhu, G., Klee, C. B., and Bax, A., 1992. Science, 256:632–638.
10. Meador, W. E., Means, A. R., and Quiocho, F. A., 1992. Science, 257:1251–1255.
11. Heidorn, D. B., and Trewhella, J., 1988. Biochemistry, 27:909–915.
12. Yao, Y., Schoeneich, C., and Squier, T. C., 1994. Biochemistry, 33:7797–7810.
13. Sun, H., Yin, D., and Squier, T. C., 1999. Biochemistry, 38:12266–12279.
14. Tjandra, N., Kuboniwa, H., and Bax, A., 1995. Eur. J. Biochem, 230:1014–1024.
15. Mehler, E. R., Pascular-Ahuir, J. R., and Weinstein, H., 1991. Prot. Eng, 4:625–617.
16. Vorherr, T., Kessler, O., Mark, A., and Carafoli, E., 1992. Eur. J. Biochem, 204:913–937.
17. van derSpoel, D., Groot, B. L.d., Hayward, S., Berendsen, H. J. C., and Vogel, H. J., 1996. Prot. Sci, 5:2044–2053.
18. Wriggers, W., Mehler, E., Pitici, F., Weinstein, H., and Schulten, K. S., 1998. Biophys. J, 74:16221639
19. Vigil, D., Gallagher, S. C., Trewhella, J., and Garcia, A. E., 2001. Biophys. J, 80:2082–2092.
20. Yang, C., Jas, G. S., and Kuczera, K., 2001. J. Biomol. Struct. Dyn., in press
21. Grubmueller, H., 1996. SOLVATE 1.0program Munich:Ludwig-Maximilians University.
22. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L., 1983. J. Chem. Phys, 79:926–935.
23. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C., 1977. J. Comp. Phys, 23:327–341.
24. Barth, E., Kuczera, K., Leimkuhler, B., and Skeel, R. D., 1995. J. Comp. Chem, 16:1192–1209.
25. Allen, M. P., and Tildesley, D. J., 1987. Computer Simulations of Liquids London:Oxford Science Publications.
26. Feller, S. E., Zhang, Y., and Pastor, R. W., 1995. J. Chem. Phys, 103:4613–4621.
27. Brooks, B. R., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M., 1983. J. Comp. Chem, 4:187–217.
28. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., and Karplus, M., 1998. J. Phys. Chem. B, 102:3386–3616.
29. Sagui, C., and Darden, T. A., 1999. Annu. Rev. Biophys. Biomol. Struct., 28:155–179.
30. Lee, B., and Richards, F. M., 1971. J. Mol. Biol, 55:379–400.
31. Lipari, G., and Szabo, A., 1982. J. Am. Chem. Soc, 104:4559–4570.
32. McQuarrie, D. A., 1976. Statistical Mechanics. New York:Harper and Row.
33. McConnell, J., 1980. Rotational Brownian Motion and Dielectric Theory London:Academic Press.
34. Ehrenberg, M., and Rigler, R., 1972. Chem. Phys. Lett, 14:539–544.
35. Chuang, T. J., and Eisenthal, K. B., 1972. J. Chem. Phys., 57:5094–5097.
36. Shoemaker, D. P., Garland, C. W., and Nibler, J. W., 1996. Experiments in Physical Chemistry., 6 edition New York:The McGraw-Hill Companies, Inc.
37. Amadei, A., Linssen, A. B. M., Van Aalten, D. M.F., and Berendsen, H. J. C., 1996. J. Biomol. Struct. Dyn, 13:615–626.
38. Berendsen, H. J. C., 1999. “ Molecular dynamics simulations:The limits and beyond ”. In Computational Molecular Dynamics:Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering Edited by:Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A. E., Reich, S., and Skeel, R. D., 3–36. Berlin:Springer. In, editors, pages
39. Yang, C., and Kuczera, K., 2001. Images and animations of calmodulin dynamics in solution. http://oolung.chem.ukans.edu/~kuczera/1cll/1cll.html
40. Barlow, D. J., and Thornton, J. M., 1988. J. Mol. Biol., 201:601–619.
41. Linse, S., Helmersson, A., and Forson, S., 1991. J. Biol. Chem, 266:8050–8054.
42. Yao, Y., Yin, D., Jas, G., Kuczera, K., Williams, T. D., Schöneich, C., and Squier, T. C., 1996. Biochemistry, 35:2767–2787.
43. Yin, D., Kuczera, K., and Squier, T. C., 2000. Chem. Res. Toxicol, 13:103–110.
44. Sharov, V. S., and Schoeneich, C. S., 2000. Free Radical Biology & Medicine, 29:986–994.
45. Yuan, T., Ouyang, H., and Vogel, H. J., 1999. J. Biol. Chem., 274:8411–8420.
46. Torre, J. G.d.l., and Carrasco, B., 2000. Biophys. J., 78:719–730.
47. Ikura, M., Spera, S., Barbato, G., Kay, L. E., Krinks, M., and Bax, A., 1991. Biochemistry, 30:92169228
48. Barbato, G., Ikura, M., Kay, L. E., Pastor, R. W., and Bax, A., 1992. Biochemistry, 31:5269–5278.
49. Takusagawa, F., DCAL. a program for crystal contact calculations
50. Kraulis, P. J., 1991. J. Appl. Cryst., 24:946–950.
51. Aqvist, J., 1986. Comput. Chem, 10:97–99.