Rational choice of molecular dynamics simulation parameters through the use of the three-dimensional autocorrelation method: Application to calmodulin flexibility study

Protein Engineering

Volumn 9, Issue 11, 1996, Pages 959-976

  Yasri, Abdelaziz ^a   Chiche, Laurent ^b   Haiech, Jacques ^b   Grassy, Gerard ^a  

^a Synt:em   (France)

^b CNRS   (France)

Author keywords

Calmodulin; Conformation clustering; Conformational autocorrelation method; Molecular dynamics; Multivariate statistical analysis

Indexed keywords

CALMODULIN;

ARTICLE; CORRELATION FUNCTION; DIELECTRIC CONSTANT; GEOMETRY; HEATING; INTERMETHOD COMPARISON; MECHANICS; MOLECULAR DYNAMICS; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; TIME;

EID: 0029823282     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/9.11.959     Document Type: Article

References (66)

1. Afshar, M., Caves, L.S.D., Guimard, L., Hubbard, R.E., Calas, B., Grassy, G. and Haiech, J. (1994) J. Mol. Biol., 244, 554-571.
2. Åqvist, J. and Tapia, O. (1990) Biopolymers, 30, 205-209.
3. Arnold, G.E. and Ornstein, R.L. (1994) Proteins: Struct. Funct. Genet., 18, 19-33.
4. Babu, Y., Buggs, C. and Cook, W. (1988) J. Mol. Biol., 204, 191-204.
5. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R. (1984) J. Chem. Phys., 81, 3648-3690.
6. Biosym (1993) Insight II 2.2.0. Biosym Technologies, San Diego, CA.
7. Boczko, E.M. and Brooks, C.L. (1995) Science, 269, 393-396.
8. Bowie, J.U., Lüthy, R. and Eisenberg, D. (1991) Science, 253, 164-170.
9. Brooks, C.L., Karplus, M. and Pettit, B.M. (1988) Proteins: a Theoretical Perspective of Dynamics. Structure and Thermodynamics. Wiley, New York,
10. Broto, P., Moreau, G. and Vandycke, C. (1984) Eur. J. Med. Chem., 19, 66-70.
11. Chatfield, C. and Collins, A.J. (1980) Introduction to Multivariate Analysis. Chapman & Hall, London.
12. Chattopadhyaya, R., Meador, W., Means, A. and Quiocho, F. (1992) J. Mol. Biol., 228, 1177-1192.
13. Chothia, C. (1976) J. Mol. Biol., 105, 1-14.
14. Clementi, S., Cruciani, G., Riganelli, D., Valigi, R., Costantine, G., Baroni, M. and Wold, S. (1993) Pharm. Pharmacol. Lett., 3, 5-8.
15. Cregut, D., Liautard, J.-P. and Chiche, L. (1994) Protein Engng, 7, 1333-1344.
16. Daggett, V. and Levitt, M. (1993a) J. Mol. Biol. 232, 600-619.
17. Daggett, V. and Levitt, M. (1993b) Annu. Rev. Biophys. Biomol. Struct., 22, 353-380.
18. Daggett, V. and Levitt, M. (1994) Curr. Opin. Struct. Biol., 4, 291-295.
19. Diamond, R. (1974) J. Mol. Biol., 82, 371-391.
20. Elofsson, A. and Nilsson, L. (1993) J. Mol. Biol., 233, 766-780.
21. Ernest, L.M., Pascual-Ahuir, J.-L. and Weinstein, H. (1991) Protein Engng, 4, 625-637.
22. Fechteler, T., Dengler, U. and Schomburg, D. (1995) J. Mol. Biol., 253, 114-131.
23. Ghose, A.K., Pritchett, A. and Crippen, G.M. (1988) J. Comput. Chem., 7, 565-577.
24. Gilson, M.K. (1995) J. Comput. Chem., 16, 1081-1095.
25. Gordon, H.L. and Somorjai, R.L. (1992) Proteins: Struct. Funct. Genet., 14, 249-264.
26. Grassy, G. and Bonnafous, M. (1988) Chemom. Intell. Lab. Syst., 5, 221-231.
27. Guenot, J. and Kollman, P. (1992) Protein Sci., 1, 1185-1205.
28. Guenot, J. and Kollman, P.A. (1993) J. Comput. Chem., 14, 295-311.
29. Hao, M.H., Pincus, M.R., Rackovsky, S. and Scheraga, H.A. (1993) Biochemistry, 32, 9614-9631.
30. Hartsough, D.S. and Merz, K.M. (1993) J. Am. Chem. Soc., 115, 6529-6537.
31. Hayward, S., Kitao, A. and Go, N. (1994) Protein Sci., 3, 936-943.
32. Hempel, J.C., Fine, R.M., Hassan, M., Ghoul, W., Guaragna, A., Koerber, S.C., Li, Z. and Hagler, A.T. (1995) Biopolymers, 36, 283-301.
33. Holm, L. and Sander, C. (1993) J. Mol. Biol., 233, 123-138.
34. Howard, A.E. and Kollman, P. (1992) Protein Sci., 1, 1173-1184.
35. Hunenberger, P.H., Mark, A.E. and Vangunsteren, W.F. (1995) Proteins: Struct. Funct. Genet., 21, 196-213.
36. Ikura, M., Kay, L.E., Krinks, M. and Bax, A. (1991) Biochemistry, 30, 5498-5504.
37. Ikura, M., Clore, G.M., Gronenborn, A.M., Zhu, G., Klee, C.B. and Bax, A. (1992) Science, 256, 632-638.
38. Karpen, M.E., Tobias, D.J. and Brooks, C.L. (1993) Biochemistry, 32, 412-420.
39. Karplus, M. and Sali, A. (1995) Curr. Opin. Struct. Biol., 5, 58-73.
40. Klee, C.B. and Vanaman, T. (1982) Adv. Protein Chem., 35, 213-321.
41. Komeiji, Y., Uebayasi, M., Someya, J. and Yamato, I. (1993) Proteins, 16, 268-277.
42. Kraulis, P.J. (1991) J. Appl. Crystallogr., 24, 946-950.
43. Kruger, P., Strabburger, W., Wollmer, A. and van Gunsteren, W.F. (1985) Eur. Biophys. J., 13, 77-88.
44. Lee, B. and Richards, F.M. (1971) J. Mol. Biol., 55, 379-400.
45. Levitt, M. (1983a) J. Mol. Biol., 168, 595-620.
46. Levitt, M. (1983b) J. Mol. Biol., 168, 621-657.
47. Makinen, M.W., Troyer, J.M., Werff, H.v.d., Berendsen, H.J.C. and Gunsteren, W.F.V. (1989) J. Mol. Biol., 207, 201-216.
48. McCammon, J.A. and Harvey, S.C. (1987) Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
49. Means, A.R. (1988) Recent Prog. Horm. Res., 223-262.
50. Oxford Molecular (1993) TSAR 2.31: Tools for Structure-Activity Relationships. Oxford Molecular, Oxford.
51. Pearlman, D.A., Case, D.A., Caldwell, J.C., Seibel, G.L., Chandra Singh, U., Weiner, P. and Kollman, P.A. (1991) AMBER 4.0. UCSF, University of California, San Francisco, CA.
52. Rao, S., Wu, S., Satyshur, K., Ling, K., Kung, C. and Sundaralingam, M. (1993) Protein Sci., 2, 436-447.
53. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comput. Phys., 23, 327.
54. Schiffer, C.A., Caldwell, J.W., Kollman, P.A. and Stroud, R.M. (1993) Mol. Simulat., 10, 121.
55. Shenkin, P.S. and McDonald, D.Q. (1994) J. Comput. Chem., 15, 899-916.
56. Sklenar, H., Etchebest, C. and Lavery, R. (1989) Proteins: Struct. Funct. Genet., 6, 46-60.
57. Smith, K.C. and Honig, B. (1994) Proteins: Struct. Funct. Genet., 18, 119-132.
58. Solmajer, T. and Mehler, E.L. (1991) Protein Engng, 4, 911-917.
59. Stouten, P.F.W., Froemmel, C., Nakamura, H. and Sander, C. (1993) Mol. Simulat., 10, 97-120.
60. Swaminathan, S., Ravishanker, G., Beveridge, D.L., Lavery, R., Etchebest, C. and Sklenar, H. (1990) Proteins: Struct. Funct. Genet, 8, 179-193.
61. Taylor, D., Sack, J., Maune, J., Beckingham, K. and Quiocho, F. (1991) J. Mol. Chem., 266, 21375-21380.
62. Troyer, J.M. and Cohen, F.E. (1995) Proteins: Struct. Funct. Genet., 23, 97-110.
63. van Gunsteren, W.F. and Berendsen, H.J.C. (1990) Angew. Chem., Int., Ed. Engl., 29, 992-1023.
64. van Gunsteren, W.F. and Mark, A.E. (1992) Eur. J. Biochem., 204, 947-961.
65. Wagener, M., Sadowski, J. and Gasteiger, J. (1995) J. Am. Chem. Soc., 117, 7769-7775.
66. Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A. (1986) J. Comput. Chem., 7, 230-252.