On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 18, 2004, Pages 6957-6962

  Delarue, Marc ^a   Dumas, Philippe ^b  

^a INSTITUT PASTEUR   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

F ACTIN; HEMOGLOBIN; PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; IMAGE RECONSTRUCTION; LIGAND BINDING; MACROMOLECULE; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; RIBOSOME; STRUCTURE ACTIVITY RELATION; VIRUS PARTICLE; X RAY CRYSTALLOGRAPHY;

CARRIER PROTEINS; COMPUTER SIMULATION; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; PROTEINS; X-RAY DIFFRACTION;

EID: 2342518038     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0400301101     Document Type: Article

References (43)

1. Go, N., Noguti, T. & Nishikawa, T. (1983) Proc. Natl. Acad. Sci. USA 80, 3696-3700.
2. Brooks, B. R. & Karplus, M. (1983) Proc. Natl. Acad. Sci. USA 80, 6571-6575.
3. Levitt, M., Sander, C. & Stern, P. S. (1985) J. Mol. Biol. 181, 423-447.
4. Tirion, M. M. (1996) Phys. Rev. Lett. 77, 1905-1908.
5. Krebs, W. G., Alexandrov, V., Wilson, C. A., Echols, N., Yu, H. & Gerstein, M. (2002) Proteins 48, 682-695.
6. Tama, F. & Sanejouand, Y.-H. (2001) Protein Eng. 14, 1-6.
7. Delarue, M. & Sanejouand, Y.-H. (2002) J. Mol. Biol. 320, 1011-1024.
8. Xu, C., Tobi, D. & Bahar, I. (2003) J. Mol. Biol. 333, 153-168.
9. Tama, F., Valle, M., Frank, J. & Brooks, C. L., 3rd. (2003) Proc. Natl. Acad. Sci. USA 100, 9319-9323.
10. Tama, F. & Brooks, C. L., 3rd. (2002) J. Mol. Biol. 318, 733-747.
11. Hinsen, K. (1998) Proteins 33, 417-429.
12. Bahar, I., Atligan, A. R. & Erman, B. (1997) Fold. Des. 2, 173-181.
13. Atligan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O. & Bahar, I. (2001) Biophys. J. 80, 505-515.
14. Kundu, S., Melton, J. S., Sorensen, D. C. & Philipps Jr., G. N. (2002) Biophys. J. 83, 723-732.
15. Tama, F., Gadea, F. X., Marques, O. & Sanejouand, Y.-H. (2000) Proteins 41, 1-7.
16. Brünger, A. T. (1992) Nature 355, 472-475.
17. Navaza, J. (1994) Acta Crystallogr. A 50, 157-163.
18. Kidera, A. & Go, N. (1990) Proc. Natl. Acad. Sci. USA 87, 3718-3722.
19. Diamond, R. (1990) Acta Crystallogr. A 46, 425-435.
20. Tirion, M. M., ben-Avraham, D., Lorenz, M. & Holmes, K. C. (1995) Biophys. J. 68, 5-12.
21. Press, W. H., Flannery, B. P., Teukolsky, S. A. & Vetterling, W. T. (1992) Numerical Recipes: The Art of Scientific Computing (Cambridge Univ. Press, Cambridge, U.K.).
22. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S. et al. (1998) Acta Crystallogr. D 54, 905-921.
23. CCP4 (1994) Acta Crystallogr. D 50, 760-763.
24. Doruker, P. & Jernigan, R. L. (2003) Proteins 53, 174-181.
25. Rossmann, M. G. (2000) Acta Crystallogr. D 56, 1341-1349.
26. Roseman, A. M. (2000) Acta Crystallogr. D 56, 1332-1340.
27. Navaza, J., Lepault, J., Rey, F. A., Alvarez-Rua, C. & Borge, J. (2002) Acta Crystallogr. D 58, 1820-1825.
28. McLachlan, A. D. (1982) Acta Crystallogr. A 38, 871-873.
29. Jones, A. T. & Kleywegt, G. (1995) Structure 3, 535-540.
30. Kolodny, R., Koehl, P., Guibas, L. & Levitt, M. (2002) J. Mol. Biol. 323, 297-307.
31. Jones, T. A., Zou, J. Y. & Cowan, S. W. (1991) Acta Crystallogr. A 47, 110-119.
32. Koehl, P. & Delarue, M. (1994) J. Mol. Biol. 239, 249-275.
33. Ming, D., Kong, Y., Lambert, M. A., Huang, Z. & Ma, J. (2002) Proc. Natl. Acad. Sci. USA 99, 8620-8625.
34. Ming, D., Kong, Y., Wakil, S. J., Brink, J. & Ma, J. (2002) Proc. Natl. Acad. Sci. USA 99, 7895-7899.
35. Tama, F., Wriggers, W. & Brooks, C. L. 3rd. (2002) J. Mol. Biol. 321, 297-305.
36. Svergun, D. I. & Koch, M. H. J. (2002) Curr. Opin. Struct. Biol. 12, 654-660.
37. Walter, D., Cohen, F. E. & Doniach, S. (2000) J. Appl. Crystallogr. 33, 350-363.
38. Delarue, M., Samama, J. P., Mourey, L. & Moras, D. (1990) Acta Crystallogr. B 46, 550-556.
39. Navaza, J. & Saludjian, P. (1997) Methods Enzymol. 276, 581-594.
40. Brünger, A. T. (1990) Acta Crystallogr. A 46, 46-57.
41. Read, R. J. (1997) Methods Enzymol. 277, 110-128.
42. Delarue, M. & Orland, H. (2000) Acta Crystallogr. A 56, 562-574.
43. Zeng, W. & Doniach, S. (2003) Proc. Natl. Acad. Sci. USA 100, 13253-13258.