Meaningful refinement of polyalanine models using rigid-body simulated annealing: Application to the structure determination of the A31P Rop mutant

Acta Crystallographica Section D: Biological Crystallography

Volumn 55, Issue 7, 1999, Pages 1301-1308

  Glykos, Nicholas M ^a   Kokkinidis, Michael ^a,b  

^a INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

^b UNIVERSITY OF CRETE   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; RNA BINDING PROTEIN; ROP PROTEIN, COLE1 PLASMID;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; MUTATION; PLASMID; PROTEIN CONFORMATION;

BACTERIAL PROTEINS; BACTERIOCIN PLASMIDS; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; RNA-BINDING PROTEINS;

BACTERIA (MICROORGANISMS);

EID: 0033166327     PISSN: 09074449     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0907444999004989     Document Type: Article

References (48)

1. Abrahams, J. P. & Leslie, A. G. W. (1996). Acta Cryst. D52, 30-42.
2. Adams, P. D., Braig, K., Rice, L. M. & Brünger, A. T. (1996). In Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.
3. Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Proc. Natl Acad. Sci. USA, 94, 5018-5023.
4. Banner, D. W., Kokkinidis, M. & Tsernoglou, D. (1987). J. Mol. Biol. 196, 657-675.
5. Bricogne, G. & Irwin, J. (1996). In Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.
6. Brünger, A. T. (1990). Acta Cryst. A46, 46-57.
7. Brünger, A. T. (1992a). X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. Connecticut: Yale University Press.
8. Brünger, A. T. (1992b). Nature (London), 355, 472-474.
9. Brünger, A. T. (1997). Methods Enzymol. 277, 366-396.
10. Brünger, A. T., Adams, P. D. & Rice, L. M. (1998). Curr. Opin. Struct. Biol. 8, 606-611.
11. Butterworth, S., Lamzin, V. S. & Wilson, K. S. (1996). In Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.
12. Castagnoli, L., Scarpa, M., Kokkinidis, M., Banner, D. W., Tsernoglou, D. & Cesareni, G. (1989). EMBO J. 8, 621-629.
13. Castagnoli, L., Vetriani, C. & Cesareni, G. (1994). J. Mol. Biol. 237, 378-387.
14. Cohen, C. & Parry, D. A. D. (1990). Proteins, 7, 1-15.
15. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
16. Cowtan, K. (1994). Jnt CCP4 ESF/EACBM Newslett. Protein Crystallogr. 31, 34-38.
17. Eberle, W., Pastore, A., Sander, C. & Rosch, P. (1991). J. Biomol. NMR, 1, 71-82.
18. Esnouf, R. M. (1997). J. Mol. Graph. 15, 132-134.
19. Gamblin, S. J., Rodgers, D. W. & Stehle, T. (1996). In Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.
20. Glykos, N. M., Cesareni, G. & Kokkinidis, M. (1999). In the press.
21. Jones, T A., Zou, J. Y., Cowan, S. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
22. Kamtekar, S. & Hecht, M. H. (1995). FASEB J. 9, 1013-1022.
23. Kokkinidis, M., Vlassi, M., Papanikolaou, Y., Kotsifaki, D., Kingswell, A., Tsernoglou, D. & Hinz, H.-J. (1993). Proteins, 16, 214-216.
24. Lamzin, V. S. & Wilson, K. S. (1993). Acta Cryst. D49, 129-147.
25. Lamzin, V. S. & Wilson, K. S. (1997). Methods Enzymol. 277, 269-305.
26. Laskowksi, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
27. Lassalle, M. W., Hinz, H.-J., Wenzel, H., Vlassi, M., Kokkinidis, M. & Cesareni, G. (1998). J. Mol. Biol. 279, 987-1000.
28. Munson, M., Anderson, K. S. & Regan, L. (1997). Fold. Des. 2, 77-87.
29. Munson, M., Balasubramanian, S., Fleming, K. G., Nagi, A. D., O'Brien, R., Sturtevant, J. M. & Regan, L. (1996). Protein Sci. 5, 1584-1593.
30. Murshudov, G. N., Dodson, E. J. & Vagin, A. A. (1996). In Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.
31. Nagi, A. D. & Regan, L. (1997). Fold. Des. 2, 67-75.
32. Navaza, J. (1987). Acta Cryst. A43, 645-653.
33. Otwinowski, Z. (1991). In Proceedings of the CCP4 Study Weekend, Isomorphous Replacement and Anomalous Scattering, edited by W. Wolf, P. R. Evans & A. G. W. Leslie. Warrington: Daresbury Laboratory.
34. Pannu, N. S. & Read, R. J. (1996). Acta Cryst. A47, 110-119.
35. Papanikolaou, Y., Kotsifaki, D., Fadouloglou, V., Glykos, N. M., Cesareni, G. & Kokkinidis, M. (1999). Submitted.
36. Perrakis, A., Sixma, T. K., Wilson, K. S. & Lamzin, V. S. (1997). Acta Cryst. D52, 659-668.
37. Peters, K., Hinz, H.-J. & Cesareni, G. (1997). Biol. Chem. 378, 1141-1152.
38. Polisky, B. (1988). Cell, 55, 929-932.
39. Predki, P. F., Agrawal, V., Brünger, A. T. & Regan, L. (1996). Nature Struct. Biol. 3, 54-58.
40. Predki, P. F., Nayak, L. M., Gottlieb, M. B. C. & Regan, L. (1995). Cell, 80, 41-50.
41. Read, R. J. (1986). Acta Cryst. A42, 140-149.
42. Read, R. J. (1997). Methods Enzymol. 277, 110-128.
43. Rice, L. M. & Brünger, A. T. (1994). Proteins, 19, 277-290.
44. Smith, G. D. (1996). In Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.
45. Steif, C., Hinz, H.-J. & Cesareni, G. (1995). Proteins, 23, 83-96.
46. Vlassi, M., Steif, C., Weber, P., Tsernoglou, D., Wilson, K. S., Hinz, H.-J. & Kokkinidis, M. (1994). Nature Struct. Biol. 1, 706-716.
47. Wang, B.-C. (1985). Methods Enzymol. 115, 90-112.
48. Zhang, K. Y. J. & Main, P. (1990). Acta Cryst. A46, 377-381.