Simulations of the T⇆R conformational transition in aspartate transcarbamylase

Protein Engineering

Volumn 12, Issue 4, 1999, Pages 285-295

  Roche, Olivier ^a   Field, Martin J ^a  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

Author keywords

Allosteric transition; Aspartate transcarbamylase; Mutant proteins; Targeted molecular dynamics simulations; Tertiary and quaternary structural changes

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE; DIMER; PROTEIN SUBUNIT;

ARTICLE; CONFORMATIONAL TRANSITION; ESCHERICHIA COLI; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SIMULATION; SITE DIRECTED MUTAGENESIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; KINETICS; PROTEIN CONFORMATION; STATISTICAL MODEL; TEMPERATURE; TIME;

ESCHERICHIA COLI;

ASPARTATE CARBAMOYLTRANSFERASE; CATALYTIC DOMAIN; ESCHERICHIA COLI; KINETICS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE; TIME FACTORS;

EID: 0032588951     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/12.4.285     Document Type: Article

References (50)

1. Allen, M. and Tildesley, D. (1987) Computer Simulations of Liquids. Oxford University Press, Oxford, pp. 78-82.
2. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977). J. Mol. Biol., 112, 535-554.
3. Brooks, B., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M. (1983) J. Comput. Chem., 4, 187-217.
4. Brünger, A.T. and Karplus, M. (1988) Proteins: Struct. Funct. Genet., 4, 148-156.
5. Dembowski, N.J., Newton, C.J. and Kantrowitz, E.R. (1990) Biochemistry, 29, 3716-3723.
6. Díaz, J.F., Wroblowski, B., Schlitter, J. and Engelborghs, Y. (1997) Proteins: Struct. Funct. Genet., 28, 434-451.
7. Ech-Cherif El-Kettani, M.A. and Durup, J. (1992) Biopolymers, 32, 516-524.
8. Elber, R. and Karplus, M. (1987) Chem. Phys. Lett., 139, 375-385.
9. Gouaux, J.E., Stevens, R.C. and Lipscomb, W.N. (1990) Biochemistry, 29, 7702-7715.
10. Guilbert, C., Perahia, D. and Mouawad, L. (1995) Comput. Phys. Commun., 91, 263-273.
11. Ha, Y. and Allewell, N.M. (1998) Proteins: Struct. Funct. Genet., 33, 430-443.
12. Hervé, G. (1989) Allosteric Enzymes: Aspartate Transcarbamylase from Escherichia coli. CRC Press, Boca Raton, FL, pp. 61-79.
13. Hinsen, K. (1997) The Molecular Modeling Toolkit: a case study of a large scientific application in Python. In Proceedings of the 6th International Python Conference, pp. 29-35.
14. Ho Lee, B., Ley, B.W., Kantrowitz, E.R., O'Leary, M.H. and Wedler, F.C. (1995) J. Biol. Chem., 270, 15620-15627.
15. Humphrey, W., Dalke, A. and Schluten, K. (1996) J. Mol. Graphics, 14, 33-38.
16. Jacoby, E., Kruger, P., Schlitter, J., Roper, D. and Wollmer, A. (1996) Protein Engng, 9, 113-125.
17. Kabsch, W. (1976) Actda Crystallogr., Sect. A, 32, 922-923.
18. Kabsch, W. (1978) Acta Crystallogr., Sect. A, 34, 827-828.
19. Kantrowitz, E.R. and Lipscomb, W.N. (1990) Trends Biochem. Sci., 15, 53-59.
20. Ke, H.M., Lipscomb, W.N., Cho, Y. and Honzatko, R.B. (1988) J. Mol. Biol., 204, 725-747.
21. Kim, K.H., Pan, Z., Honzatko, R.B., Ke, H.M. and Lipscomb, W.N. (1987) J. Mol. Biol., 196, 853-875.
22. Kneller, G.R. (1991) Mol. Simul., 7, 113-119.
23. Kosman, R.P., Gouaux, J.E. and Lipscomb, W.N. (1993) Proteins: Struct. Funct. Genet., 15, 147-176.
24. Krause, K.L., Volz, K.W. and Lipscomb, W.N. (1985) Proc. Natl Acad. Sci. USA, 82, 1643-1647.
25. Krause, K.L., Volz, K.W. and Lipscomb, W.N. (1987) J. Mol. Biol., 193, 527-553.
26. Ladjimi, M.M., Middleton, S.A., Kelleher, K.S. and Kantrowitz, E.R. (1988) Biochemistry, 27, 268-276.
27. Lazaridis, T., Tobias, D.J., Brooks, C.L., III and Paulatis, M.E. (1990) J. Chem. Phys., 95, 7612-7624.
28. Lipscomb, W.N. (1992) Proc. Robert A. Welch Found. Conf. Chem. Res., 36, 103-143.
29. Lipscomb, W.N. (1994) Adv. Enzymol. Relat. Areas Mol. Biol., 68, 67-151.
30. Loncharich, R.J. and Brooks, B.R. (1989) Proteins: Struct. Funct. Genet., 6, 32-45.
31. Ma, J. and Karplus, M. (1997) Proc. Natl Acad. Sci. USA, 94, 11905-11910.
32. Merritt, E.A. and Murphy, M. (1994) Acta Crystallogr., Sect. D, 50, 869-873.
33. Monod, J., Wyman, J. and Changeux, J.P. (1965) J. Mol. Biol., 12, 88-118.
34. Mouawad, L. and Perahia, D. (1996) J. Mol. Biol., 258, 393-410.
35. Newton, C.J. and Kantrowitz, E.R. (1990) Biochemistry, 29, 1444-1451.
36. Ryckaert, J.P. (1985) Mol. Phys., 55, 549-556.
37. Schlitter, J., Engels, M., Kruger, P., Jacoby, E. and Wollmer, A. (1993) Mol. Simul., 10, 291-308.
38. Steinbach, P.J. and Brooks, B.R. (1994) J. Comput. Chem., 15, 667-683.
39. Stevens, R.C., Gouaux, J.E. and Lipscomb, W.N. (1990) Biochemistry, 29, 7691-7701.
40. Svergun, D.L., Barberato, C., Koch, M.H.J., Fetler, L. and Vachette, P. (1997) Proteins: Struct. Funct. Genet., 27, 110-117.
41. Tanner, J.J., Smith, P.E. and Krause, K.L. (1993) Protein Sci., 2, 927-935.
42. Tauc, P., Keiser, R.T., Kantrowitz, E.R. and Vachette, P. (1994) Protein Sci., 3, 1998-2004.
43. Thiry, L. and Hervé, G. (1978) J. Mol. Biol., 125, 515-534.
44. Thomas, A., Field, M.J., Mouawad, L. and Perahia, D. (1996a) J. Mol. Biol., 257, 1070-1087.
45. Thomas, A., Field, M.J., And Perahia, D. (1996b) J. Mol. Biol., 261, 490-506.
46. Thomas, A., Hinsen, K., Field, M.J. and Perahia, D. (1999) Proteins: Struct. Funct. Genet., 34, 96-112.
47. Tsuruta, H., Vachette, P. and Kantrowitz, E. (1998) Proteins: Struct. Funct. Genet., 31, 383-390.
48. Van Vliet, F., Xi, X.G., De Staercke, C., De Wannamaeker, B., Jacobs, A., Cherfils, J., Ladjimi, M.M., Hervé, G. and Cunin, R. (1991) Proc. Natl Acad. Sci. USA, 88, 9180-9183.
49. Wroblowski, B., Diaz, J.F., Schlitter, J. and Engelborghs, Y. (1997) Protein Engng, 10, 1163-1174.
50. Xi, X.G., Van Vliet, F., Ladjimi, M.M., De Wannamaeker, B., De Staerke, C., Glansdorff, N., Piérard, A., Cunin, R. and Hervé, G. (1991) J. Mol. Biol., 220, 789-799.