Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B

Protein Engineering

Volumn 13, Issue 1, 2000, Pages 21-26

  Gargallo, R ^b   Oliva, B ^a   Querol, E ^a   Aviles F X ^a,b  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Electrostatics; Molecular dynamics; Procarboxypeptidase B; Reaction field; Salt effects

Indexed keywords

CARBOXYPEPTIDASE B;

ARTICLE; ELECTRIC FIELD; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; SIMULATION; SWINE;

SUIDAE; SUS SCROFA;

EID: 0033975655     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/13.1.21     Document Type: Article

References (23)

1. Berendsen, H.J.C. (1993) In Van Gunsteren, W.F., Weiner, P.K. and Wilkinson, A.J. (eds), Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, Vol. 2. Leiden, ESCOM, pp. 161-181.
2. Cheatham, I.T.E., Miller, J.L., Fox, T., Darden, T.A. and Kollman, P.A. (1995) J. Am. Chem. Soc., 117, 4193-4194.
3. Coll, M., Guasch, A., Avilés, F.X. and Huber, R. (1991) EMBO J., 10, 1-9.
4. Conejo-Lara, F., Sánchez-Ruiz, J.M., Mateo, P.L., Burgos, F.J., Vendrell, J. and Avilés, F.X. (1991) Eur. J. Biochem., 200, 663-670.
5. Gilson,M.K. (1995) Curr. Opin. Struct. Biol., 5, 216-223.
6. Goto, Y., Takahashi, N. and Fink, A.L. (1990) Biochemistry, 29, 3480-3488.
7. Hendsch, Z.S. and Tidor, B. (1994) Protein Sci., 3, 211-226.
8. Honig, B. and Yang, A.W. (1995) Adv. Protein Chem., 46, 27-58.
9. Kohn, W.D., Kay, C.M. and Hodges, R.S. (1997) J. Mol. Biol., 267, 1039-1052.
10. Levitt, M. and Lifson, S. (1969) J. Mol. Biol., 46, 269-279.
11. Luty, B.A., Davis, M.E., Tironi, I.G. and Van Gunsteren, W.F. (1994) Mol. Simul., 14, 11-20.
12. Martí-Renom, M.A., Mas, J.M., Oliva, B., Querol, E. and Avilés, F.X. (1998) Protein Engng, 11, 101-110.
13. Roxström, G., Velázquez, I., Paulino, M. and Tapia, O. (1998) J. Phys. Chem. B, 102, 1828-1832.
14. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comp. Chem., 23, 327-341.
15. Saito, M. (1994) J. Chem. Phys., 101, 4055-4061.
16. Screiber, H. and Steinhauer, O. (1992) Biochemistry, 31, 5856-5860.
17. Sindelar, C.V., Hendsch, Z.S. and Tidor, B. (1998) Protein Sci., 7, 1898-1914.
18. Talbot, J.A. and Hodges, R.S. (1982) Acc. Chem. Res., 15, 224-230.
19. Tironi, I.G., Sperb, R., Smith, P.E. and Van Gunsteren, W.F. (1995) J. Chem. Phys., 102, 5451-5459.
20. van Gunsteren, W.F. and Berendsen, H.J.C. (1977) Mol. Phys., 34, 1311-1327.
21. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P. and Tironi, I.G. (1996) In Groningen Molecular Simulation (GROMOS) Library Manual. BIOMOS B.V., Zürich.
22. Wimley, W.C., Gawrisch, K., Creamer, T.P. and White, S.H. (1996) Proc. Natl Acad. Sci. USA, 93, 2985-2990.
23. Zhou, N.E., Kay, C.M. and Hodges, R.S. (1992) Biochemistry, 31, 5739-5746.