Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase

Journal of Computational Chemistry

Volumn 17, Issue 14, 1996, Pages 1598-1611

  Cummins, Peter L ^a   Gready, Jill E ^a,b  

^a UNIVERSITY OF SYDNEY   (Australia)

^b Biology and Environment   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001142724     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19961115)17:14<1598::AID-JCC2>3.0.CO;2-G     Document Type: Article

References (38)

1. T. Solmajer and E. L. Mehler, Prof. Eng., 4, 911 (1991).
2. G. E. Arnold and R. L. Ornstein, Proteins, 18, 19 (1994).
3. K. A. Sharp, In Computer Simulation of Biomolecular Systems, Vol. 2, W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden, 1993, pp. 147-160.
4. B. von Freyberg and W. Braun, J. Comput. Chem., 5, 510 (1993).
5. F. Floris and J. Tomasi, J. Comput. Chem., 10, 616 (1989).
6. W. F. van Gunsteren and H. J. C. Berendsen, J. Mol. Biol., 176, 559 (1984).
7. C. F. Wong and J. A. McCammon, Israel J. Chem., 27, 211 (1986).
8. P. Ahlström, O. Teleman, and B. Jönsson, J. Am. Chem. Soc., 110, 4198 (1988).
9. Y. Komeiji, M. Uebayasi, J. Someya, and I. Yamato, Proteins, 16, 268 (1993).
10. D. S. Harlsough and K. M. Merz, J. Am. Chem. Soc., 115, 6529 (1993).
11. M. Berkowitz and J. A. McCammon, Chem. Phys. Lett., 90, 215 (1982).
12. C. L. Brooks, A. Brunger, and M. Karplus, Biopolymers, 24, 843 (1985).
13. M. Mezei and D. L. Beveridge, Ann. NY Acad. Sci., 482, 1 (1986).
14. C. A. Reynolds, P. M. King, and W. G. Richards, Mol. Phys., 76, 251 (1992).
15. R. L. Blakley, In Folates and Pterins, Chemistry and Biochemistry of Folates, Vol. 1. R. L. Blakley and S. J. Benkovic, Eds., Wiley, New York, 1984, pp. 191-253.
16. V. Thibault, M. J. Koen, and J. E. Gready, Biochemistry, 24, 4761 (1985).
17. M. T. G. Ivery and J. E. Gready, Biochemistry, 34, 3724 (1995).
18. M. T. G. Ivery and J. E. Gready, J. Med. Chem., 37, 4211 (1994).
19. J. E. Gready, In Chemistry and Biology of Pteridines 1989, H.-Ch Curtius, S. Ghisla, and N. Blau, Eds., de Gruyter, Berlin, 1990, pp. 23-30.
20. P. L. Cummins and J. E. Gready, Proteins Struct. Funct. Genet., 15, 426 (1993).
21. P. L. Cummins and J. E. Gready, J. Comput.-Aided Mol, Design, 7, 535 (1993).
22. T. Solmajer and E. L. Mehler, Int. J. Quant. Chem., 44, 291 (1992).
23. K. S. Kim, Chem. Phys. Lett., 156, 261 (1989).
24. S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem., 7, 230 (1986).
25. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984).
26. P. L. Cummins, K. Ramnarayan, U. C. Singh, and J. E. Gready, J. Am. Chem. Soc., 113, 8247 (1991).
27. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902 (1985).
28. P. L. Cummins and J. E. Gready, J. Comput. Chem., 15, 704 (1994).
29. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys., 79, 926 (1983).
30. A. T. Hagler, S. Lifson, and P. Dauber, J. Am. Chem. Soc., 101, 5122 (1979).
31. A. T. Hagler, J. R. Maple, T. S. Thacher, G. B. Fitzgerald, and U. Dinur, In Computer Simulation of Biomolecular Systems, W. F. van Gunsteren and P. K. Weiner, Eds., ESCOM, Leiden, 1989, pp. 149-167.
32. S. Hirono and P. A. Kollman, J. Mol. Biol., 212, 196 (1990).
33. M. A. McTigue, J. F. Davies, B. T. Kaufman, and J. Kraut, Biochemistry, 31, 7264 (1992).
34. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys., 81, 3684 (1984).
35. W. F. van Gunsteren and H. J. C. Berendsen, Mol. Phys., 34, 1311 (1977).
36. J. J. Wendoloski and J. B. Matthews, Proteins Struct. Funct. Genet., 5, 313 (1989).
37. J. Geunot and P. A. Kollman, Protein Sci., 1, 1185 (1992).
38. P. E. Smith and W. F. van Gunsteren, In Computer Simulation of Biomolecular Systems, Vol. 2, W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden, 1993, pp. 182-212.