Calculation of the reaction pathway for the aromatic ring flip in methotrexate complexed to dihydrofolate reductase

Journal of Physical Chemistry

Volumn 100, Issue 7, 1996, Pages 2510-2518

  Verma, Chandra S ^a   Fischer, Stefan ^b   Caves, Leo S D ^a   Roberts, Gordon C K ^c   Hubbard, Roderick E ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000715079     PISSN: 00223654     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp952574+     Document Type: Article

References (42)

1. Bolin, J. T.; Filman, D. J.; Matthews, D. A.; Hamlin, R. C.; Kraut, J. J. Biol. Chem. 1982, 257, 13650.
2. Clore, G. M.; Gronenborn, A. M.; Birdsall, B.; Feeney, J.; Roberts, G. C. K. Biochem. J. 1984, 217, 659.
3. Northrup, S. H.; Pear, M. R.; Lee, C.-Y.; McCammon, J, A.; Karplus, M. Proc. Natl. Acad, Sci. U.S.A. 1982, 79, 4035.
4. McCammon, J, A.; Lee, C.-Y.; Northrup, S. H. J. Am. Chem. Soc. 1983, 105, 2232.
5. McCammon, J, A.; Harvey, S. C. Dynamics of proteins and nucleic acids; Cambridge University Press: Cambridge, U.K., 1985.
6. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: a theoretical perspective of dynamics, structure and thermodynamics; Advances in Chemical Physics; John Wiley & Sons: New York, 1985; Vol. 71.
7. Ghosh, I.; McCammon, J. A. Biophys. J. 1987, 51, 637.
8. Haydock, C. J. Chem. Phys., 1993, 91, 8199.
9. Smart, O. S.; Akins, J.; Blow, D. M. Protein: Struct., Funct., Genet. 1992, 13, 100.
10. Fischer, S.; Michnick, S.; Karplus, M. Biochemistry 1993, 32, 13280.
11. Lazaridis, T.; Paulaitis, M. E. J. Am. Chem. Soc. 1994, 116, 1546.
12. Fischer, S., Ph.D. Thesis, Harvard University, Cambridge, MA, 1992.
13. Czerminski, R.; Elber, R. Int. J. Quantum Chem. 1990, 24, 167.
14. Choi, C.; Elber, R. J. Chem. Phys. 1991, 94, 751.
15. Lazaridis, T.; Tobias, T. J.; Brooks, C. L., III; Paulaitis, M. E. J. Chem. Phys. 1991, 95, 7612.
16. Smart, O. S. Chem. Phys. Lett. 1994, 222, 503.
17. Fischer, S.; Karplus, M. Chem. Phys. Lett. 1992, 194, 252.
18. Fischer, S.; Dunbrack, R. L., Jr.; Karplus, M. J. Am. Chem. Soc. 1994, 116, 11931.
19. Fischer, S.; Grootenhuis, P. D. J.; Groenen, L. C.; van Hoorn, W. P.; van Veggel, F. C. J. M.; Reinhoudt, D. N.; Karplus, M. J. Am. Chem. Soc. 1995, 117, 1611.
20. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
21. Brooks, C. L., III. Personal communication.
22. Momany, F. A.; Rone, R. J. Comput. Chem. 1992, 13, 888.
23. Lonchariach, R. J.; Brooks, B. R. Proteins: Struct., Funct., and Genet. 1989, 6, 32.
24. Guenot, J.; Kollman, P. A. Protein Sci. 1992, 1, 1185.
25. Guenot, J.; Kollman, P. A. J. Comput. Chem. 1993, 14, 295.
26. Jorgensen, W. L.; Chandrasekhar, J.; Medura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 926.
27. Bruccoleri, R. E.; Karplus, M. J. Comput. Chem. 1986, 7, 165.
28. Gerothanassis, I. P.; Birdsall, B.; Bauer, C. J.; Frenkiel, T. A.; Feeney, J. J. Mol. Biol. 1992, 26, 549.
29. Brown, K. A.; Kraut, J. Faraday Discuss. Chem. Soc. 1992, 93, 217.
30. MacKerell, A. D., Jr.; Nilsson, L.; Rigler, R.; Saenger, W. Biochemistry 1988, 27, 4547.
31. McDonald, J. J.; Brooks, C. L., III. J. Am. Chem. Soc. 1992, 114, 2062.
32. Kraut, J.; Matthews, M. A. In Biological macromolecules and assemblies; Jurnaak, F. A., McPherson, A., Eds.; John Wiley & Sons: New York, 1987; Vol. 3, pp 1-72.
33. Fischer, S. Manuscript in preparation.
34. (a) Stewart, J. J. P. MOPAC (version 6.0). QCPE No. 455.
35. (b) Stewart, J. J. P. J. Comput.-Aided Mol. Des. 1990, 4, 1.
36. Dewar, M. J. S.; Zoebisch, E. J.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902.
37. Hammond, S. J.; Birdsall, B.; Feeney, J.; Searle, M. S.; Roberts, G. C. K.; Cheung, H. T. A. Biochemistry 1987, 26, 8585.
38. Bystroff, C., Oatley, S. J., Kraut, J. Biochemistry 1990, 29, 3263.
39. Berne, B. J.; Borkovec, M.; Straub, J. E. J. Phys. Chem. 1988, 92, 3711.
40. Elber, R. J. Chem. Phys. 1990, 93, 4312.
41. Curtis, N.; Moore, S.; Birdsall, B.; Bloxsidge, J.; Gibson C. L.; Jones, J.; Feeney, J. Biochem. J. 1994, 303, 401.
42. Oldfield, T. J. J. Mol. Graphics 1992, 10, 247.