Accurate QM/MM free energy calculations of enzyme reactions: Methylation by catechol O-methyltransferase

Journal of Chemical Theory and Computation

Volumn 1, Issue 6, 2005, Pages 1240-1251

  Rod, Thomas H ^a   Ryde, Ulf ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33646508010     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct0501102     Document Type: Article

References (56)

1. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196-1202.
2. Chandrasekhar, J.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 2974-2975.
3. Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154-163.
4. Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184-189.
5. Muller, R. P.; Warshel, A. J. Phys. Chem. 1995, 99, 17516-17524.
6. Štrajbl, M.; Hong, G.; Warshel, A. J. Phys. Chem. B 2002, 106, 13333-13343.
7. Iftimie, R.; Salahub, D.; Wei, D.; Schofield, J. J. Chem. Phys. 2000, 113, 4852-4862.
8. Iftimie, R.; Schofield, J. J. Chem. Phys. 2001, 114, 6763-6773.
9. Iftimie, R.; Schofield, J. J. Chem. Phys. 2001, 115, 5891-5902.
10. Iftimie, R.; Salahub, D.; Schofield, J. J. Chem. Phys. 2003, 119, 11285-11297.
11. Iftimie, R.; Schofield, J. Int. J. Quantum Chem. 2003, 91, 404-413.
12. Bandyopadhyay, P. J. Chem. Phys. 2005, 122, 091102.
13. Stanton, R. V.; Peräkylä, M.; Bakowies, D.; Kollman, P. A. J. Am. Chem. Soc. 1998, 120, 3448-3457.
14. Kuhn, B.; Kollman, P. A. J. Am. Chem. Soc. 2000, 122, 2586-2596.
15. Kollman, P. A.; Kuhn, B.; Donini, O.; Perakyla, M.; Stanton, R.; Bakowies, D. Acc. Chem. Res. 2001, 34, 72-79.
16. Zhang, Y.; Liu, H.; Yang, W. J. Chem. Phys. 2000, 112, 3483-3492.
17. Zhang, Y.; Liu, H.; Yang, W. Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions. In Macromolecules-Challenges and Applications; Schlick, T., Gan, H. H., Eds.; Springer-Verlag's Lecture Series in Computational Science and Engineering, Springer: New York, 2002.
18. Liu, H.; Zhang, Y.; Yang, W. J. Am. Chem. Soc. 2000, 122, 6560-6570.
19. Cisneros, G. A.; Liu, H.; Zhang, Y.; Yang, W. J. Am. Chem. Soc. 2003, 125, 10384-10393.
20. Ishida, T.; Kato, S. J. Am. Chem. Soc. 2003, 125, 12035-12048.
21. Ishida, T.; Kato, S. J. Am. Chem. Soc. 2004, 126, 7111-7118.
22. Bentzien, J.; Muller, R. P.; Florián, J.; Warshel, A. J. Phys. Chem. B 1998, 102, 2293-2301.
23. Olsson, M. H. M.; Hong, G.; Warshel, A. J. Am. Chem. Soc. 2003, 125, 5025-5039.
24. Warshel, A. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425-443.
25. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218-6226.
26. Wood, R. H.; Yezdimer, E. M.; Sakane, S.; Barriocanal, J. A.; Doren, D. J. J. Chem. Phys. 1999, 110, 1329-1337.
27. Sakane, S.; Yezdimer, E. M.; Liu, W.; Barriocanal, J. A.; Doren, D. J.; Wood, R. H. J. Chem. Phys. 2000, 113, 2583-2593.
28. Sakane, S.; Liu, W.; Doren, D. J.; Shock, E. L.; Wood, R. H. Geochim. Cosmochim. Acta 2001, 65, 4067-4075.
29. Liu, W.; Sakane, S.; Wood, R. H.; Doren, D. J. J. Phys. Chem. A 2002, 106, 1409-1418.
30. Wood, R. H.; Liu, W.; Doren, D. J. J. Phys. Chem. A 2002, 106, 6689-6693.
31. Ming, Y.; Lai, G.; Tong, C.; Wood, R. H.; Doren, D. J. J. Chem. Phys. 2004, 121, 773-777.
32. Rod, T. H.; Ryde, U. Phys. Rev. Lett. 2005, 94, 138302.
33. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426.
34. Beveridge, D. L.; Di Capua, F. M. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
35. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Commit. Chem. 1983, 4, 187-217.
36. Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720-1735.
37. Ryde, U. J. Comput.-Aided Mol. Des. 1996, 10, 153-164.
38. Hohenberg, P.; Kohn, W. Phys. Rev. 1964, 136, B864-B871.
39. Vidgren, J.; Svensson, L. A.; Liljas, A. Nature 1994, 368, 354-358.
40. Rasmussen, T.; Nilsson, K.; Ryde, U. in preparation.
41. Case, D. A. et al. AMBER 7, University of California, San Francisco, 2002.
42. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165-169.
43. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
44. Frisch, M. J. et al. Gaussian 98 (Revision A.1), Gaussian, Inc., Pittsburgh, PA, 11998.
45. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Commit. Phys. 1977, 23, 327-341.
46. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, Jr., K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
47. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
48. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
49. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868.
50. Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Theor. Chem. Acc. 1997, 97, 119-124.
51. In doing this, it should be ensured that the same grid size is employed in the nonself-consistent calculation as in the last iteration of the self-consistent calculation. In Turbomole notation, we used the grid size 'm3' for the self-consistent calculations, meaning that grid size 3 is used for the very last iteration.
52. Standard errors were computed using a bootstrap procedure.
53. Schultz, E.; Nissinen, E. Biochem. Phamacol. 1989, 38, 3953-3956.
54. Eichkorn, K.; Treutler, O.; Öhm, H.; Häser, M.; Ahlrichs, R. Chem. Phys. Lett. 1995, 240, 283-289.
55. We note that the gap between the distributions of the PC and TSC is closed when all simulations are included. This indicates that inclusion of the enzyme and solvent degrees of freedom into the reaction coordinate would not change the barrier height significantly. The lack of a profound hysteresis further supports this point.
56. Lu, Z.; Yang, W. J. Chem. Phys. 2004, 121, 89-100. CT0501102