Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

Journal of the American Chemical Society

Volumn 125, Issue 6, 2003, Pages 1532-1540

  Devi Kesavan, Lakshmi S ^a   Gao, Jiali ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOPHILIC DISPLACEMENT;

ACTIVATION ENERGY; CATALYST ACTIVITY; DEHALOGENATION; ENZYMES; FREE ENERGY; HYDROGEN BONDS; HYDROPHOBICITY; ISOTOPES; REACTION KINETICS;

MOLECULAR DYNAMICS;

ALKANE DERIVATIVE; CHLORIDE ION; DEHALOGENASE; DICHLOROETHANE; ENZYME; ISOTOPE; UNCLASSIFIED DRUG; WATER;

ARTICLE; CATALYSIS; DEHALOGENATION; DISPERSION; ENZYME KINETICS; ENZYME MECHANISM; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MOLECULAR MODEL; QUANTUM MECHANICS; SIMULATION; SOLVATION;

AMINO ACID SUBSTITUTION; CHLORINE; HYDROGEN BONDING; HYDROLASES; ISOTOPES; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; QUANTUM THEORY; STOCHASTIC PROCESSES; THERMODYNAMICS; XANTHOBACTER;

EID: 0037433269     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja026955u     Document Type: Article

References (74)

1. National Institute for Occupational Safety and Health 1978, Current Intelligence Bulletin # 25, Publication No. 79-146, 91-100.
2. Janssen, D. B.; Scheper, A.; Dijkhuizen, L.; Witholt, B. Appl. Environ. Microbiol 1985, 49, 673-677.
3. Wischnak, C.; Muller, R. Biotechnology, 2nd ed. 2000, 11b, 241-271.
4. Ridder, I. S.; Dijkstra, B. W. Cattech. 2000, 3, 126-142.
5. Franken, S. M.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W. The EMBO J. 1991, 10, 1297-1302.
6. Stucki, G.; Thuer, M. Environ. Sci. Technol. 1995, 29, 2339-45.
7. Verschueren, K. H.; Seljee, F.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W. Nature 1993, 363, 693-8.
8. Schindler, J. F.; Naranjo, P. A.; Honaberger, D. A.; Chang, C.; Brainard, J. R.; Vanderberg, L. A.; Unkefer, C. J. Biochemistry 1999, 38, 5772-5778.
9. Schanstra, J. P.; Janssen, D. B. Biochemistry 1996, 35, 5624-5632.
10. Schanstra, J. P.; Kingman, J.; Janssen, D. B. J. Biol. Chem. 1996, 271, 14747-14753.
11. Pries, F.; Kingma, J.; Krooshof, G. H.; Jeronimus-Stratingh, M.; Bruins, A. P.; Janssen, D. B. J. Biol. Chem. 1995, 270, 10405-10411.
12. Kennes, C.; Pries, F.; Krooshof, G. H.; Bokma, E.; Kingma, J.; Janssen, D. B. Eur. J. Biochem. 1995, 228, 403-407.
13. Damborsky, J.; Kuty, M.; Nemec, M.; Koca, J. J. Chem. Inf. Comput. Sci. 1997, 37, 562-568.
14. Damborsky, J.; Bohac, M.; Prokop, M.; Kuty, M.; Koca, J. Prot. Eng. 1998, 11, 901-907.
15. Dombrosky, J.; Koca, J. Prot. Eng. 1999, 12, 989-998.
16. Kuty, M.; Damborsky, J.; Prokop, M.; Koca, J. J. Chem. Inf. Comput. Sci. 1998, 38, 736-741.
17. Lightstone, F. C.; Zheng, Y.; Bruice, T. C. Bio. Org. Chem. 1998, 26, 169-174.
18. Lightstone, F. C.; Zheng, Y.; Bruice, T. C. J. Am. Chem. Soc. 1998, 120, 5611-5621.
19. Lau, E. Y.; Kahn, K.; Bash, P. A.; Bruice, T. C. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9937-9942.
20. Lewandowicz, A.; Rudzinski, J.; Tronstad, L.; Widersten, M.; Ryberg, P.; Matsson, O.; Paneth, P. J. Am. Chem. Soc. 2001, 123, 4550-4555.
21. Lightstone, F. C.; Zheng, Y.; Maulitz, A. H.; Bruice, T. C. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 8417-8420.
22. Gao, J.; Xia, X. Science 1992, 258, 631-5.
23. Gao, J. Methods and applications of combined quantum mechanical and molecular mechanical potentials: Lipkowitz, K. B., Boyd, D. B., Ed.; VCH: New York, 1995; Vol. 7, pp 119-185.
24. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-49.
25. Field, M. J.; Bash, P., A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733.
26. Stanton, R. V.; Little, L. R.; Merz, K. M., Jr. J. Phys. Chem. 1995, 99, 17 344-17348.
27. Alhambra, C.; Corchado, J.; Sanchez, M. L.; Gao, J.; Truhlar, D. G. J. Am. Chem. Soc. 2000, 122, 8197-8203.
28. Alhambra, C.; Gao, J.; Corchado, J. C.; Villa, J.; Truhlar, D. G. J. Am. Chem. Soc. 1999, 121, 2253-2258.
29. Alhambra, C.; Corchado, J.; Sanchez, M. L.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G. Journal of Physical Chemistry B 2001, 105, 11 326-11 340.
30. Shurki, A.; Strajbl, M.; Villa, J.; Warshel, A. J. Am. Chem. Soc. 2002, 124, 4097-4107.
31. Keuning, S.; Janssen, D. B.; Witholt, B. J. Bacteriol. 1985, 163, 635-639.
32. Verschueren, K. H. G.; Franken, S. M.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W. J. Mol. Biol. 1993, 232, 856-72.
33. Prince, R. C. TIBS 1994, 19, 3-4.
34. Benning, M. M.; Taylor, K. L.; Liu, R.-Q.; Yang, G.; Xiang, H.; Wesenberg, G.; Dunaway-Mariano, D.; Holden, H. M. Biochemistry 1996, 35, 8103-8109.
35. Janssen, D. B.; Schanstra, J. P. Curr. Opin. Biotech 1994, 5, 253-259.
36. Krooshof, G. H.; Ridder, I. S.; Tepper, A. W. J. W.; Vos, G. J.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W.; Janssen, D. B. Biochemistry 1998, 37, 15 013-15 023.
37. Schanstra, J. P.; Ridder, I. S.; Heimeriks, G. J.; Rink, R.; Poelarends, G. J.; Kalk, K. H.; Dijkstra, B. W.; Janssen, D. B. Biochemistry 1996, 35, 13 186-13 195.
38. Brooks, C. L., III.; Karplus, M. J. Chem. Phys. 1983, 79, 6312-25.
39. Bruenger, A. T.; Brooks. C. L., III.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 8458-62.
40. Berkowitz, M.; McCammon, J. A. Chem. Phys. Lett. 1982, 90, 215-217.
41. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
42. Singh, U. C.; Kollman, P. A. J. Comput. Chem. 1986, 7, 718-730.
43. Liu, H.; Zhang, Y.; Yang, W. J. Am. Chem. Soc. 2000, 122, 6560-6570.
44. Gao, J.; Thompson, M. A. Combined Quantum Mechanical and Molecular Mechanical Methods; American Chemical Society: Washington, DC, 1998; Vol. 712.
45. Stewart, J. J. P. Comput. Chem. 1989, 10, 209-220.
46. Truhlar, D. G.; Gao, J.; Alhambra, C.; Garcia-Viloca, M.; Corchado, J.; Sanchez, M. L.; Villa, J. Acc. Chem. Res. 2002, ACS, ASAP.
47. Liu, H.; Mueller-Plathe, F.; van Gunsteren, W. F. J. Mol. Biol. 1996, 261, 454-469.
48. Monard, G.; Merz, K. M., Jr. Acc. Chem. Res. 1999, 32, 904-911.
49. Bash, P. A.; Field, M. J.; Davenport, R. C.; Petsko, G. A.; Ringe, D.; Karplus, M. Biochemistry 1991, 30, 5826-32.
50. Mulholland, A. J.; Richards, W. G. ACS Symp. Ser. 1999, 721, 448-461.
51. Colonna-Cesari, F.; Perahia, D.; Karplus, M.; Eklund, H.; Branden, C. I.; Tapia, O. J. Biol. Chem. 1986, 261, 15273-8.
52. Maulitz, A. H.; Lightstone, F. C.; Zheng, Y.; Bruice, T. C. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 6591-6595.
53. Curtiss, L. A.; Raghavachari, K.; Trucks, G. W.; Pople, J. A. J. Chem. Phys. 1991, 94, 7221-30.
54. Cunningham, M. A.; Ho, L. L.; Nguyen, D. T.; Gillilan, R. E.; Bash, P. A. Biochemistry 1997, 36, 4800-4816.
55. Alhambra, C.; Luz Sanchez, M.; Corchado, J.; Gao, J.; Truhlar, D. G. Chem. Phys. Lett. 2001, 347, 512-518.
56. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
57. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-35.
58. Gao, J.; Amara, P.; Alhambra, C.; Field, M. J. J. Phys. Chem. A 1998, 102, 4714-4721.
59. Amara, P.; Field, M. J.; Alhambra, C.; Gao, J. Theor. Chem. Acc. 2000, 104, 336-343.
60. Valleau, J. P.; Torrie, G. M. A Guide to Monte Carlo for Stastistical Mechanics: 2. Byways.; Berne, B. J., Ed.; Plenum: New York, 1977; Vol. 5, pp 169-194.
61. Bartels, C.; Karplus, M. J. Phys. Chem. B 1998, 102, 865-880.
62. Ryckaert, J. P.; Cicotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-337.
63. Pellerite, M. J.; Brauman, J. I. J. Am. Chem. Soc. 1983, 105, 2672-80.
64. Okamoto, K.; Kita, T.; Araki, K.; Shingu, H. Bull. Chem. Soc. Jpn 1967, 40, 1912-1916.
65. Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154-63.
66. Warshel, A.; Florian, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5950-5955.
67. Ingold, C. K. Structure and Mechanism in Organic Chemistry; 2nd ed.; Cornell University: Ithaca, New York, 1969.
68. Dewar, M. J. S.; Dieter, K. M. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 2225-2229.
69. Gao, J.; Truhlar, D. G. Ann. Rev. Phys. Chem. 2002, 53, 467-505.
70. Garcia-Viloca, M.; Alhambra, C.; Truhlar, D. G.; Gao, J. J. Chem. Phys. 2001, 114, 9953-9958.
71. Ladanyi, B. M.; Stratt, R. M. J. Phys. Chem. 1995, 99, 2502-11.
72. Larsen, R. E.; Goodyear, G.; Stratt, R. M. J. Chem. Phys. 1996, 104, 2987-3002.
73. Corchado, J, C.; Chuang, Y.-Y.; Fast, P. L.; Villa, J.; Coitino, E. L.; Hu, W.-P.; Liu, Y.-P.; Lynch, G. C.; Nguyen, K. A.; Jackels, C. F.; Gu, M. Z.; Rossi, I.; Clayton, S.; Melissas, V. S.; Steckler, R.; Grarrett, B. C.; Isaacson, A. D.; Truhlar, D. G. 7.9.1 ed.; University of Minnesota: Minneapolis, 1998.
74. Truhlar, D. G.; Garrett, B. C. Annu. Rev. Phys. Chem. 1984, 35, 159-89.