Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations

Journal of the American Chemical Society

Volumn 133, Issue 31, 2011, Pages 12050-12062

  López Canut, Violeta ^a   Roca, Maite ^a   Bertrán, Juan ^c   Moliner, Vicent ^b   Tuñón, Iñaki ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSITAT JAUME I   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ALKALINE HYDROLYSIS; ALKALINE PHOSPHATASE; ALKYL GROUPS; CATALYTIC SITES; COORDINATION SHELLS; DIESTERS; DISSOCIATIVE MECHANISMS; LEAVING GROUPS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; MONOESTERS; OXYGEN ATOM; P-NITROPHENYL PHOSPHATE; PHOSPHATE GROUP; PHOSPHODIESTERS; PHOSPHOESTERS; PROMISCUOUS ACTIVITY; REACTION MECHANISM; THEORETICAL STUDY; WATER MOLECULE;

ESCHERICHIA COLI; ESTERS; HYDROLYSIS; MOLECULAR DYNAMICS; MOLECULAR MODELING; OXYGEN; REACTION KINETICS;

PHOSPHATASES;

ALKALINE PHOSPHATASE; ESTER DERIVATIVE; MAGNESIUM; METHYL 4 NITROPHENYLPHOSPHATE; OXYGEN; PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CHEMICAL REACTION; CRYSTAL STRUCTURE; DISSOCIATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME SUBSTRATE; ESCHERICHIA COLI; HYDROLYSIS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MUTATIONAL ANALYSIS; NONHUMAN; PROTEIN INTERACTION; QUANTUM MECHANICS;

ALKALIES; ALKALINE PHOSPHATASE; CATALYTIC DOMAIN; ENZYME ACTIVATION; ESCHERICHIA COLI; HYDROLYSIS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; QUANTUM THEORY;

EID: 79961136627     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja2017575     Document Type: Article

References (66)

1. Gerlt, J. A.; Babbitt, P. C. Annu. Rev. Biochem. 2001, 70, 209-246
2. OBrien, P. J.; Herschlag, D. Chem. Biol. 1999, 6, R91-R105
3. Khersonsky, O.; Roodveldt, C.; Tawfik, D. S. Curr. Opin. Chem. Biol. 2006, 10, 498-508
4. Jensen, R. A. Annu. Rev. Microbiol. 1976, 30, 409-425
5. Zalatan, J. G.; Herschlag, D. J. Am. Chem. Soc. 2006, 128, 1293-1303
6. Boyer, P. D.; Cross, R. L.; Momsen, W. Proc. Natl. Acad. Sci. U.S.A. 1973, 70, 2837-2839
7. Admiraal, S. J.; Herschlag, D. Chem. Biol. 1995, 2, 729-739
8. Cleland, W. W.; Hengge, A. C. Chem. Rev. 2006, 106, 3252-3278
9. Benkovic, S. J.; Schray, K. J. In The Enzymes; Boyer, P. D., Ed.; Academic Press: New York, 1973; Vol. III; pp 201-238.
10. Vetter, I. R.; Wittinghofer, A. Q. Rev. Biophys. 1999, 32, 1-56
11. Ahn, N. Chem. Rev. 2001, 101, 2207-2208
12. Zalatan, J. G.; Catrina, I.; Mitchell, R.; Grzyska, P. K.; OBrien, P. J.; Herschlag, D.; Hengge, A. C. J. Am. Chem. Soc. 2007, 129, 9789-9798
13. Catrina, I.; OBrien, P. J.; Purcell, J.; Nikolic-Hughes, I.; Zalatan, J. G.; Hengge, A. C.; Herschlag, D. J. Am. Chem. Soc. 2007, 129, 5760-5765
14. Nikolic-Hughes, I.; Rees, D. C.; Herschlag, D. J. Am. Chem. Soc. 2004, 126, 11814-11819
15. Yang, K. C.; Metcalf, W. W. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7919-7924
16. OBrien, P. J.; Herschlag, D. Biochemistry 2001, 40, 5691-5699
17. Coleman, J. E. Annu. Rev. Biophys. Biomol. Struct. 1992, 21, 441-483
18. Stefan, C.; Jansen, S.; Bollen, M. Trends Biochem. Sci. 2005, 30, 542-550
19. Goding, J. W.; Grobben, B.; Slegers, H. Biochim. Biophys. Acta 2003, 1638, 1-19
20. Zalatan, J. G.; Fenn, T. D.; Brunger, A. T.; Herschlag, D. Biochemistry 2006, 45, 9788-9803
21. Lassila, J. K.; Herschlag, D. Biochemistry 2008, 47, 12853-12859
22. Zalatan, J. G.; Fenn, T. D.; Herschlag, D. J. Mol. Biol. 2008, 384, 1174-1189
23. Kim, E. E.; Wyckoff, H. W. J. Mol. Biol. 1991, 218, 449-464
24. Stec, B.; Holtz, K. M.; Kantrowitz, E. R. J. Mol. Biol. 2000, 299, 1303-1311
25. Klahn, M.; Rosta, E.; Warshel, A. J. Am. Chem. Soc. 2006, 128, 15310-15323
26. Rosta, E.; Kamerlin, S. C. L.; Warshel, A. Biochemistry 2008, 47, 3725-3735
27. Zalatan, J. G.; Catrina, I.; Mitchell, R.; Grzyska, P. K.; OBrien, P. J.; Herschlag, D.; Hengge, A. C. J. Am. Chem. Soc. 2007, 129, 9789-9798
28. Hollfelder, F.; Herschlag, D. Biochemistry 1995, 34, 12255-12264
29. McWhirter, C.; Lund, E. A.; Tanifum, E. A.; Feng, G.; Sheikh, Q. I.; Hengge, A. C.; Williams, N. H. J. Am. Chem. Soc. 2008, 130, 13673-13682
30. Martí, S.; Moliner, V.; Tuñón, I. J. Chem. Theory Comput. 2005, 1, 1008-1016
31. Gao, J. In Reviews in Computational Chemistry; Kenny, B.; Lipkowitz, D. B. B., Eds.; Wiley: New York, 1995; pp 119-185.
32. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249
33. Gao, J. L.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467-505
34. López-Canut, V.; Martí, S.; Bertrán, J.; Moliner, V.; Tuñón, I. J. Phys. Chem. B 2009, 113, 7816-7824
35. López-Canut, V.; Ruiz-Pernía, J.; Tuñón, I.; Ferrer, S.; Moliner, V. J. Chem. Theory Comput. 2009, 5, 439-442
36. López-Canut, V.; Roca, M.; Bertrán, J.; Moliner, V.; Tuñón, I. J. Am. Chem. Soc. 2010, 132, 6955-6963
37. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. J. Mol. Biol. 1994, 238, 415-436
38. Field, M. J.; Amara, P.; David, L.; Rinaldo, D., Laboratoire de Dynamique Moleculaire, Institut de Biologie Structurale, Grenoble, France, Personal communication, 2004.
39. OBrien, P. J.; Herschlag, D. Biochemistry 2002, 41, 3207-3225
40. Bas, D. C.; Rogers, D. M.; Jensen, J. H. Proteins: Struct., Funct., Bioinf. 2008, 73, 765-783
41. Li, H.; Robertson, A. D.; Jensen, J. H. Proteins: Struct., Funct., Bioinf. 2005, 61, 704-721
42. Singh, U. C.; Kollman, P. A. J. Comput. Chem. 1986, 7, 718-730
43. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733
44. Nam, K.; Cui, Q.; Gao, J. L.; York, D. M. J. Chem. Theory Comput. 2007, 3, 486-504
45. Nam, K.; Gao, J. L.; York, D. M. J. Am. Chem. Soc. 2008, 130, 4680-4691
46. Pranata, J.; Wierschke, S. G.; Jorgensen, W. L. J. Am. Chem. Soc. 1991, 113, 2810-2819
47. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657-1666
48. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
49. Field, M. J. A Practical Introduction to the Simulation of Molecular Systems, 1 st ed.; Cambridge University Press: Cambridge, U.K., 1999.
50. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282
51. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199
52. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
53. Pauling, L. The Nature of the Chemical Bond; Cornell University Press: Ithaca, NY, 1960.
54. Representative snapshots are selected on the basis of the mean square deviations of some distances to the average values. Selected distances include the bond breaking and forming distances and hydrogen bond distances analyzed in the text.
55. Gu, Y. L.; Kar, T.; Scheiner, S. J. Am. Chem. Soc. 1999, 121, 9411-9422
56. Pedzisa, L.; Hay, B. P. J. Org. Chem. 2009, 74, 2554-2560
57. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
58. Frisch, M. J.; Headgordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 275-280
59. Frisch, M. J.; Headgordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 281-289
60. Murphy, J. E.; Tibbitts, T. T.; Kantrowitz, E. R. J. Mol. Biol. 1995, 253, 604-617
61. Kaneko, Y.; Hayashi, N.; Tohe, A.; Banno, I.; Oshima, Y. Gene 1987, 58, 137-148
62. Xu, X.; Kantrowitz, E. R. Biochemistry 1991, 30, 7789-7796
63. Hulett, F. M.; Kim, E. E.; Bookstein, C.; Kapp, N. V.; Edwards, C. W.; Wyckoff, H. W. J. Biol. Chem. 1991, 266, 1077-1084
64. Murphy, J. E.; Kantrowitz, E. R. Mol. Microbiol. 1994, 12, 351-357
65. Shibasaki, K.; Fujii, A.; Mikami, N.; Tsuzuki, S. J. Phys. Chem. A 2006, 110, 4397-4404
66. Note that a bulkier R′ group could require a different selection to replace Lys328.