How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab Initio QM/MM study

Journal of the American Chemical Society

Volumn 127, Issue 5, 2005, Pages 1553-1562

  Cheng, Yuhui ^a   Zhang, Yingkai ^b   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CATALYSIS; COMPUTER SIMULATION; DISSOCIATION; MAGNESIUM PRINTING PLATES; MOLECULAR DYNAMICS; POSITIVE IONS; PROBABILITY DENSITY FUNCTION; REACTION KINETICS;

GLYCINE; PHOSPHORYLATION REACTION; PROTEIN KINASE (PKA); SUBSTRATE PEPTIDES;

ENZYMES;

ADENOSINE TRIPHOSPHATE; CYCLIC AMP DEPENDENT PROTEIN KINASE; GLYCINE; MAGNESIUM; PEPTIDE;

AB INITIO CALCULATION; ARTICLE; CATALYSIS; CHEMICAL BINDING; CHEMICAL MODEL; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ELECTRICITY; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; MUTATION; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTON TRANSPORT; TECHNIQUE; WILD TYPE;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BINDING SITES; CATALYSIS; CYCLIC AMP-DEPENDENT PROTEIN KINASES; ELECTROSTATICS; KINETICS; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; QUANTUM THEORY;

EID: 13444303958     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0464084     Document Type: Article

References (66)

1. Johnson, D. A.; Akamine, P.; Radzio-Andzelm, E.; Madhusudan; Taylor, S. S. Chem. Rev. 2001, 101, 2243-2270.
2. Walsh, D. A.; Perkins, J. P.; Krebs, E. G. J. Biol. Chem. 1968, 243, 3763-3774.
3. Shoji, S.; Titani, K.; Demaille, J. G.; Fischer, E. H. J. Biol. Chem. 1979, 254, 6211-6214.
4. Slice, L. W.; Taylor, S. S. J. Biol. Chem. 1989, 264, 20940-20946.
5. Gibbs, C. S.; Zoller, M. J. J. Biol. Chem. 1991, 266, 8923-8931.
6. Gibbs, C. S.; Knighton, D. R.; Sowadski, J. M.; Taylor, S. S.; Zoller, M. J. J. Biol. Chem. 1992, 267, 4806-4814.
7. Adams, J. A.; McGlone, M. L.; Gibson, R.; Taylor, S. S. Biochemistry 1995, 34, 2447-2454.
8. Yonemoto, W.; McGlone, M. L.; Grant, B.; Taylor, S. S. Protein Eng. 1997, 10, 915-925.
9. Grant, B. D.; Adams, J. A. Biochemistry 1996, 35, 2022-2029.
10. Hemmer, W.; McGlone, M.; Tsigelny, I.; Taylor, S. S. J. Biol. Chem. 1997, 272, 16946-16954.
11. Aimes, R. T.; Hemmer, W.; Taylor, S. S. Biochemistry 2000, 39, 8325-8332.
12. Seifert, M. H. J.; Breitenlechner, C. B.; Bossemeyer, D.; Huber, R.; Holak, T. A.; Engh, R. A. Biochemistry 2002, 41, 5968-5977.
13. Lew, J.; Coruh, N.; Tsigelny, I.; Garrod, S.; Taylor, S. S. J. Biol. Chem. 1997, 272, 1507-1513.
14. Shaffer, J.; Adams, J. A. Biochemistry 1999, 38, 12072-12079.
15. Cheng, X. D.; Shaltiel, S.; Taylor, S. S. Biochemistry 1998, 37, 14005-14013.
16. Madhusudan; Akamine, P.; Xuong, N. H.; Taylor, S. S. Nat. Struct. Biol. 2002, 9, 273-277.
17. Bossemeyer, D.; Engh, R. A.; Kinzel, V.; Ponstingl, H.; Huber, R. EMBO J. 1993, 12, 849-859.
18. Yang, J.; Ten eyck, L. F.; Xuong, N. H.; Taylor, S. S. J. Mol. Biol. 2004, 336, 473-487.
19. Madhusudan; Trafny, E. A.; Xuong, N. H.; Adams, J. A.; Teneyck, L. F.; Taylor, S. S.; Sowadski, J. M. Protein Sci. 1994, 3, 176-187.
20. Zheng, J. H.; Knighton, D. R.; Xuong, N. H.; Taylor, S. S.; Sowadski, J. M.; Teneyck, L. F. Protein Sci. 1993, 2, 1559-1573.
21. Yoon, M. Y.; Cook, P. F. Biochemistry 1987, 26, 4118-4125.
22. Zhou, J.; Adams, J. A. Biochemistry 1997, 36, 2977-2984.
23. Hanks, S. K.; Quinn, A. M. Methods Enzymol. 1991, 200, 38-62.
24. Knighton, D. R.; Cadena, D. L.; Zheng, J. H.; Teneyck, L. F.; Taylor, S. S.; Sowadski, J. M.; Gill, G. N. Structural features that specify tyrosine kinase-activity deduced from homology modeling of the epidermal growth-factor receptor. Proc. Natl. Acad. Sci. U.S.A. 1993, 90 (11).
25. Li, F.; Gangal, M.; Juliano, C.; Gorfain, E.; Taylor, S. S.; Johnson, D. A. J. Mol. Biol. 2002, 315, 459-469.
26. Hart, J. C.; Sheppard, D. W.; Hillier, I. H.; Burton, N. A. Chem. Commun. 1999, 79-80.
27. Hart, J. C.; Hillier, I. H.; Burton, N. A.; Sheppard, D. W. J. Am. Chem. Soc. 1998, 120, 13535-13536.
28. Hutter, M. C.; Helms, V. Protein Sci. 1999, 8, 2728-2733.
29. Sheppard, D. W.; Burton, N. A.; Hillier, I. H. THEOCHEM 2000, 506, 35-44.
30. Hirano, Y.; Hata, M.; Hoshino, T.; Tsuda, M. J. Phys. Chem. B 2002, 106, 5788-5792.
31. Ginalski, K.; Grochowski, P.; Lesyng, B.; Shugar, D. Int. J. Quantum Chem. 2002, 90, 1129-1139.
32. Cavalli, A.; De vivo, M.; Recanatini, M. Chem. Commun. 2003, 1308-1309.
33. Valiev, M.; Kawai, R.; Adams, J. A.; Weare, J. H. J. Am. Chem. Soc. 2003, 125, 9926-9927.
34. Diaz, N.; Field, M. J. J. Am. Chem. Soc. 2004, 126, 529-542.
35. Henkelman, G.; LaBute, M. X.; Tung, C. S.; Fenimore, P. W.; McMahon, B. H. To be published.
36. Hur, S.; Bruice, T. C. The near attack conformation approach to the study of thechorismate to prephenate reaction. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (21).
37. Zhang, Y. K.; Lee, T. S.; Yang, W. T. J. Chem. Phys. 1999, 110, 46-54.
38. Zhang, Y. K.; Liu, H. Y.; Yang, W. T. J. Chem. Phys. 2000, 112, 3483-3492.
39. Zhang, Y.; Liu, H.; Yang, W. Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions. In Methods for Macromolecular Modeling; Schlick, T., et al., Eds.; Springer-Verlag: 2001.
40. Liu, H. Y.; Zhang, Y. K.; Yang, W. T. J. Am. Chem. Soc. 2000, 122, 6560-6570.
41. Zhang, Y. K.; Kua, J.; McCammon, J. A. J. Am. Chem. Soc. 2002, 124, 10572-10577.
42. Zhang, Y. K.; Kua, J.; McCammon, J. A. J. Phys. Chem. B 2003, 107, 4459-4463.
43. Cisneros, G. A.; Liu, H. Y.; Zhang, Y. K.; Yang, W. T. J. Am. Chem. Soc. 2003, 125, 10384-10393.
44. Cisneros, G. A.; Wang, M.; Silinski, P.; Fitzgerald, M. C.; Yang, W. T. Biochemistry 2004, 43, 6885-6892.
45. Case, D. A. et al. Amber 7.0; University of California: San Francisco, CA, 2002.
46. Vriend, G. J. Mol. Graphics 1990, 8, 52-56.
47. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
48. Meagher, K. L.; Redman, L. T.; Carlson, H. A. J. Comput. Chem. 2003, 24, 1016-1025.
49. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
50. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
51. Williams, I. H.; Maggiora, G. M. THEOCHEM 1982, 6, 365-378.
52. Ponder, J. W. TINKER, Software Tools for Molecular Design, version 3.6; The most updated version for the TINKER program can be obtained from J. W. Ponder's World Wide Web site at http://dasher.wustl.edu/tinker., February 1998.
53. Mildvan, A. S. Proteins 1997, 29, 401-416.
54. Kim, K.; Cole, P. A. J. Am. Chem. Soc. 1997, 119, 11096-11097.
55. Kim, K.; Cole, P. A. J. Am. Chem. Soc. 1998, 120, 6851-6858.
56. Williams, D. M.; Cole, P. A. J. Am. Chem. Soc. 2002, 124, 5956-5957.
57. Parang, K.; Till, J. H.; Ablooglu, A. J.; Kohanski, R. A.; Hubbard, S. R.; Cole, P. A. Nat. Struct. Biol. 2001, 8, 37-41.
58. Granot, J.; Mildvan, A. S.; Bramson, H. N.; Kaiser, E. T. Biochemistry 1980, 19, 3537-3543.
59. Cook, A.; Lowe, E. D.; Chrysina, E. D.; Skamnaki, V. T.; Oikonomakos, N. G.; Johnson, L. N. Biochemistry 2002, 41, 7301-7311.
60. Ablooglu, A. J.; Frankel, M.; Rusinova, E.; Ross, J. B. A.; Kohanski, R. A. J. Biol. Chem. 2001, 276, 46933-46940.
61. Poyner, R. R.; Larsen, T. M.; Wong, S. W.; Reed, G. H. Arch. Biochem. Biophys. 2002, 401, 155-163.
62. Moore, M. J.; Kanter, J. R.; Jones, K. C.; Taylor, S. S. J. Biol. Chem. 2002, 277, 47878-47884.
63. Moore, M. J.; Adams, J. A.; Taylor, S. S. J. Biol. Chem. 2003, 278, 10613-10618.
64. Adams, J. A.; Taylor, S. S. Biochemistry 1992, 31, 8516-8522.
65. Herberg, F. W.; Doyle, M. L.; Cox, S.; Taylor, S. S. Biochemistry 1999, 38, 6352-6360.
66. Hanks, S. K.; Hunter, T. FASEB J. 1995, 9, 576-596.