Conformational dependence of a protein kinase phosphate transfer reaction

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 43, 2005, Pages 15347-15351

  Henkelman, Graeme ^a   LaBute, Montiago X ^b   Tung, Chang Shung ^b   Fenimore, P W ^b   McMahon, Benjamin H ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Protein dynamics; Quantum chemistry; Reaction kinetics

Indexed keywords

CYCLIC AMP DEPENDENT PROTEIN KINASE; PHOSPHATE; PROTEIN KINASE; SERINE;

ARTICLE; CATALYSIS; CHEMICAL REACTION KINETICS; CRYSTALLIZATION; DENSITY FUNCTIONAL THEORY; ENERGY TRANSFER; ENZYME ACTIVE SITE; ENZYME CONFORMATION; MOLECULAR DYNAMICS; PHOSPHATE TRANSPORT; PHOSPHORYLATION; PRIORITY JOURNAL; QUANTUM CHEMISTRY; STRUCTURE ANALYSIS;

BINDING SITES; CYCLIC AMP-DEPENDENT PROTEIN KINASES; PHOSPHATES; PROTEIN CONFORMATION;

EID: 27344450414     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0506425102     Document Type: Article

References (39)

1. Smith, C. M., Radzio-Andzelm, E., Madhusudan, Akamine, P. & Taylor, S. S. (1999) Prog. Biophys. Mol. Biol. 71, 313-341.
2. Johnson, L. N. & Lewis, R. J. (2001) Chem. Rev. 101, 2209-2242.
3. Pearson, R. B. & Kemp, B. E. (1991) Methods Enzymol. 200, 62-81.
4. Songyang, Z., Lu, K. P., Kwon, Y. T., Tsai, L. H., Filhol, O., Cochet, C., Brickey, D. A., Soderling, T. R., Bartleson, C., Graves, D. J., et. al. (1996) Mol. Cell. Biol. 16, 6486-6493.
5. Pinna, L. A. & Ruzzene, M. (1996) Biochim. Biophys. Acta 1314, 191-225.
6. Brinkworth, R. I., Breinl, R. A. & Kobe, B. (2003) Proc. Natl. Acad. Sci. USA 100, 74-79.
7. Austin R. H., Beeson, K. W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I. C. (1975) Biochemistry 14, 5355-5373.
8. Agmon, N. & Hopfield, J. J. (1983) J. Chem. Phys. 79, 2042-2053.
9. Agmon, N. & Hopfield, J. J. (1983) J. Chem. Phys. 78, 6947-6959.
10. Vojtechovsky, J., Chu, K., Berendzen, J., Sweet, R. M. & Schlichting, I. (1999) Biophys. J. 77, 2153-2174.
11. McMahon, B. H., Stojkovic, B. P., Hay, P. J., Martin, R. L. & Garcia, A. E. (2000) J. Chem. Phys. 113, 6831-6850.
12. Fenimore, P. W., Frauenfelder, H., McMahon, B. H. & Parak, F. G. (2002) Proc. Natl. Acad. Sci. USA 99, 16047-16051.
13. Fenimore, P. W., Frauenfelder, H., McMahon, B. H. & Young, R. D. (2004) Proc. Natl. Acad. Sci. USA 101, 14408-14413.
14. Zheng, J., Knighton, D. R., Ten Eyck, L. F., Karlsson, R., Xuong, N. H., Taylor, S. S. & Sowadski, J. M. (1993) Biochemistry 32, 2154-2161.
15. Madhusudan, Akamine P., Xuong, N. H. & Taylor S. S. (2002) Nat. Struct. Biol. 9, 273-277.
16. Valiev, M., Weare, J. H., Adams, J. A. & Kawai, R. (2003) J. Am. Chem. Soc. 125, 9926-9927.
17. Kresse, G. & Hafner, J. (1993) Phys. Rev. B 47, R558-R561.
18. Kresse, G. & Hafner, J. (1994) Phys. Rev. B 49, 14251-14269.
19. Kresse, G. & Furthmüller, J. (1996) Comput. Mater. Sci. 6, 15-50.
20. Kresse, G. & Furthmüller, J. (1996) Phys. Rev. B 54, 11169-11186.
21. Vanderbilt, D. (1990) Phys. Rev. B 41, 7892-7895.
22. Jónsson, H., Mills, G. & Jacobsen, K. W. (1998) in Classical and Quantum Dynamics in Condensed Phase Simulations, eds. Berne, B. J., Ciccotti, G. & Coker, D. F. (World Scientific, Singapore), pp. 385-404.
23. Henkelman, G. & Jońsson, H. (2000) J. Chem. Phys. 113, 9978-9985.
24. Henkelman, G., Uberuaga, B. P. & Jónsson, H. (2000) J. Chem. Phys. 113, 9901-9904.
25. Henkelman, G. & Jónsson, H. (1999) J. Chem. Phys. 111, 7010-7022.
26. Nemeth, K. & Challacombe, M. (2004) J. Chem. Phys. 121, 2877-2885.
27. Frauenfelder, H., Sligar, S. & Wolynes, P. (1991) Science 254, 1598-1603.
28. Florian, J., Goodman, M. F. & Warshel, A. (2005) Proc. Natl. Acad. Sci. USA 102, 6819-6824.
29. Cheng, Y. H., Zhang, Y. K. & McCammon, J. A. (2005) J. Am. Chem. Soc. 127, 1553-1562.
30. Warshel, A. (2003) Annu. Rev. Biophys. Biomol. Struct. 32, 425-443.
31. Hanggi, F., Talkner, P. & Borkovec, M. (1990) Rev. Mod. Phys. 62, 251-341.
32. Frauenfelder, H. & Wolynes, P. G. (1985) Science 229, 337-345.
33. Zheng, C., Makarov, V. & Wolynes, P. G. (1996) J. Am. Chem. Soc. 118, 2818-2824.
34. Hur, S. & Bruice, T. C. (2003) Proc. Natl. Acad. Sci. USA 100, 12015-12020.
35. Johnson, J. B., Lamb, D. C., Frauenfelder, H., Mueller, J. D., McMahon, B. H., Nienhaus, G. U. & Young, R. D. (1996) Biophys. J. 71, 1563-1573.
36. McMahon, B. H., Muller, J. D., Wraight, C. A. & Nienhaus, G. U. (1998) Biophys. J. 74, 2567-2587.
37. Yang, J., Ten Eyck, L. F., Xuong, N. H. & Taylor, S. S. (2004) J. Mol. Biol. 336, 473-487.
38. Clementi, C., Garcia, A. E. & Onuchic, J. N. (2003) J. Mol. Biol. 326, 933-954.
39. Galburt, E. A. & Stoddard, B. L. (2001) Phys. Today 54, 33-39.