Computational studies of the farnesyltransferase ternary complex part II: The conformational activation of farnesyldiphosphate

Biochemistry

Volumn 46, Issue 43, 2007, Pages 12375-12381

  Cui, Guanglei ^a   Merz Jr , Kenneth M ^a  

^a University of Florida   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; COMPUTATIONAL METHODS; CONFORMATIONS; MUTAGENESIS; REACTION KINETICS; THERMODYNAMICS;

FARNESYLDIPHOSPHATES; FARNESYLTRANSFERASE TERNARY COMPLEX; PRENYLATION; TERNARY COMPLEX;

ENZYME KINETICS;

MAGNESIUM; PROTEIN FARNESYLTRANSFERASE;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENERGY; ENZYME ACTIVATION; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME MECHANISM; HYDROGEN BOND; PRIORITY JOURNAL; THERMODYNAMICS; WILD TYPE;

FARNESYLTRANSTRANSFERASE; MODELS, MOLECULAR; MOLECULAR CONFORMATION; POLYISOPRENYL PHOSPHATES; SESQUITERPENES;

EID: 35648982863     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701324t     Document Type: Article

References (38)

1. Adjei, A. A. (2001) Blocking oncogenic Ras signaling for cancer therapy, J. Natl. Cancer I 93, 1062-1074.
2. Resh, M. (1996) Regulation of cellular signaling by fatty acid acylation and prenylation of signal transduction proteins, Cell. Signaling 8, 403-412.
3. Roskoski, R. (2003) Protein prenylation: a pivotal posttranslational process, Biochem. Bioph. Res. Co. 303, 1-7.
4. Seabra, M. (1998) Membrane association and targeting of prenylated Ras-like GTPases, Cell. Signaling 10, 167-172.
5. Sinensky, M. (2000) Recent advances in the study of prenylated proteins, Bba-Mol. Cell. Biol. L 1484, 93-106.
6. Zhang, F. L., and Casey, P. J. (1996) Annu. Rev. Biochem. 65, 241-269.
7. Caponigro, F., Casale, M., and Bryce, J. (2003) Farnesyl transferase inhibitors in clinical development, Expert Opin. Invest. Drugs 12, 943-954.
8. Doll, R. J., Kirschmeier, P., and Bishop, W. R. (2004) Farnesyltransferase inhibitors as anticancer agents: Critical crossroads, Curr. Opin. Drug. Discovery Dev. 7, 478-486.
9. Huang, C. Y., and Rokosz, L. (2004) Farnesyltransferase inhibitors: recent advances, Expert Opin. Ther. Pat. 14, 175-186.
10. Khuri, F. R., Glisson, B. S., Kim, E. S., Statkevich, P., Thall, P. F., Meyers, M. L., et al. (2004) Phase I study of the farnesyltransferase inhibitor lonafarnib with paclitaxel in solid tumors, Clin. Cancer Res. 10, 2968-2976.
11. Rao, S., Cunningham, D., de Gramont, A., Scheithauer, W., Smakal, M., Humblet, Y., et al. (2004) Phase III double-blind placebo-controlled study of farnesyl transferase inhibitor R115777 in patients with refractory advanced colorectal cancer, J. Clin. Oncol. 22, 3950-3957.
12. Taveras, A. G., Kirschmeier, P., and Baum, C. M. (2003) SCH-66336 (Sarasar (R)) and other benzocycloheptapyridyl farnesyl protein transferase inhibitors: Discovery, biology and clinical observations, Curr. Top. Med. Chem. 3, 1103-1114.
13. Hightower, K. E., De, S., Weinbaum, C., Spence, R. A., and Casey, P. J. (2001) Lysine(164)alpha of protein farnesyltransferase is important for both CaaX substrate binding and catalysis, Biochem. J. 360, 625-631.
14. Wu, Z., Demma, M., Strickland, C. L., Radisky, E. S., Poulter, C. D., Le, H. V., and Windsor, W. T. (1999) Farnesyl protein transferase: Identification of K164 alpha and Y300 beta as catalytic residues by mutagenesis and kinetic studies, Biochemistry 38, 11239-11249.
15. Pickett, J. S., Bowers, K. E., Hartman, H. L., Fu, H. W., Embry, A. C., Casey, P. J., and Fierke, C. A. (2003) Kinetic studies of protein farnesyltransferase mutants establish active substrate conformation, Biochemistry 42, 9741-9748.
16. Dunten, P., Kammlott, U., Crowther, R., Weber, D., Palermo, R., and Birktoft, J. (1998) Protein farnesyltransferase: Structure and implications for substrate binding, Biochemistry 37, 7907-7912.
17. Long, S. B., Casey, P. J., and Beese, L. S. (1998) Cocrystal structure of protein farnesyltransferase complexed with a farnesyl diphosphate substrate, Biochemistry 37, 9612-9618.
18. Long, S. B., Casey, P. J., and Beese, L. S. (2000) The basis for K-Ras4B binding specificity to protein farnesyl-transferase revealed by 2 angstrom resolution ternary complex structures, Struct. Fold. Des. 8, 209-222.
19. Long, S. B., Casey, P. J., and Beese, L. S. (2002) Reaction path of protein farnesyltransferase at atomic resolution, Nature 419, 645-650.
20. Long, S. B., Hancock, P. J., Kral, A. M., Hellinga, H. W., and Beese, L. S. (2001) The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics, Proc. Natl. Acad. Sci. U.S.A. 98, 12948-12953.
21. Park, H. W., Boduluri, S. R., Moomaw, J. F., Casey, P. J., and Beese, L. S. (1997) Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution, Science 275, 1800-1804.
22. Strickland, C. L., Windsor, W. T., Syto, R., Wang, L., Bond, R., Wu, Z., Schwartz, J., Le, H. V., Beese, L. S., and Weber, P. C. (1998) Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue, Biochemistry 37, 16601-16611.
23. Pais, J. E., Bowers, K. E., and Fierke, C. A. (2006) Measurement of the alpha-secondary kinetic isotope effect for the reaction catalyzed by mammalian protein farnesyltransferase, J. Am. Chem. Soc. 128, 15086-15087.
24. Lenevich, S. X. J., Hosokawa, A., Cramer, C. J., and Distefano, M. D. (2007) Transition state analysis of model and enzymatic prenylation reactions, J. Am. Chem. Soc. 129, 5796-5797.
25. Daan Frenkel, B. S. (2002) Understanding Molecular Simulation: From Algorithms to Applications, Vol. 1, 2 ed., Academic Press.
26. Cui, G., Wang, B., and Merz, K. M., Jr. (2005) Computational studies of the farnesyltransferase ternary complex part I: substrate binding, Biochemistry 44, 16513-16523.
27. Saderholm, M. J., Hightower, K. E., and Fierke, C. A. (2000) Role of metals in the reaction catalyzed by protein farnesyltransferase, Biochemistry 39, 12398-12405.
28. Case, D. A., Darden, T. A., Cheatham, T. E. III, Simmerling, C. L., Wang, J., Duke, R. E., et al. (2004) AMBER 8.
29. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., et al. (2003) Gaussian 03.
30. Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the RESP model, J. Phys. Chem. 97, 10269-10280.
31. Wang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A. (2004) Development and testing of a general amber force field, J. Comput. Chem. 25, 1157-1174.
32. Kumar, S., Bouzida, D., Swendsen, R., Kollman, P., and Rosenberg, J. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules .1. the method, J. Comput. Chem. 13, 1011-1021.
33. 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., and Kollman, P. A. (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules, J. Am. Chem. Soc. 117, 5179-5197.
34. Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, W. F., Dinola, A., and Haak, J. R. (1984) Molecular-dynamics with coupling to an external bath, J. Chem. Phys. 81, 3684-3690.
35. Andrea, T. A., Swope, W. C., and Andersen, H. C. (1983) The role of long ranged forces in determining the structure and properties of liquid water, J. Chem. Phys. 79, 4576-4584.
36. Grossfield, A. (2003) Weighted histogram analysis method, http://dasher.wustl.edu/alan/wham/.
37. Roux, B. (1995) The calculation of the potential of mean force using computer simulations, Comput. Phys. Commun. 91, 275-282.
38. Reid, T. S., Terry, K. L., Casey, P. J., and Beese, L. S. (2004) Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity, J. Mol. Biol. 343, 417-433.