Functionally important conformations of the met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations

Journal of the American Chemical Society

Volumn 131, Issue 15, 2009, Pages 5642-5647

  Arora, Karunesh ^a   Brooks, Charles L ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BARRIER HEIGHTS; BINDING POCKETS; CATALYTIC REACTIONS; COFACTOR; CONFORMATIONAL CHANGE; CONFORMATIONAL STATE; DIHYDROFOLATE; DIHYDROFOLATE REDUCTASE; ENERGY PROFILE; FREE ENERGY LANDSCAPE; LIGAND BINDING; QUANTITATIVE ESTIMATES; REACTION RATE THEORY; REACTIVE GROUP; TERNARY COMPLEX; THERMAL FLUCTUATIONS; TWO-STATE;

CATALYSIS; CONFORMATIONS; ENZYMES; FREE ENERGY; REACTION RATES;

BINDING ENERGY;

DIHYDROFOLATE REDUCTASE; DIHYDROFOLIC ACID; METHIONINE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; DRUG DERIVATIVE; FOLIC ACID; LIGAND; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIFFUSION COEFFICIENT; ENZYME STRUCTURE; LIGAND BINDING; THERMODYNAMICS; BINDING SITE; CHEMISTRY; KINETICS; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION;

BINDING SITES; FOLIC ACID; KINETICS; LIGANDS; NADP; PROTEIN BINDING; PROTEIN CONFORMATION; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS;

EID: 67849095470     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja9000135     Document Type: Article

References (53)

1. Huennekens, F. M. Protein Sci. 1996, 5, 1201-1208.
2. Blakely, R. L. In Chemistry and Biochemistry of Folates. In folates and pterins; Blakely, R. L., Benkovic, S. J., Eds.; Wiley: New York, 1984; Vol. 3, pp 191-253.
3. (a) Radkiewicz, J. L.; Brooks, C. L., III. J. Am. Chem. Soc. 2000, 122, 225-231.
4. (b) Agarwal, P. K.; Billeter, S. R.; Rajagopalan, P. T. R.; Benkovic, S. J.; Hammes-Schiffer, S. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2794-2799.
5. (c) Rod, T. H.; Brooks, C. L., III. J. Am. Chem. Soc. 2003, 125, 8718-8719.
6. (d) Rod, T. H.; Radkiewicz, J. L.; Brooks, C. L., III. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6980-6985.
7. (e) Thorpe, I. F.; Brooks, C. L., III. J. Phys. Chem. B 2003, 107, 14042-14051.
8. (f) Thorpe, I. F.; Brooks, C. L., III. Proteins: Struct. Funct. Genet. 2004, 57, 444-457.
9. (g) Thorpe, I. F.; Brooks, C. L., III. J. Am. Chem. Soc. 2005, 127, 12997-13006.
10. (h) Okazaki, K.; Koga, N.; Takada, S.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11844-11849.
11. (i) Chen, J.; Dima, R. I.; Thirumalai, D. J. Mol. Biol. 2007, 374, 250-266.
12. (a) Fierke, C. A.; Johnson, K. A.; Benkovic, S. J. Biochemistry 1987, 26, 4085-4092.
13. (b) Epstein, D. M.; Benkovic, S. J.; Wright, P. E. Biochemistry 1995, 34, 11037-11048.
14. (c) Cannon, W. R.; Singleton, S. F.; Benkovic, S. J. Nat. Struct. Biol. 1996, 3, 821-833.
15. (d) Miller, G. P.; Benkovic, S. J. Biochemistry 1998, 37, 6327-6335.
16. (e) Miller, G. P.; Wahnon, D. C.; Benkovic, S. J. Biochemistry 2001, 40, 867-875.
17. (f) Osborne, M. J.; Schnell, J.; Benkovic, S. J.; Dyson, H. J.; Wright, P. E. Biochemistry 2001, 40, 9846-9859.
18. (g) Rajagopalan, P. T. R.; Lutz, S.; Benkovic, S. J. Biochemistry 2002, 41, 12618-12628.
19. (h) Osborne, M. J.; Venkitakrishnan, R. P.; Dyson, H. J.; Wright, P. E. Protein Sci. 2003, 12, 2230-2238.
20. (i) Schnell, J. R.; Dyson, H. J.; Wright, P. E. Biochemistry 2004, 43, 374-383.
21. (j) Venkitakrishnan, R. P.; Zaborowski, E.; McElheny, D.; Benkovic, S. J.; Dyson, H. J.; Wright, P. E. Biochemisty 2004, 43, 16046-16055.
22. (k) McElheny, D.; Schnell, J. R.; Lansing, J. C.; Dyson, H. J.; Wright, P. E. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 5032-5037.
23. (l) Boehr, D. D.; McElheny, D.; Dyson, H. J.; Wright, P. E. Science 2006, 313, 1638-1642.
24. (m) Boehr, D. D.; Dyson, H. J.; Wright, P. E. Biochemistry 2008, 47, 9227-33.
25. Sawaya, M. R.; Kraut, J. Biochemistry 1997, 36, 586-603.
26. Benkovic, S. J.; Fierke, C. A.; Naylor, A. M. Science 1988, 239, 1105-1110.
27. (a) Volkman, B. F.; Lipson, D.; Wemmer, D. E.; Kern, D. Science 2001, 291, 2429-33.
28. (b) Okazaki, K.-I.; Takada, S. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11182-11187.
29. Arora, K.; Brooks, C. L., III Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18496-18501.
30. Banavali, N. K.; Roux, B. J. Am. Chem. Soc. 2005, 127, 6866-6876.
31. (a) Kitahara, R.; Sareth, S.; Yamada, H.; Ohmae, E.; Gekko, K.; Akasaka, K. Biochemistry 2000, 39, 12789-12795.
32. (b) Ohmae, E.; Tatsuta, M.; Abe, F.; Kato, C.; Tanaka, N.; Kunugi, S.; Gekko, K. Biochim. Biophys. Acta. 2008, 1784, 1115-21.
33. (a) Wu, Y.-D.; Houk, K. N. J. Am. Chem. Soc. 1987, 109, 2226-2227.
34. (b) Shrimpton, P.; Allemann, R. K. Protein Sci. 2002, 11, 1442-1451.
35. Khavrutskii, I.; Price, D.; Lee, J.; Brooks, C. L., III. Protein. Sci. 2007, 16, 1087-100.
36. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196-1202.
37. Cameron, C. E.; Benkovic, S. J. Biochemistry 1997, 36, 15792-15800.
38. Adams, J. A.; Fierke, C. A.; Benkovic, S. J. Biochemistry 1991, 30, 11046-11054.
39. Caratzoulas, S.; Mincer, J. S.; Schwartz, S. D. J. Am. Chem. Soc. 2002, 124, 3270-3276.
40. Laidler, K. J. Chemical Kinetics; Prentice Hall: New Jersey, 1987; Vol. 3.
41. Hanggi, P.; Talkner, P.; Borkovec, M. Rev. Mod. Phys. 1990, 62, 251-341.
42. Best, R.; Hummer, G. Phys. Rev. Lett. 2006, 96, 228104-228108.
43. Hummer, G.; Garćia, A.; Garde, S. Phys. Rev. Lett. 2000, 85, 2637-2640.
44. Hamelberg, D.; Shen, T.; McCammon, J. A. J. Chem. Phys. 2006, 125, 094905-094912.
45. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Chem. 1977, 23, 327-341.
46. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
47. MacKerell, A. D., Jr. J. Phys. Chem. B 1998, 102, 3586-3616.
48. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J. Am. Chem. Soc. 2004, 126, 698-699.
49. Chu, J.-W.; Trout, B. L.; Brooks, B. R. J. Chem. Phys. 2003, 119, 12708-12717.
50. (a) Michael, S. L.; Salsbury, F. R., Jr.; Brooks, C. L., III. J. Chem. Phys. 2002, 116, 10606-10614.
51. (b) Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. J. Comput. Chem. 2003, 24, 1348-1356.
52. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
53. Hummer, G. New J Phys. 2005, 7, 34-48.