Free-energy landscape of enzyme catalysis

Biochemistry

Volumn 47, Issue 11, 2008, Pages 3317-3321

  Benkovic, Stephen J ^a   Hammes, Gordon G ^b   Hammes Schiffer, Sharon ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; FREE ENERGY;

CATALYTIC NETWORKS; ENZYME MECHANISMS; TRANSITION STATES;

CATALYST ACTIVITY;

DIHYDROFOLATE REDUCTASE; ENZYME;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME BINDING; ENZYME CONFORMATION; ENZYME MECHANISM; LIGAND BINDING; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN FOLDING;

CATALYSIS; ESCHERICHIA COLI PROTEINS; KINETICS; PROTEIN CONFORMATION; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS;

EID: 40849097646     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800049z     Document Type: Article

References (41)

1. Koshland, D. E., Jr. (1960) The active site and enzyme action. Adv. Enzymol. 22, 45-97.
2. Hammes, G. G. (1982) Enzyme Catalysis and Regulation, Academic Press, New York.
3. Fersht, A. (1999) Structure and Mechanism in Protein Science. A Guide to Enzyme Catalysis and Protein Folding, Freeman, New York.
4. Hammes, G. G. (2002) Multiple conformational changes in enzyme catalysis. Biochemistry 41, 8221-8228.
5. Benkovic, S. J., and Hammes-Schiffer, S. (2003) A perspective on enzyme catalysis. Science 301, 1196-1202.
6. Nagel, Z., and Klinman, J. P. (2006) Tunneling and dynamics in enzymatic hydride transfer. Chem. Rev. 106, 3095-3118.
7. Hammes-Schiffer, S., and Benkovic, S. J. (2006) Relating protein motion to catalysis. Annu. Rev. Biochem. 75, 519-541.
8. Purich, D. L. (1996) Contemporary Enzyme Kinetics and Mechanism, 2nd ed., Academic Press, New York.
9. Smiley, R. D., and Hammes, G. G. (2006) Single molecule studies of enzyme mechanisms. Chem. Rev. 106, 3080-3094.
10. English, B. P., Min, W., Van Oijen, A. M., Lee, K. T., Luo, G. B., Sun, H. Y., Cherayil, B. J., Kou, S. C., and Xie, X. S. (2006) Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nat. Chem. Biol. 2, 87-94.
11. Palmer, A. G. (2004) NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 104, 3623-3640.
12. Boehr, D. D., McElheny, D., Dyson, H. J., and Wright, P. E. (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638-1642.
13. Watt, E. D., Shimada, H., Kovrigin, E. L., and Loria, J. P. (2007) The mechanism of rate-limiting motions in enzyme function. Proc. Natl. Acad. Sci. U.S.A. 104, 11981-11986.
14. Eisenmesser, E. Z., Millet, O., Labeikovsky, W., Korzhnev, D. M., Wolf-Watz, M., Bosco, D. A., Skalicky, J. J., Kay, L. E., and Kern, D. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117-121.
15. Henzler-Wildman, K. A., Thai, V., Lei, M., Ott, M., Wolf-Watz, M., Fenn, T., Pozharski, E., Wilson, M. A., Petsko, G. A., Karplus, M., Hubner, C. G., and Kern, D. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450, 838-844.
16. Warshel, A. (1991) Computer Modeling of Chemical Reactions in Enzymes and Solutions, John Wiley and Sons, Inc., New York.
17. Hammes-Schiffer, S. (2002) Impact of enzyme motion on activity. Biochemistry 41, 13335-13343.
18. Cui, Q., and Karplus, M. (2002) Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: A study of models and realistic systems. J. Phys. Chem. B 106, 7927-7947.
19. Garcia-Viloca, M., Gao, J., Karplus, M., and Truhlar, D. G. (2004) How enzymes work: Analysis by modern rate theory and computer simulations. Science 303, 186-195.
20. Merlo, C., Dill, K. A., and Weikl, T. R. (2005) φ values in protein-folding kinetics have energetic and structural components. Proc. Natl. Acad. Sci. U.S.A. 102, 10171-10175.
21. Fierke, C. A., Johnson, K. A., and Benkovic, S. J. (1987) Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry 26, 4085-4092.
22. Penner, M. H., and Frieden, C. (1987) Kinetic analysis of the mechanism of Escherichia coli dihydrofolate reductase. J. Biol. Chem. 262, 15908-15914.
23. Sawaya, M. R., and Kraut, J. (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry 36, 586-603.
24. Schnell, J. R., Dyson, H. J., and Wright, P. E. (2004) Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu. Rev. Biophys. Biomol. Struct. 33, 119-140.
25. Zhang, Z. Q., Rajagopalan, P. T. R., Selzer, T., Benkovic, S. J., and Hammes, G. G. (2004) Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate. Proc. Natl. Acad. Sci. U.S.A. 101, 2764-2769.
26. Sikorski, R. S., Wang, L., Markham, K. A., Rajagopalan, P. T. R., Benkovic, S. J., and Kohen, A. (2004) Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis. J. Am. Chem. Soc. 126, 4778-4779.
27. Antikainen, N. M., Smiley, R. D., Benkovic, S. J., and Hammes, G. G. (2005) Conformation coupled enzyme catalysis: Single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry 44, 16835-16843.
28. Radkiewicz, J. L., and Brooks, C. L., III (2000) Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase. J. Am. Chem. Soc. 122, 225-231.
29. Agarwal, P. K., Billeter, S. R., Rajagopalan, P. T. R., Benkovic, S. J., and Hammes-Schiffer, S. (2002) Network of coupled promoting motions in enzyme catalysis. Proc. Natl. Acad. Sci. U.S.A. 99, 2794-2799.
30. Agarwal, P. K., Billeter, S. R., and Hammes-Schiffer, S. (2002) Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis. J. Phys. Chem. B 106, 3283-3293.
31. Wong, K. F., Watney, J. B., and Hammes-Schiffer, S. (2004) Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase. J. Phys. Chem. B 108, 12231-12241.
32. Garcia-Viloca, M., Truhlar, D. G., and Gao, J. (2003) Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase. Biochemistry 42, 13558-13575.
33. Liu, H., and Warshel, A. (2007) The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry 46, 6011-6025.
34. Cameron, C. E., and Benkovic, S. J. (1997) Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry 36, 15792-800.
35. Wang, L., Goodey, N. M., Benkovic, S. J., and Kohen, A. (2006) Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc. Natl. Acad. Sci. U.S.A. 103, 15753-15758.
36. Rajagopalan, P. T. R., Lutz, S., and Benkovic, S. J. (2002) Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates. Biochemistry 41, 12618-12628.
37. Goodey, N. M., and Benkovic, S. J. unpublished results.
38. Kou, S. C., Cherayil, B. J., Min, W., English, B. P., and Xie, X. S. (2005) Single-molecule Michaelis-Menten equations. J. Phys. Chem. B 109, 19068-19081.
39. Osborne, M. J., Schnell, J., Benkovic, S. J., Dyson, H. J., and Wright, P. E. (2001) Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism. Biochemistry 40, 9846-9859.
40. Watney, J. B., Agarwal, P. K., and Hammes-Schiffer, S. (2003) Effect of mutation on enzyme motion in dihydrofolate reductase. J. Am. Chem. Soc. 125, 3745-3750.
41. Wong, K. F., Selzer, T., Benkovic, S. J., and Hammes-Schiffer, S. (2005) Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc. Natl. Acad. Sci. U.S.A. 102, 6807-6812.