Two parallel pathways in the kinetic sequence of the dihydrofolate reductase from mycobacterium tuberculosis

Biochemistry

Volumn 50, Issue 32, 2011, Pages 7045-7056

  Czekster, Clarissa M ^a   Vandemeulebroucke, An ^a   Blanchard, John S ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC CYCLES; DIHYDROFOLATE; DIHYDROFOLATE REDUCTASE; ENERGETIC BARRIERS; ENERGY PROFILE; KINETIC ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; ONE-CARBON UNITS; PARALLEL PATHWAYS; PH DEPENDENCE; PRODUCT RELEASE; RATE-LIMITING STEPS; STEADY STATE; TEMPERATURE STUDY; TETRAHYDROFOLATES; TURNOVER NUMBER; WILD TYPES;

ACTIVATION ENERGY; RATE CONSTANTS; SYNTHESIS (CHEMICAL);

KINETICS;

DIHYDROFOLATE REDUCTASE;

ARTICLE; CATALYSIS; ENZYME KINETICS; HUMAN; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PH; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STEADY STATE; TEMPERATURE; WILD TYPE;

BIOCATALYSIS; ESCHERICHIA COLI; KINETICS; MARKOV CHAINS; MYCOBACTERIUM TUBERCULOSIS; PROTEIN BINDING; RECOMBINANT PROTEINS; TETRAHYDROFOLATE DEHYDROGENASE;

MYCOBACTERIUM TUBERCULOSIS;

EID: 80051486812     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200608n     Document Type: Article

References (38)

1. Kompis, I. M., Islam, K., and Then, R. L. (2005) DNA and RNA synthesis: Antifolates Chem. Rev. 105, 593-620 (Pubitemid 40351635)
2. McGuire, J. J. (2003) Anticancer antifolates: Current status and future directions Curr. Pharm. Des. 9, 2593-2613 (Pubitemid 37456011)
3. Hitchings, G. H., Jr. (1989) Nobel lecture in physiology or medicine-1988. Selective inhibitors of dihydrofolate reductase In Vitro Cell. Dev. Biol. 25, 303-310 (Pubitemid 19149487)
4. Ionescu, R. M., Smith, V. F., O'Neill, J. C., Jr., and Matthews, C. R. (2000) Multistate equilibrium unfolding of Escherichia coli dihydrofolate reductase: Thermodynamic and spectroscopic description of the native, intermediate, and unfolded ensembles Biochemistry 39, 9540-9550 (Pubitemid 30626345)
5. Hammes-Schiffer, S. and Benkovic, S. J. (2006) Relating protein motion to catalysis Annu. Rev. Biochem. 75, 519-541 (Pubitemid 44118042)
6. 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 (Pubitemid 44414038)
7. Czekster, C. M., Vandemeulebroucke, A., and Blanchard, J. S. (2011) Kinetic and Chemical Mechanism of the Dihydrofolate Reductase from Mycobacterium tuberculosis Biochemistry 50, 367-375
8. 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
9. Appleman, J. R., Beard, W. A., Delcamp, T. J., Prendergast, N. J., Freisheim, J. H., and Blakley, R. L. (1990) Unusual transient- and steady-state kinetic behavior is predicted by the kinetic scheme operational for recombinant human dihydrofolate reductase J. Biol. Chem. 265, 2740-2748
10. Thillet, J., Adams, J. A., and Benkovic, S. J. (1990) The kinetic mechanism of wild-type and mutant mouse dihydrofolate reductases Biochemistry 29, 5195-5202 (Pubitemid 20189161)
11. Andrews, J., Fierke, C. A., Birdsall, B., Ostler, G., Feeney, J., Roberts, G. C. K., and Benkovic, S. J. (1989) A kinetic study of wild-type and mutant dihydrofolate reductases from Lactobacillus casei Biochemistry 28, 5743-5750 (Pubitemid 19183709)
12. Margosiak, S. A., Appleman, J. R., Santi, D. V., and Blakley, R. L. (1993) Dihydrofolate reductase from the pathogenic fungus Pneumocystis carinii: Catalytic properties and interaction with antifolates Arch. Biochem. Biophys. 305, 499-508 (Pubitemid 23282938)
13. Liang, P. H. and Anderson, K. S. (1998) Kinetic reaction scheme for the dihydrofolate reductase domain of the bifunctional thymidylate synthase-dihydrofolate reductase from Leishmania major Biochemistry 37, 12206-12212 (Pubitemid 28411306)
14. Lee, J., Yennawar, N. H., Gam, J., and Benkovic, S. J. (2010) Kinetic and Structural Characterization of Dihydrofolate Reductase from Streptococcus pneumoniae Biochemistry 49, 195-206
15. Argyrou, A., Vetting, M. W., Aladegbami, B., and Blanchard, J. S. (2006) Mycobacterium tuberculosis dihydrofolate reductase is a target for isoniazid Nat. Struct. Mol. Biol. 13, 408-413 (Pubitemid 43881580)
16. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein Protein Sci. 4, 2411-2423
17. Morrison, J. F. (1969) Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors Biochim. Biophys. Acta 185, 269-286
18. Morrison, J. F. and Stone, S. R. (1988) Mechanism of the reaction catalyzed by dihydrofolate reductase from Escherichia coli: pH and deuterium isotope effects with NADPH as the variable substrate Biochemistry 27, 5499-5506
19. Johnson, K. A. (1992) Transient state kinetic analysis of enzyme reaction pathways Enzymes 20, 1-61
20. Hiromi, K. (1979) Kinetics of Fast Enzyme Reactions: Theory and Practice, Halsted Press, New York.
21. Cleland, W. W. and Northrop, D. B. (1999) Energetics of substrate binding, catalysis, and product release Methods Enzymol. 308, 3-27 (Pubitemid 29418897)
22. Winzor, D. J. and Jackson, C. M. (2006) Interpretation of the temperature dependence of equilibrium and rate constants J. Mol. Recognit. 19, 389-407 (Pubitemid 44437530)
23. Johnson, K. A., Simpson, Z. B., and Blom, T. (2009) Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data Anal. Biochem. 387, 20-29
24. Johnson, K. A., Simpson, Z. B., and Blom, T. (2009) FitSpace Explorer: An algorithm to evaluate multidimensional parameter space in fitting kinetic data Anal. Biochem. 387, 30-41
25. Qi, F., Dash, R. K., Han, Y., and Beard, D. A. (2009) Generating rate equations for complex enzyme systems by a computer-assisted systematic method BMC Bioinf. 10, 238
26. Stewart, W. J. (2009) Probability, Markov Chains, Queues, and Simulation: The Mathematical Basis of Performance Modeling, Princeton University Press, Princeton, NJ.
27. Northrop, D. B. (1975) Steady-state analysis of kinetic isotope effects in enzymic reactions Biochemistry 14, 2644-2651
28. Carey, F. A. and Sundberg, R. J. (2000) Advanced Organic Chemistry, Part A: Structures and Mechanisms, 4th ed., Kluwer Academic, New York.
29. Johnson, K. A. (1992) Transient-state kinetic analysis of enzyme reaction pathways Enzymes 20, 1-61
30. Gore, M. G. and Bottomley, S. P. (2000) Stopped-flow fluorescence spectroscopy. In Spectrophotometry and spectrofluorimetry (Gore, M. G., Ed.) p 368, Oxford University Press, New York.
31. Cleland, W. W. (1982) The use of pH studies to determine chemical mechanisms of enzyme-catalyzed reactions Methods Enzymol. 87, 390-405
32. Maglia, G., Javed, M. H., and Allemann, R. K. (2003) Hydride transfer during catalysis by dihydrofolate reductase from Thermotoga maritima Biochem. J. 374, 529-535 (Pubitemid 37094113)
33. Chock, P. B. and Gutfreund, H. (1988) Reexamination of the kinetics of the transfer of NADH between its complexes with glycerol-3-phosphate dehydrogenase and with lactate dehydrogenase Proc. Natl. Acad. Sci. U.S.A. 85, 8870-8874 (Pubitemid 19001807)
34. Fersht, A. (1999) Structure and Mechanism in Protein Science, W. H. Freeman and Co., New York.
35. Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Dien, S. J. V., and Rabinowitz, J. D. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli Nat. Chem. Biol. 5, 593-599
36. Gopinathan, K. P., Sirsi, M., and Ramakrishnan, T. (1963) Nicotin-amide-adenine nucleotides of Mycobacterium tuberculosis H37Rv Biochem. J. 87, 444-448
37. Nakano, T., Spencer, H. T., Appleman, J. R., and Blakley, R. L. (1994) Critical role of phenylalanine 34 of human dihydrofolate reductase in substrate and inhibitor binding and in catalysis Biochemistry 33, 9945-9952 (Pubitemid 24286069)
38. Cleland, W. W. and Northrop, D. B. (1999) Energetics of substrate binding, catalysis, and product release Methods Enzymol. 308, 3-27 (Pubitemid 29418897)