Triple isotopic labeling and kinetic isotope effects: Exposing H-transfer steps in enzymatic systems

Biochemistry

Volumn 50, Issue 29, 2011, Pages 6462-6468

  Sen, Arundhuti ^a   Yahashiri, Atsushi ^a   Kohen, Amnon ^a  

^a The University of Iowa   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC FUNCTIONS; COMPARATIVE STUDIES; DIHYDROFOLATE; ENZYMATIC SYSTEM; EXPERIMENTAL ERRORS; HYDROGEN ISOTOPE; ISOTOPIC LABELING; ISOTOPOLOGUES; KINETIC ISOTOPE EFFECTS; MECHANISM AND KINETICS; MODEL REACTIONS; OBSERVED DATA; RATE LIMITING; STEADY-STATE ANALYSIS; SYNTHETIC TECHNIQUES;

CARRIER MOBILITY; ENZYME KINETICS; HYDROGEN; KINETICS;

ISOTOPES;

DIHYDROBIOPTERIN; DIHYDROFOLIC ACID; ISOTOPE;

ARTICLE; CATALYSIS; CHEMICAL REACTION KINETICS; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; ENZYME ANALYSIS; ERROR; ISOTOPE LABELING; PRIORITY JOURNAL; REDUCTION;

BIOCATALYSIS; ESCHERICHIA COLI; HYDROGEN; ISOTOPE LABELING; KINETICS; NADP; PROTEIN STRUCTURE, SECONDARY; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 79960492493     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi2003873     Document Type: Article

References (35)

1. Cook, P. F. and Cleland, W. W. (2007) Enzyme Kinetics and Mechanism, Garland Science, New York.
2. Parkin, D. W. (1991) Methods for the determination of competitive and noncompetitive kinetic isotope effects, in Enzyme Mechanism from Isotope Effects (Cook, P. F., Ed.) pp 269-290, CRC Press, Boca Raton, FL.
3. Kohen, A. (2006) Kinetic isotope effects as probes for hydrogen tunneling in enzyme catalysis, in Isotope Effects in Chemistry and Biology (Kohen, A. and Limbach, H. H., Eds.) pp 743-764, CRC Press, Boca Raton, FL.
4. Cleland, W. W. (2006) Enzyme mechanism from isotope effects, in Isotope Effects in Chemistry and Biology (Kohen, A. and Limbach, H. H., Eds.) pp 915-930, CRC Press, Boca Raton, FL.
5. Marlier, J. F., Robins, L. I., Tucker, K. A., Rawlings, J., Anderson, M. A., and Cleland, W. W. (2010) A kinetic and isotope effect investigation of the urease-catalyzed hydrolysis of hydroxyurea Biochemistry 49, 8213-8219
6. Zhang, Y., Luo, M., and Schramm, V. L. (2009) Transition states of Plasmodium falciparum and human orotate phosphoribosyltransferases J. Am. Chem. Soc. 131, 4685-4694
7. Sen, A. and Kohen, A. (2010) Enzymatic tunneling and kinetic isotope effects: chemistry at the crossroads J. Phys. Org. Chem. 23, 613-619
8. Northrop, D. B. (1975) Steady-state analysis of kinetic isotope effects in enzymic reactions Biochemistry 14, 2644-2651
9. Northrop, D. B. (1991) Intrinsic isotope effects in enzyme-catalyzed reactions, in Enzyme Mechanism from Isotope Effects (Cook, P. F., Ed.) pp 181-202, CRC Press, Boca Raton, FL.
10. Swain, C. G., Stivers, E. C., Reuwer, J. F., and Schaad, L. J. (1958) Use of hydrogen isotope effects to identify the attacking nucleophile in the enolization of ketones catalyzed by acetic acid J. Am. Chem. Soc. 80, 5885-5893
11. Siebrand, W. and Smedarchina, Z. (2005) Generalized Swain-Schaad relations including tunneling and temperature dependence Chem. Phys. Lett. 410, 370-376 (Pubitemid 40929433)
12. Streitwieser, A., Jagow, R. H., Fahey, R. C., and Suzuki, S. (1958) Kinetic isotope effects in the acetolyses of deuterated cyclopentyl tosylates J. Am. Chem. Soc. 80, 2326-2332
13. Northrop, D. B. and Duggleby, R. G. (1990) Calculations of intrinsic isotope effects and the detection of tunneling in enzyme-catalyzed reactions Bioorg. Chem. 18, 435-439
14. Yahashiri, A., Howell, E. E., and Kohen, A. (2008) Tuning of the H-transfer coordinate in primitive versus well-evolved enzymes ChemPhysChem 9, 980-982
15. Howell, E. E. (2005) Searching sequence space: two different approaches to dihydrofolate reductase catalysis ChemBioChem 6, 590-600 (Pubitemid 40873755)
16. 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
17. Nagel, Z. D. and Klinman, J. P. (2009) A 21st-century revisionists view at a turning point in enzymology Nat. Chem. Biol. 5, 543-550 and references therein.
18. Blakley, R. L. (1960) Crystalline dihydropteroylglutamic acid Nature 188, 231-232
19. 2H]NADPH J. Labelled Compd. Radiopharm. 52, 463-466
20. Markham, K. A., Sikorski, R. S., and Kohen, A. (2004) Synthesis and utility of 14C-labeled nicotinamide cofactors Anal. Biochem. 325, 62-67 (Pubitemid 38050267)
21. McCracken, J. A., Wang, L., and Kohen, A. (2004) Synthesis of R and S tritiated reduced beta-nicotinamide adenine dinucleotide 2′-phosphate Anal. Biochem. 324, 131-136 (Pubitemid 37491133)
22. Markham, K. A., Sikorski, R. S., and Kohen, A. (2003) Purification, analysis, and preservation of reduced nicotinamide adenine dinucleotide 2′-phosphate Anal. Biochem. 322, 26-32 (Pubitemid 37188552)
23. Miller, G. P., Wahnon, D. C., and Benkovic, S. J. (2001) Interloop contacts modulate ligand cycling during catalysis by Escherichia coli dihydrofolate reductase Biochemistry 40, 867-875 (Pubitemid 32108578)
24. Wang, L., Tharp, S., Selzer, T., Benkovic, S. J., and Kohen, A. (2006) Effects of a distal mutation on active site chemistry Biochemistry 45, 1383-1392 (Pubitemid 43214803)
25. Schramm, V. L. (2007) Binding isotope effects: boon and bane Curr. Opin. Chem. Biol. 11, 529-536 (Pubitemid 47588998)
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 (Pubitemid 38490135)
27. Pu, J., Ma, S., Gao, J., and Truhlar, D. G. (2005) Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase J. Phys. Chem. B 109, 8551-8556 (Pubitemid 40750883)
28. Melander, L. and Saunders, W. H. (1987) Reaction Rates of Isotopic Molecules, R.E. Krieger, Malabar, FL.
29. Truhlar, D. G. (2010) Tunneling in enzymatic and nonenzymatic hydrogen transfer reactions J. Phys. Org. Chem. 23, 660-676
30. Cha, Y., Murray, C. J., and Klinman, J. P. (1989) Hydrogen tunneling in enzyme reactions Science 243, 1325-1330 (Pubitemid 19085368)
31. Kohen, A. (2007) Current issues in enzymatic hydrogen transfer from carbon: Tunneling and coupled motion from kinetic isotope effects, in Hydrogen Transfer Reactions (Hynes, J. T., Limbach, H. H., Klinman, J. P., and Schowen, R. L., Eds.) pp 1311-1340, Wiley-VCH, Weinheim.
32. Nagel, Z. D. and Klinman, J. P. (2010) Tunneling and dynamics in enzymatic hydride transfer Chem. Rev. 110, PR41-PR67
33. Roston, D. and Kohen, A. (2010) Elusive transition state of alcohol dehydrogenase unveiled Proc. Natl. Acad. Sci. U.S.A. 107, 9572-9577
34. Bandaria, J., Cheatum, C., and Kohen, A. (2009) Examination of enzymatic H-tunneling through kinetics and dynamics J. Am. Chem. Soc. 131, 10151-10155
35. Agrawal, N., Hong, B., Mihai, C., and Kohen, A. (2004) Vibrationally enhanced hydrogen tunneling in the Escherichia coli thymidylate synthase catalyzed reaction Biochemistry 43, 1998-2006 (Pubitemid 38233262)