Locating the rate-determining step(s) for three-step hydrolase-catalyzed reactions with dynafit

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1784, Issue 5, 2008, Pages 827-833

  Zhang, Daoning ^a   Kovach, Ildiko M ^a   Sheehy, John Paul ^a  

^a CATHOLIC UNIVERSITY OF AMERICA   (United States)

Author keywords

Blood cascade enzymes; Elementary rate constants; Enzyme kinetics; Progress curve; Proton inventories; Solvent isotope effects

Indexed keywords

ACTIVATED PROTEIN C; AMINO ACID DERIVATIVE; ANILIDE; BLOOD CLOTTING FACTOR 10A; BUFFER; DEUTERIUM; HYDROCHLORIC ACID; HYDROLASE; THROMBIN;

ANALYTIC METHOD; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; CONCENTRATION (PARAMETERS); ENZYME MECHANISM; ERROR; HYDROLYSIS; MATHEMATICAL COMPUTING; MICHAELIS MENTEN KINETICS; PH; PRIORITY JOURNAL; TEMPERATURE;

ANIMALS; CATALYSIS; DEUTERIUM; FACTOR XA; HUMANS; HYDROLASES; HYDROLYSIS; KINETICS; RABBITS; REPRODUCIBILITY OF RESULTS; SOFTWARE; SUBSTRATE SPECIFICITY;

EID: 41949100471     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2008.02.004     Document Type: Article

References (36)

1. Kuzmic P. Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal. Biochem. 237 (1996) 260-273
2. Garfinkel D., Ching S.W., Adelman M., and Clark P. Techniques and problems in the construction of computer models of biochemical systems including real enzymes. Ann. N. Y. Acad. Sci. 128 (1966) 1054-1068
3. Barshop B.A., Wrenn R.F., and Frieden C. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM-A flexible. Portable Syst., Anal. Biochem. 130 (1983) 134-145
4. Zimmerle C.T., and Frieden C. Analysis of progress curves by simulations generated by numerical integration. Biochem. J. 258 (1989) 381-387
5. Duggleby R.G. Quantitative analysis of enzyme progress curves by non-linear regression. Methods Enzymol. 249 (1995) 61-90
6. Goudar C.T., Sonnad J.R., and Duggleby R.G. Parameter estimation using a direct solution of the integrated Michaelis-Menten equation. Biochim. Biophys. Acta 1429 (1999) 377-383
7. Fersht A. Structure and Mechanism in Protein Science (1999), W. H. Freeman and Co., NY, NY 1-631
8. Hedstrom L. Serine protease mechanism and specificity. Chem. Rev. 102 (2002) 4501-4524
9. Brouwer A.C., and Kirsch J.F. Investigation of diffusion-limited rates of chymotrypsin reactions by viscosity variation. Biochemistry 21 (1982) 1302-1307
10. Stone S.R., Betz A., and Hofsteenge J. Mechanistic studies on thrombin catalysis. Biochemistry 30 (1991) 9841-9848
11. +-activated enzyme. Biochemistry 31 (1992) 11721-11730
12. Picozzi M., Landolfi R., and Decristofaro R. Effects of protons on the thrombin-fibrinogen interaction. Eur. J. Biochem. 219 (1994) 1013-1021
13. Hopfner K.P., and Di Cera E. Energetics of thrombin-fibrinogen interaction. Biochemistry 31 (1992) 11567-11571
14. Vindigni A., and Di Cera E. Release of fibrinopeptides by the slow and fast forms of thrombin. Biochemistry 35 (1996) 4417-4426
15. Dicera E., De Cristofaro R., Albright D.J., and Fenton J.W. Linkage between proton binding and amidase activity in human a-thrombin - effect of ions and temperature. Biochemistry 30 (1991) 7913-7924
16. Zhang D., and Kovach I.M. Deuterium solvent isotope effect and proton-inventory studies of factor Xa-catalyzed reactions. Biochemistry 45 (2006) 14175-14182
17. Enyedy E.J., and Kovach I.M. Proton inventory studies of thrombin-catalyzed reactions of substrates with selected P and P′ sites. J. Am. Chem. Soc. 126 (2004) 6017-6024
18. Lottenberg R., Christensen U., Jackson C.M., and Coleman P.L. Assay of coagulation proteases using peptide chromogenic and fluorogenic substrates. Methods Enzymol. 28 (1981) 341-361
19. Sala N., Owen G.W., and Collen D. A functional assay of Protein C in human plasma. Blood 63 (1984) 671-675
20. Leatherbarrow R.J. GraFit User's Guide. 1992 (1992), Ertihacus Sofware Ltd., Staines, U.K
21. Lottenberg R., and Jackson C.M. Solution composition dependent variation in extinction coefficients for p-nitroaniline. Biochim. Biophys. Acta 742 (1983) 558-564
22. Johnson M.L., and Faunt L.M. Parameter estimation by least-squares methods. Methods Enzymol. 210 (1994) 1-37
23. Johnson M.L. Why, when, and how biochemists should use least squares. Anal. Biochem. 206 (1992) 215-225
24. Venkatasubban K.S., and Schowen R.L. The proton inventory technique. CRC Crit. Rev. Biochem. 17 (1985) 1-44
25. Stein R.L., Elrod J.P., and Schowen R.L. Correlate variations in enzyme-derived and substrate -derived structures of catalytic transition states. implications for the catalytic strategy of acyl-transfer enzymes. J. Am. Chem. Soc. 105 (1983) 2446-2452
26. Stein R.L., Strimpler A.M., Hori H., and Powers J.C. Catalysis by human leukocyte elastase: proton inventory as a mechanistic probe. Biochemistry 26 (1987) 1305-1314
27. Alvarez F.J., and Schowen R.L. Mechanistic deductions from solvent isotope effects. In: Buncel E., and Lee C.C. (Eds). Isotopes in Organic Chemistry (1987), Elsevier, Amsterdam 1-60
28. Kresge A.J., More O., and Powell M.F. Solvent isotopes effects, fractionation factors and mechanisms of proton transfer reactions. In: Buncel E., and Lee C.C. (Eds). Isotopes in Organic Chemistry (1987), Elsevier, Amsterdam 177-273
29. Scholten J.D., Hogg J.L., and Raushel F.M. Methyl chymotrypsin catalyzed hydrolysis of specific substrate esters indicate multiple proton catalysis is possible with a modified charge relay triad. J. Am. Chem. Soc. 110 (1988) 8246-8247
30. Schowen R.L. Structural and energetic aspects of protolytic catalysis by enzymes: charge-relay catalysis in the function of serine proteases. In: Liebman J.F., and Greenberg A. (Eds). Mechanistic Principles of Enzyme Activity (1988), VCH Publishers, New York 119-168
31. Schowen K.B., Limbach H.H., Denisov G.S., and Schowen R.L. Hydrogen bonds and proton transfer in general-catalytic transition state stabilization in enzyme catalysis. Biochim. Biophys. Acta 1458 (2000) 43-62
32. Quinn D.M., and Sutton L.D. Theoretical basis and mechanistic utility of solvent isotope effects. In: Cook P.F. (Ed). Enzyme Mechanism from Isotope Effects (1991), CRC Press 73-126
33. Zhang D., and Kovach I.M. Full and partial deuterium solvent isotope effect studies of α-thrombin-catalyzed reactions of natural substrates. J. Am. Chem. Soc (2005) 3760-3766
34. 2O mixtures. Adv. Phys. Org. Chem. 7 (1969) 259-331
35. 2O mixtures. Pure Appl. Chem. 8 (1964) 243-258
36. Quinn D.M. Acetylcholinesterase: enzyme structure, reaction dynamics, and virtual transition states. Chem. Rev. 87 (1987) 955-975