Quantitative full time course analysis of nonlinear enzyme cycling kinetics

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Cao, Wenxiang ^a   De La Cruz, Enrique M ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; ENZYME SPECIFICITY; KINETICS; METABOLISM;

ALGORITHMS; COMPUTER SIMULATION; ENZYMES; KINETICS; MODELS, BIOLOGICAL; SUBSTRATE SPECIFICITY;

EID: 84884272899     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep02658     Document Type: Article

References (44)

1. Miao, Y., Chen, J. Y., Jiang, X. & Huang, Z. Kinetic studies on the product inhibition of enzymatic lignocellulose hydrolysis. Appl Biochem Biotechnol 167, 358-366 (2012).
2. Strompen, S. et al. Kinetic investigation of a solvent-free, chemoenzymatic reaction sequence towards enantioselective synthesis of a beta-amino acid ester. Biotechnol Bioeng 109, 1479-1489 (2012).
3. Demirhan, E., Apar, D. K. & Ozbek, B. A kinetic study on sesame cake protein hydrolysis by Alcalase. J Food Sci 76, C64-67 (2011).
4. Bezerra, R. M., Dias, A. A., Fraga, I. & Pereira, A. N. Cellulose hydrolysis by cellobiohydrolase Cel7A shows mixed hyperbolic product inhibition. Appl Biochem Biotechnol 165, 178-189 (2011).
5. Cornish-Bowden, A. Fundamentals of Enzyme Kinetics. Third edn, (Portland Press, 2004).
6. Michaelis, L.,Menten, M. L., Johnson, K. A. & Goody, R. S. The original Michaelis constant: translation of the 1913 Michaelis-Menten paper. Biochemistry 50, 8264-8269 (2011).
7. Cornish-Bowden, A. The use of the direct linear plot for determining initial velocities. Biochem J 149, 305-312 (1975).
8. Atkins, G. L. & Nimmo, I. A. The reliability of Michaelis constants and maximum velocities estimated by using the integrated Michaelis-Menten equation. Biochem J 135, 779-784 (1973).
9. Cooper, B. F. & Rudolph, F. B. Product inhibition applications. Methods Enzymol 249, 188-211 (1995).
10. Briggs, G. E. & Haldane, J. B. A Note on the Kinetics of Enzyme Action. Biochem J 19, 338-339 (1925).
11. Michaelis, L. & Menten, M. L. Die Kinetik der Invertinwirkung. Biochem Z 49, 333-369 (1913).
12. Cao, W. et al. Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins. J Mol Biol 409, 399-414 (2011).
13. De La Cruz, E. M., Sweeney, H. L. & Ostap, E. M. ADP inhibition of myosin V ATPase activity. Biophys J 79, 1524-1529 (2000).
14. Henn, A., Cao, W., Hackney, D. D. & De La Cruz, E. M. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J Mol Biol 377, 193-205 (2008).
15. De La Cruz, E. M., Ostap, E. M. & Sweeney, H. L. Kinetic mechanism and regulation of myosin VI. J Biol Chem 276, 32373-32381 (2001).
16. Robblee, J. P.,Olivares, A. O.&de la Cruz, E. M. Mechanismof nucleotide binding to actomyosin VI: evidence for allosteric head-head communication. J Biol Chem 279, 38608-38617 (2004). (Pubitemid 39296016)
17. Saunders, L. P. et al. Kinetic analysis of autotaxin reveals substrate-specific catalytic pathways and a mechanism for lysophosphatidic acid distribution. J Biol Chem 286, 30130-30141 (2011).
18. Robblee, J. P., Cao, W., Henn, A., Hannemann, D. E. & De La Cruz, E. M. Thermodynamics of nucleotide binding to actomyosin V and VI: a positive heat capacity change accompanies strong ADP binding. Biochemistry 44, 10238-10249 (2005). (Pubitemid 41076819)
19. De La Cruz, E. M. & Ostap, E. M. Kinetic and equilibrium analysis of the myosin ATPase. Methods Enzymol 455, 157-192 (2009).
20. Fernley, H. N. Statistical estimations in enzyme kinetics. The integrated Michaelis equation. Eur J Biochem 43, 377-378 (1974).
21. Nimmo, I. A. & Atkins, G. L. A comparison of two methods for fitting the integrated Michaelis-Menten equation. Biochem J 141, 913-914 (1974).
22. Cornish-Bowden, A. J. Analysis of progress curves in enzyme kinetics. Biochem J 130, 637-639 (1972).
23. Schwert, G. W. Use of integrated rate equations in estimating the kinetic constants of enzyme-catalyzed reactions. J Biol Chem 244, 1278-1284 (1969).
24. Schwert, G. W. The estimation of kinetic constants for the lactate dehydrogenase system by the use of integrated rate equations. J Biol Chem 244, 1285-1290 (1969).
25. Huang, H. T. & Niemann, C. The Kinetics of the a-Chymotrypsin Catalyzed Hydrolysis of Acetyl- and Nicotinyl-L-tryptophanamide in Aqueous Solutions at 25u and pH 7.91. J Am Chem Soc 73, 1541-1548 (1951).
26. Boeker, E. A. Integrated rate equations for enzyme-catalysed first-order and second-order reactions. Biochem J 223, 15-22 (1984).
27. Michaelis, L. & Rona, P. DieWirkungsbedingungen der Maltase aus Bierhefe. Ill. Uber die Natur der verschiedenartigen Hemmungen der Fermentwirkunge. Biochem Z 60, 62-78 (1914).
28. Michaelis, L. & Pechstein, H. Uber die verschiedenartige Natur der Hernmungen der Invertasewirkung. biochem Z 60, 79-90 (1914).
29. Alberty, R. A. & Koerber, B. M. Studies of the Enzyme Fumarase. VII.1 Series Solutions of Integrated Rate Equations for Irreversible and Reversible Michaelis- Menten Mechanisms2. J Am Chem Soc 79, 6379-6382 (1957).
30. Orsi, B. A. & Tipton, K. F. Kinetic analysis of progress curves. Methods Enzymol 63, 159-183 (1979).
31. Walter, C. The role of the concentration of the products in integrated rate equations. Arch Biochem Biophys 102, 14-20 (1963).
32. Darvey, I. G. &Williams, J. F. Integrated Steady-State Rate Equations for Enzyme- Catalyzed Reactions. Biochim Biophys Acta 85, 1-10 (1964).
33. Philo, R. D. & Selwyn, M. J. Use of progress curves to investigate product inhibition in enzyme-catalysed reactions. Application to the soluble mitochondrial adenosine triphosphatase. Biochem J 135, 525-530 (1973).
34. Darvey, I. G., Shrager, R. & Kohn, L. D. Integrated steady state rate equations and the determination of individual rate constants. J Biol Chem 250, 4696-4701 (1975).
35. Duggleby, R. G. & Morrison, J. F. The analysis of progress curves for enzymecatalysed reactions by non-linear regression. Biochim Biophys Acta 481, 297-312 (1977). (Pubitemid 8082580)
36. Duggleby, R. G. & Wood, C. Analysis of progress curves for enzyme-catalysed reactions. Automatic construction of computer programs for fitting integrated rate equations. Biochem J 258, 397-402 (1989). (Pubitemid 19075510)
37. Boeker, E. A. Integrated rate equations for irreversible enzyme-catalysed firstorder and second-order reactions. Biochem J 226, 29-35 (1985).
38. Henri, V. Lois générales de láction des diastases. (Librairie Scientifique A. Hermann, 1903).
39. Barshop, B. A., Wrenn, R. F. & Frieden, C. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM-a flexible, portable system. Anal Biochem 130, 134-145 (1983).
40. Johnson, K. A. Fitting enzyme kinetic data with KinTek Global Kinetic Explorer. Methods Enzymol 467, 601-626 (2009).
41. Johnson, K. A. in The Enzymes Vol. 20 (ed Sigman David, S.) 1-61 (Academic Press, 1992).
42. Henn, A. & De La Cruz, E. M. Vertebrate myosin VIIb is a high duty ratio motor adapted for generating and maintaining tension. J Biol Chem 280, 39665-39676 (2005). (Pubitemid 41713926)
43. De La Cruz, E. M.,Wells, A. L., Sweeney, H. L.&Ostap, E. M. Actin and light chain isoform dependence of myosin V kinetics. Biochemistry 39, 14196-14202 (2000).
44. Bradley, M. J. & De La Cruz, E. M. Analyzing ATP utilization by DEAD-Box RNA helicases using kinetic and equilibrium methods. Methods Enzymol 511, 29-63 (2012).