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George A Bruque - One of the best experts on this subject based on the ideXlab platform.

  • biosynthesis of deoxynucleoside triphosphates dctp and dttp Reaction mechanism and kinetics
    Enzyme and Microbial Technology, 2005
    Co-Authors: George A Bruque
    Abstract:

    Abstract The enzyme Reaction mechanism and kinetics for biosyntheses of deoxycytidine triphosphate (dCTP) and deoxythymidine triphosphate (dTTP) from the corresponding deoxycytidine diphosphate (dCDP) and deoxythymidine diphosphate (dTDP) catalyzed by pyruvate kinase were studied. The kinetic model for the two synthetic Reactions was found to follow the Bi–Bi random rapid equilibrium mechanism similar to that of the biosynthesis of deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP) from the corresponding deoxyadenosine diphosphate (dADP) and deoxyguanosine diphosphate (dGDP). Kinetic constants involved in the Reactions including the Maximum Reaction Velocity, the Michaelis–Menten constants, and the inhibition constants for dCTP and dTTP biosyntheses were experimentally determined. This enzyme Reaction requires Mg 2+ ion and the optimal Mg 2+ concentration was also determined. The experimental results showed a good agreement with the simulation results obtained from the kinetic model developed. The kinetics of the four biosynthetic Reactions for deoxynucleoside triphosphates (dNTP) including dATP, dGTP, dCTP, and dTTP from the corresponding deoxynucleoside diphosphates (dNDP) including dADP, dGDP, dCDP, and dTDP were analyzed. The results suggest that the binding kinetics of phosphoenolpyruvate (PEP) and pyruvate are similar for all four biosynthetic Reactions. The affinity of the dNDP substrates to enzyme is of the same order of magnitude as the corresponding dNTP as inhibitors. The order of reactivity and substrate specificity for dNDP is dADP > dGDP > dCDP > dTDP in the pyruvate kinase (PK) Reactions. The results obtained from this study can be applied to bioreactor design and production of dCTP and dTTP for biosynthesis of DNA at a significantly lower cost compared to the currently available chemical method.

Dewey D. Y. Ryu - One of the best experts on this subject based on the ideXlab platform.

  • Biosynthesis Reaction mechanism and kinetics of deoxynucleoside triphosphates, dATP and dGTP.
    Biotechnology and bioengineering, 2005
    Co-Authors: Jie Bao, Dewey D. Y. Ryu
    Abstract:

    The enzyme Reaction mechanism and kinetics for biosyntheses of deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP) from the corresponding deoxyadenosine diphosphate (dADP) and deoxyguanosine diphosphate (dGDP) catalyzed by pyruvate kinase were studied. A kinetic model for this synthetic Reaction was developed based on a Bi-Bi random rapid equilibrium mechanism. Kinetic constants involved in this pyruvate kinase catalyzed phosphorylation Reactions of deoxynucleoside diphosphates including the Maximum Reaction Velocity, Michaelis-Menten constants, and inhibition constants for dATP and dGTP biosyntheses were experimentally determined. These kinetic constants for dATP and dGTP biosyntheses are of the same order of magnitude but significantly different between the two Reactions. Kinetic constants involved in ATP and GTP biosyntheses as reported in literature are about one order of magnitude different from those involved in dATP and dGTP biosyntheses. This enzyme Reaction requires Mg2+ ion and the optimal Mg2+ concentration was also determined. The experimental results showed a very good agreement with the simulation results obtained from the kinetic model developed. This kinetic model can be applied to the practical application of a pyruvate kinase Reaction system for production of dATP and dGTP. There is a significant advantage of using enzymatic biosyntheses of dATP and dGTP as compared to the chemical method that has been in commercial use. © 2005 Wiley Periodicals, Inc.

Jie Bao - One of the best experts on this subject based on the ideXlab platform.

  • Biosynthesis Reaction mechanism and kinetics of deoxynucleoside triphosphates, dATP and dGTP.
    Biotechnology and bioengineering, 2005
    Co-Authors: Jie Bao, Dewey D. Y. Ryu
    Abstract:

    The enzyme Reaction mechanism and kinetics for biosyntheses of deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP) from the corresponding deoxyadenosine diphosphate (dADP) and deoxyguanosine diphosphate (dGDP) catalyzed by pyruvate kinase were studied. A kinetic model for this synthetic Reaction was developed based on a Bi-Bi random rapid equilibrium mechanism. Kinetic constants involved in this pyruvate kinase catalyzed phosphorylation Reactions of deoxynucleoside diphosphates including the Maximum Reaction Velocity, Michaelis-Menten constants, and inhibition constants for dATP and dGTP biosyntheses were experimentally determined. These kinetic constants for dATP and dGTP biosyntheses are of the same order of magnitude but significantly different between the two Reactions. Kinetic constants involved in ATP and GTP biosyntheses as reported in literature are about one order of magnitude different from those involved in dATP and dGTP biosyntheses. This enzyme Reaction requires Mg2+ ion and the optimal Mg2+ concentration was also determined. The experimental results showed a very good agreement with the simulation results obtained from the kinetic model developed. This kinetic model can be applied to the practical application of a pyruvate kinase Reaction system for production of dATP and dGTP. There is a significant advantage of using enzymatic biosyntheses of dATP and dGTP as compared to the chemical method that has been in commercial use. © 2005 Wiley Periodicals, Inc.

William J Riley - One of the best experts on this subject based on the ideXlab platform.

  • the thermodynamic links between substrate enzyme and microbial dynamics in michaelis menten monod kinetics
    International Journal of Chemical Kinetics, 2018
    Co-Authors: Federico Maggi, Fiona H M Tang, William J Riley
    Abstract:

    Author(s): Maggi, F; Fiona, FH; Riley, WJ | Abstract: © 2018 Wiley Periodicals, Inc. Accurate prediction of the temperature response of the Velocity v of a biochemical Reaction has wide applications in cell biology, Reaction design, and biomass yield enhancement. Here, we introduce a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to describe and link the Reaction rate and Michaelis–Menten constants (kT and K T) with the biomass yield and mortality rate (YT and δT) as explicit functions of T. The temperature control is exerted by catabolic enthalpy at low temperatures and catabolic entropy at high temperatures, whereas changes in cell and enzyme–substrate heat capacity shift the anabolic electron use efficiency eA and the Maximum Reaction Velocity vmax. We show that cells have optimal growth when the catabolic (differential) free energy of activation decreases the cell free energy harvest required to duplicate their internal structures as long as electrons for anabolism are available. With the described approach, we accurately predicted observed glucose fermentation and ammonium nitrification dynamics across a wide temperature range with a minimal number of thermodynamics parameters, and we highlight how kinetic parameters are linked to each other using first principles.

  • the thermodynamic links between substrate enzyme and microbial dynamics in michaelis menten monod kinetics
    International Journal of Chemical Kinetics, 2018
    Co-Authors: Federico Maggi, Fiona H M Tang, William J Riley
    Abstract:

    Author(s): Maggi, F; Fiona, FH; Riley, WJ | Abstract: Accurate prediction of the temperature response of the Velocity v of a biochemical Reaction has wide applications in cell biology, Reaction design, and biomass yield enhancement. Here, we introduce a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to describe and link the Reaction rate and Michaelis–Menten constants (k and K ) with the biomass yield and mortality rate (Y and δ ) as explicit functions of T. The temperature control is exerted by catabolic enthalpy at low temperatures and catabolic entropy at high temperatures, whereas changes in cell and enzyme–substrate heat capacity shift the anabolic electron use efficiency e and the Maximum Reaction Velocity v . We show that cells have optimal growth when the catabolic (differential) free energy of activation decreases the cell free energy harvest required to duplicate their internal structures as long as electrons for anabolism are available. With the described approach, we accurately predicted observed glucose fermentation and ammonium nitrification dynamics across a wide temperature range with a minimal number of thermodynamics parameters, and we highlight how kinetic parameters are linked to each other using first principles. T T T T A max

Federico Maggi - One of the best experts on this subject based on the ideXlab platform.

  • the thermodynamic links between substrate enzyme and microbial dynamics in michaelis menten monod kinetics
    International Journal of Chemical Kinetics, 2018
    Co-Authors: Federico Maggi, Fiona H M Tang, William J Riley
    Abstract:

    Author(s): Maggi, F; Fiona, FH; Riley, WJ | Abstract: © 2018 Wiley Periodicals, Inc. Accurate prediction of the temperature response of the Velocity v of a biochemical Reaction has wide applications in cell biology, Reaction design, and biomass yield enhancement. Here, we introduce a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to describe and link the Reaction rate and Michaelis–Menten constants (kT and K T) with the biomass yield and mortality rate (YT and δT) as explicit functions of T. The temperature control is exerted by catabolic enthalpy at low temperatures and catabolic entropy at high temperatures, whereas changes in cell and enzyme–substrate heat capacity shift the anabolic electron use efficiency eA and the Maximum Reaction Velocity vmax. We show that cells have optimal growth when the catabolic (differential) free energy of activation decreases the cell free energy harvest required to duplicate their internal structures as long as electrons for anabolism are available. With the described approach, we accurately predicted observed glucose fermentation and ammonium nitrification dynamics across a wide temperature range with a minimal number of thermodynamics parameters, and we highlight how kinetic parameters are linked to each other using first principles.

  • the thermodynamic links between substrate enzyme and microbial dynamics in michaelis menten monod kinetics
    International Journal of Chemical Kinetics, 2018
    Co-Authors: Federico Maggi, Fiona H M Tang, William J Riley
    Abstract:

    Author(s): Maggi, F; Fiona, FH; Riley, WJ | Abstract: Accurate prediction of the temperature response of the Velocity v of a biochemical Reaction has wide applications in cell biology, Reaction design, and biomass yield enhancement. Here, we introduce a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to describe and link the Reaction rate and Michaelis–Menten constants (k and K ) with the biomass yield and mortality rate (Y and δ ) as explicit functions of T. The temperature control is exerted by catabolic enthalpy at low temperatures and catabolic entropy at high temperatures, whereas changes in cell and enzyme–substrate heat capacity shift the anabolic electron use efficiency e and the Maximum Reaction Velocity v . We show that cells have optimal growth when the catabolic (differential) free energy of activation decreases the cell free energy harvest required to duplicate their internal structures as long as electrons for anabolism are available. With the described approach, we accurately predicted observed glucose fermentation and ammonium nitrification dynamics across a wide temperature range with a minimal number of thermodynamics parameters, and we highlight how kinetic parameters are linked to each other using first principles. T T T T A max