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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Wolfram Liebermeister1, Jannis Uhlendorf, Edda Klipp
1Institut für Biologie, Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany. wolfram.liebermeister@biologie.hu-berlin.de
Bioinformatics (Oxford, England)
|April 14, 2010
Summary
We introduce new reversible rate laws for metabolic modeling, ensuring thermodynamic consistency. These laws simplify kinetic modeling and are compatible with Systems Biology Markup Language standards.
Area of Science:
- Systems biology
- Metabolic modeling
- Biochemical kinetics
Background:
- Standard rate laws are essential for creating kinetic models of metabolic networks.
- Existing laws must be simple, general, biochemically plausible, and thermodynamically consistent.
- Thermodynamic consistency relates kinetic constants to metabolic fluxes and concentrations.
Purpose of the Study:
- To present a new family of reversible rate laws for reactions with arbitrary stoichiometries and various regulatory types.
- To ensure that parameter sets from model fitting, sampling, or optimization lead to consistent chemical equilibrium states.
- To reformulate rate laws using saturation values for simpler formulae and highlight the role of chemical potential differences.
Main Methods:
- Developed a family of reversible rate laws applicable to diverse reaction stoichiometries and regulations.
- Introduced a thermodynamically safe parameterization for these rate laws.
- Reformulated rate laws using saturation values for simplified expressions of rates and elasticities.
- Proposed standard syntax and semantic annotations for Systems Biology Markup Language (SBML) for automated handling.
Main Results:
- Presented a family of reversible rate laws, encompassing mass-action, Michaelis-Menten, and uni-uni reversible Hill kinetics as special cases.
- Demonstrated that the proposed parameterization guarantees consistent chemical equilibrium states.
- Showcased simplified formulae for rates and elasticities adjustable to stationary flux distributions.
- Highlighted the significance of chemical potential differences as thermodynamic driving forces.
- Compared the modular rate laws with the thermodynamic-kinetic modeling formalism.
- Discussed a simplified rate law where reaction rate directly depends on reaction affinity.
Conclusions:
- The new family of reversible rate laws provides a robust framework for kinetic modeling of metabolic networks.
- The thermodynamically safe parameterization ensures biochemical realism and consistency.
- The reformulation simplifies model analysis and highlights thermodynamic driving forces.
- Standardization for SBML facilitates automated implementation and broader application.
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