Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis

  title={Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis},
  author={Daniele De Martino},
  journal={Physical Biology},
  • D. Martino
  • Published 18 May 2015
  • Environmental Science
  • Physical Biology
In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium… 
The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges
The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis but leads to possibly non-convex feasible flux spaces, whose exploration needs efficient algorithms.


Genome-scale thermodynamic analysis of Escherichia coli metabolism.
A genome-scale metabolic model of Escherichia coli is constructed based on the iJR904 model developed by the Palsson Laboratory at the University of California at San Diego to facilitate the refinement of the feasible ranges for cellular parameters such as species concentrations and reaction rate constants.
Energy balance for analysis of complex metabolic networks.
Counting and Correcting Thermodynamically Infeasible Flux Cycles in Genome-Scale Metabolic Networks
This work proposes a method that accomplishes identifying and removing cycles in large reaction networks by combining a relaxation algorithm and a Monte Carlo procedure to detect loops, with ad hoc rules to eliminate them, and corrects loopy solutions to Flux Balance Analysis.
Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli
The data and analyses presented here highlight the ability to identify organizing metabolic principles from systems-level absolute metabolite concentration data, and facilitate efficient flux reversibility given thermodynamic and osmotic constraints.
Thermodynamic constraints for biochemical networks.
Thermodynamics of biochemical networks and duality theorems.
  • D. De Martino
  • Computer Science
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2013
It is demonstrated that for chemical reaction networks in the steady state the exclusion (presence) of closed reaction cycles makes possible (impossible) the definition of a chemical potential vector.
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.
The Monte Carlo sampling procedure provides a broadening of the constraint-based approach by allowing for the unbiased and detailed assessment of the impact of the applied physicochemical constraints on a reconstructed network.
Metabolic regulation and mathematical models.
The hierarchical structure of metabolic networks and the construction of efficient metabolic simulators.
  • D. Park
  • Computer Science, Physics
    Journal of theoretical biology
  • 1974
A generalized theory of the transition time for sequential enzyme reactions.
Application of the theory to coupled enzyme assays allows a definition of the minimum requirements for successful operation of the assay, and the theory can be extended to deal with sequences in which the enzyme concentration exceeds substrate concentration.