Enzyme allocation problems in kinetic metabolic networks: optimal solutions are elementary flux modes

DOI10.1016/J.JTBI.2013.11.015zbMATH Open1412.92124arXiv1308.0510OpenAlexW2048243530WikidataQ51137005 ScholiaQ51137005MaRDI QIDQ2632634FDOQ2632634

Authors: Stefan Müller, Georg Regensburger, Ralf Steuer 

Publication date: 15 May 2019

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular metabolism is limited by finite resources that are shared between all enzymes, such as cytosolic space, energy expenditure for amino-acid synthesis, or micro-nutrients. While extensive work has been done to study constrained optimization problems based only on stoichiometric information, mathematical results that characterize the optimal flux in kinetic metabolic networks are still scarce. Here, we study constrained enzyme allocation problems with general kinetics, using the theory of oriented matroids. We give a rigorous proof for the fact that optimal solutions of the non-linear optimization problem are elementary flux modes. This finding has significant consequences for our understanding of optimality in metabolic networks as well as for the identification of metabolic switches and the computation of optimal flux distributions in kinetic metabolic networks.

Full work available at URL: https://arxiv.org/abs/1308.0510

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zbMATH Keywords

enzyme kineticsoriented matroidelementary vectorconformal summetabolic optimization

Mathematics Subject Classification ID

Systems biology, networks (92C42) Cell biology (92C37) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Cites Work

• Lectures on Polytopes
• Title not available (Why is that?)
• Oriented Matroids
• A new constraint-based description of the steady-state flux cone of metabolic networks
• Title not available (Why is that?)
• Cell design in bacteria as a convex optimization problem
• Generalized mass action systems: complex balancing equilibria and sign vectors of the stoichiometric and kinetic-order subspaces
• Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism
• Is maximization of molar yield in metabolic networks favoured by evolution?
• Thermodynamic constraints for biochemical networks
• Linear programming duality: an introduction to oriented matroids
• An algebraic-combinatorial model for the identification and mapping of biochemical pathways

Cited In (12)

• Regulatory dynamic enzyme-cost flux balance analysis: a unifying framework for constraint-based modeling
• Enumeration and Cartesian product decomposition of alternate optimal fluxes in cellular metabolism
• Dynamic metabolic resource allocation based on the maximum entropy principle
• Precision and sensitivity in detailed-balance reaction networks
• Evolution of enzyme levels in metabolic pathways: a theoretical approach. I
• Why optimal states recruit fewer reactions in metabolic networks
• The steady-state assumption in oscillating and growing systems
• Optimal resource allocation enables mathematical exploration of microbial metabolic configurations
• Nonlinear multi-objective flux balance analysis of the Warburg Effect
• Sequential activation of metabolic pathways: a dynamic optimization approach
• On dynamically generating relevant elementary flux modes in a metabolic network using optimization
• Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks. I: Theoretical analysis

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