The solution space of metabolic networks: producibility, robustness and fluctuations

Abstract

Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of its main areas of application is the study of cellular metabolic networks. We briefly and selectively review the main approaches to this problem and then, building on recent work, we provide a characterization of the productive capabilities of the metabolic network of the bacterium E.coli in a specified growth medium in terms of the producible biochemical species. While a robust and physiologically meaningful production profile clearly emerges (including biomass components, biomass products, waste etc.), the underlying constraints still allow for significant fluctuations even in key metabolites like ATP and, as a consequence, apparently lay the ground for very different growth scenarios.

10 pages, prepared for the Proceedings of the International Workshop on Statistical-Mechanical Informatics, March 7-10, 2010, Kyoto, Japan

References in corpus (4)

• Structural Kinetic Modeling of Metabolic Networks
• Identifying essential genes in E. coli from a metabolic optimization principle
• Von Neumann's expanding model on random graphs
• Optimal flux states, reaction replaceability and response to knockouts in the human red blood cell

Cited by in corpus (9)

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• Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks
• Constraint satisfaction mechanisms for marginal stability and criticality in large ecosystems
• A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks
• On the Clausius formulation of the second law in stationary chemical networks through the theorems of the alternative
• Reaction networks as systems for resource allocation: A variational principle for their non-equilibrium steady states
• A weighted belief-propagation algorithm to estimate volume-related properties of random polytopes
• Boolean constraint satisfaction problems for reaction networks
• Von Neumann's growth model: statistical mechanics and biological applications