A statistical mechanics description of environmental variability in metabolic networks

DOI10.1007/S10910-013-0288-7zbMATH Open1311.92069arXiv1303.0103OpenAlexW2110697952MaRDI QIDQ2014792FDOQ2014792

Jonathan J. Crofts, Ernesto Estrada

Publication date: 16 June 2014

Published in: Journal of Mathematical Chemistry (Search for Journal in Brave)

Abstract: Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibrium within these biochemical reaction systems.

Full work available at URL: https://arxiv.org/abs/1303.0103

zbMATH Keywords

complexitycentralitymetabolic networksreturnability

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Cites Work

• Estimating the Estrada index
• The Structure of Complex Networks
• Returnability in complex directed networks (digraphs)

Cited In (1)

• A statistical thermodynamical interpretation of metabolism

Uses Software

• KEGG

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