A statistical mechanics description of environmental variability in metabolic networks

DOI10.1007/S10910-013-0288-7MaRDI QIDQ2014792zbMATH OpenOpenAlexFDO

Authors Jonathan J. Crofts, Ernesto Estrada

Publication date 16 June 2014

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

Full work available at URL https://arxiv.org/abs/1303.0103, https://strathprints.strath.ac.uk/47237/

zbMATH Keywords

complexitycentralitymetabolic networksreturnability

Mathematics Subject Classification ID

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

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.

Recommendations

• Stochastic fluctuations in metabolic pathways
• Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations
• Stochastic reaction networks within interacting compartments
• Bacterial metabolic heterogeneity: from stochastic to deterministic models
• scientific article; zbMATH DE number 3952549
• Stochastic reaction networks in dynamic compartment populations
• A statistical thermodynamical interpretation of metabolism
• scientific article; zbMATH DE number 3939156

Cites work

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

Cited in

(2)

• A statistical thermodynamical interpretation of metabolism
• Why optimal states recruit fewer reactions in metabolic networks

Describes a project that uses

Uses Software

• KEGG

This page was built for publication: A statistical mechanics description of environmental variability in metabolic networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2014792)