Energy-based analysis of biomolecular pathways

DOI10.1098/RSPA.2016.0825MaRDI QIDQ4557921zbMATH OpenOpenAlexWikidataFDO

Authors Peter J. Gawthrop, Edmund J. Crampin

Publication date 27 November 2018

Published in Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1611.02332

zbMATH Keywords

signalling networkssteady-state mass flows

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Abstract: Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network. In this work we show how pathway analysis of biomolecular networks can be extended using an energy-based approach to provide information about energy flows through the network. This energy-based approach is developed using the engineering-inspired bond graph methodology to represent biomolecular reaction networks. The approach is introduced using glycolysis as an exemplar; and is then applied to analyse the efficiency of free energy transduction in a biomolecular cycle model of a transporter protein (Sodium-Glucose Transport Protein 1, SGLT1). The overall aim of our work is to present a framework for modelling and analysis of biomolecular reactions and processes which considers energy flows and losses as well as mass transport.

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Cites work

• Bond Graph Modelling of Engineering Systems
• Bond graphs for modelling, control and fault diagnosis of engineering systems
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Cited in

(7)

• Network thermodynamics of biological systems: a bond graph approach
• SBML to bond graphs: from conversion to composition
• Open problems in mathematical biology
• Physically-plausible modelling of biomolecular systems: a simplified, energy-based model of the mitochondrial electron transport chain
• A thermodynamic framework for modelling membrane transporters
• Bond graph modelling of the cardiac action potential: implications for drift and non-unique steady states
• Energy Properties of Protein Structures in the Analysis of the Human RAB5A Cellular Activity

Describes a project that uses

Uses Software

• Octave
• Metatool
• MTT

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