Energy-based Analysis of Biomolecular Pathways

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.

References in corpus (3)

• Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws
• Hierarchical Bond Graph Modelling of Biochemical Networks
• Modular Bond-graph Modelling and Analysis of Biomolecular Systems

Cited by in corpus (6)

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• Bond Graph Representation of Chemical Reaction Networks
• Network Thermodynamical Modelling of Bioelectrical Systems: A Bond Graph Approach
• Physically-Plausible Modelling of Biomolecular Systems: A Simplified, Energy-Based Model of the Mitochondrial Electron Transport Chain
• Computing Biomolecular System Steady-states
• A thermodynamic framework for modelling membrane transporters