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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Energy-based analysis of biomolecular pathways
Peter J Gawthrop1, Edmund J Crampin1,2,3,4
1Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia.
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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