Gawthrop Peter J, Crampin Edmund J
Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia.
School of Mathematics and Statistics, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia.
Proc Math Phys Eng Sci. 2017 Jun;473(2202):20160825. doi: 10.1098/rspa.2016.0825. Epub 2017 Jun 21.
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.
将生物分子反应网络分解为途径是分析代谢和信号网络的一种强大方法。目前基于化学计量矩阵分析的方法揭示了通过网络的稳态质量流（反应速率）的信息。在这项工作中，我们展示了如何使用基于能量的方法扩展生物分子网络的途径分析，以提供有关通过网络的能量流的信息。这种基于能量的方法是使用受工程启发的键图方法开发的，用于表示生物分子反应网络。该方法以糖酵解为例进行介绍；然后应用于分析转运蛋白[钠-葡萄糖转运蛋白1（SGLT1）]的生物分子循环模型中的自由能转导效率。我们工作的总体目标是提出一个用于生物分子反应和过程建模与分析的框架，该框架考虑能量流和损失以及质量传输。
