Energy-based analysis of biomolecular pathways

被引:17
|
作者
Gawthrop, Peter J. [1 ]
Crampin, Edmund J. [1 ,2 ,3 ,4 ]
机构
[1] Univ Melbourne, Syst Biol Lab, Melbourne, Vic 3010, Australia
[2] Univ Melbourne, Sch Math & Stat, Melbourne, Vic 3010, Australia
[3] Univ Melbourne, Sch Med, Melbourne, Vic 3010, Australia
[4] Univ Melbourne, ARC Ctr Excellence Convergent Bionano Sci, Melbourne Sch Engn, Melbourne, Vic 3010, Australia
基金
澳大利亚研究理事会;
关键词
network thermodynamics; biomolecular systems; bond graph; reaction kinetics; NA+ GLUCOSE COTRANSPORTER; OXIDATIVE-PHOSPHORYLATION; ELECTROGENIC PROPERTIES; NETWORK THERMODYNAMICS; SYSTEMS; TRANSPORT; MITOCHONDRIA; MULTISCALE; EVOLUTION; DISEASE;
D O I
10.1098/rspa.2016.0825
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页数:21
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