Physically-plausible modelling of biomolecular systems: A simplified, energy-based model of the mitochondrial electron transport chain

Peter J Gawthrop; Peter Cudmore; Edmund J Crampin

doi:10.1016/j.jtbi.2020.110223

Physically-plausible modelling of biomolecular systems: A simplified, energy-based model of the mitochondrial electron transport chain

J Theor Biol. 2020 May 21:493:110223. doi: 10.1016/j.jtbi.2020.110223. Epub 2020 Feb 29.

Authors

Peter J Gawthrop¹, Peter Cudmore², Edmund J Crampin³

Affiliations

¹ Systems Biology Laboratory, Department of Biomedical Engineering, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia; Systems Biology Laboratory, School of Mathematics and Statistics, University of Melbourne, Victoria 3010, Australia. Electronic address: peter.gawthrop@unimelb.edu.au.
² Systems Biology Laboratory, Department of Biomedical Engineering, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemical and Biomedical Engineering, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia.
³ Systems Biology Laboratory, Department of Biomedical Engineering, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia; Systems Biology Laboratory, School of Mathematics and Statistics, University of Melbourne, Victoria 3010, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemical and Biomedical Engineering, Melbourne School of Engineering, University of Melbourne, Victoria 3010, Australia.

PMID: 32119969
DOI: 10.1016/j.jtbi.2020.110223

Abstract

Advances in systems biology and whole-cell modelling demand increasingly comprehensive mathematical models of cellular biochemistry. Such models require the development of simplified representations of specific processes which capture essential biophysical features but without unnecessarily complexity. Recently there has been renewed interest in thermodynamically-based modelling of cellular processes. Here we present an approach to developing of simplified yet thermodynamically consistent (hence physically plausible) models which can readily be incorporated into large scale biochemical descriptions but which do not require full mechanistic detail of the underlying processes. We illustrate the approach through development of a simplified, physically plausible model of the mitochondrial electron transport chain and show that the simplified model behaves like the full system.

Keywords: Bond graph; Computational biology; Systems biology; Thermodynamical modelling.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Physiological Phenomena
Electron Transport
Models, Biological*
Systems Biology*
Thermodynamics