A structural property for reduction of biochemical networks

Abstract Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches eit...

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Autores principales:	Anika Küken, Philipp Wendering, Damoun Langary, Zoran Nikoloski
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e3a74f9814e4466794cfb0b2ccc046b8
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spelling	oai:doaj.org-article:e3a74f9814e4466794cfb0b2ccc046b82021-12-02T15:28:52ZA structural property for reduction of biochemical networks10.1038/s41598-021-96835-12045-2322https://doaj.org/article/e3a74f9814e4466794cfb0b2ccc046b82021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96835-1https://doaj.org/toc/2045-2322Abstract Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches either restrict functionality of reduced models or do not lead to significant decreases in the number of modelled metabolites. Here, we introduce an approach for model reduction based on the structural property of balancing of complexes that preserves the steady-state fluxes supported by the network and can be efficiently determined at genome scale. Using two large-scale mass-action kinetic models of Escherichia coli, we show that our approach results in a substantial reduction of 99% of metabolites. Applications to genome-scale metabolic models across kingdoms of life result in up to 55% and 85% reduction in the number of metabolites when arbitrary and mass-action kinetics is assumed, respectively. We also show that predictions of the specific growth rate from the reduced models match those based on the original models. Since steady-state flux phenotypes from the original model are preserved in the reduced, the approach paves the way for analysing other metabolic phenotypes in large-scale biochemical networks.Anika KükenPhilipp WenderingDamoun LangaryZoran NikoloskiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anika Küken Philipp Wendering Damoun Langary Zoran Nikoloski A structural property for reduction of biochemical networks
description	Abstract Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches either restrict functionality of reduced models or do not lead to significant decreases in the number of modelled metabolites. Here, we introduce an approach for model reduction based on the structural property of balancing of complexes that preserves the steady-state fluxes supported by the network and can be efficiently determined at genome scale. Using two large-scale mass-action kinetic models of Escherichia coli, we show that our approach results in a substantial reduction of 99% of metabolites. Applications to genome-scale metabolic models across kingdoms of life result in up to 55% and 85% reduction in the number of metabolites when arbitrary and mass-action kinetics is assumed, respectively. We also show that predictions of the specific growth rate from the reduced models match those based on the original models. Since steady-state flux phenotypes from the original model are preserved in the reduced, the approach paves the way for analysing other metabolic phenotypes in large-scale biochemical networks.
format	article
author	Anika Küken Philipp Wendering Damoun Langary Zoran Nikoloski
author_facet	Anika Küken Philipp Wendering Damoun Langary Zoran Nikoloski
author_sort	Anika Küken
title	A structural property for reduction of biochemical networks
title_short	A structural property for reduction of biochemical networks
title_full	A structural property for reduction of biochemical networks
title_fullStr	A structural property for reduction of biochemical networks
title_full_unstemmed	A structural property for reduction of biochemical networks
title_sort	structural property for reduction of biochemical networks
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e3a74f9814e4466794cfb0b2ccc046b8
work_keys_str_mv	AT anikakuken astructuralpropertyforreductionofbiochemicalnetworks AT philippwendering astructuralpropertyforreductionofbiochemicalnetworks AT damounlangary astructuralpropertyforreductionofbiochemicalnetworks AT zorannikoloski astructuralpropertyforreductionofbiochemicalnetworks AT anikakuken structuralpropertyforreductionofbiochemicalnetworks AT philippwendering structuralpropertyforreductionofbiochemicalnetworks AT damounlangary structuralpropertyforreductionofbiochemicalnetworks AT zorannikoloski structuralpropertyforreductionofbiochemicalnetworks
_version_	1718387236474454016

A structural property for reduction of biochemical networks

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