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Model-based metabolism design: constraints for kinetic and stoichiometric models

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization co...

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Autores principales: Stalidzans, Egils, Seiman, Andrus, Peebo, Karl, Komasilovs, Vitalijs, Pentjuss, Agris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Portland Press Ltd. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906704/
https://www.ncbi.nlm.nih.gov/pubmed/29472367
http://dx.doi.org/10.1042/BST20170263
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author Stalidzans, Egils
Seiman, Andrus
Peebo, Karl
Komasilovs, Vitalijs
Pentjuss, Agris
author_facet Stalidzans, Egils
Seiman, Andrus
Peebo, Karl
Komasilovs, Vitalijs
Pentjuss, Agris
author_sort Stalidzans, Egils
collection PubMed
description The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed.
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spelling pubmed-59067042018-05-01 Model-based metabolism design: constraints for kinetic and stoichiometric models Stalidzans, Egils Seiman, Andrus Peebo, Karl Komasilovs, Vitalijs Pentjuss, Agris Biochem Soc Trans Review Articles The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed. Portland Press Ltd. 2018-04-17 2018-02-22 /pmc/articles/PMC5906704/ /pubmed/29472367 http://dx.doi.org/10.1042/BST20170263 Text en © 2018 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Review Articles
Stalidzans, Egils
Seiman, Andrus
Peebo, Karl
Komasilovs, Vitalijs
Pentjuss, Agris
Model-based metabolism design: constraints for kinetic and stoichiometric models
title Model-based metabolism design: constraints for kinetic and stoichiometric models
title_full Model-based metabolism design: constraints for kinetic and stoichiometric models
title_fullStr Model-based metabolism design: constraints for kinetic and stoichiometric models
title_full_unstemmed Model-based metabolism design: constraints for kinetic and stoichiometric models
title_short Model-based metabolism design: constraints for kinetic and stoichiometric models
title_sort model-based metabolism design: constraints for kinetic and stoichiometric models
topic Review Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906704/
https://www.ncbi.nlm.nih.gov/pubmed/29472367
http://dx.doi.org/10.1042/BST20170263
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