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

Biochemical Society Transactions
Egils StalidzansAgris Pentjuss

Abstract

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 informa...Continue Reading

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Citations

Apr 27, 2019·Frontiers in Microbiology·Peter C St John, Yannick J Bomble
Aug 17, 2020·PloS One·Georgios MarinosSilvio Waschina
Mar 5, 2021·Network and Systems Medicine·Massimiliano ZaninHarald H H W Schmidt
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Jul 2, 2021·Materials Today. Bio·O Burgos-MoralesW Weber
Aug 24, 2021·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Rudolfs PetrovsAgris Pentjuss

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