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

Egils Stalidzans (Corresponding Author), Andrus Seiman, Karl Peebo, Vitalijs Komasilovs, Agris Pentjuss

Research output: Contribution to journalReview articlepeer-review

32 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)261-267
Number of pages7
JournalBiochemical Society Transactions
Volume46
Issue number2
DOIs
Publication statusPublished - 17 Apr 2018
Externally publishedYes

Field of Science*

  • 1.6 Biological sciences
  • 3.1 Basic medicine
  • 1.4 Chemical sciences

Publication Type*

  • 1.1. Scientific article indexed in Web of Science and/or Scopus database

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