Fig 1 - available via license: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Content may be subject to copyright.
The topology contributing to the formation of a BC. A small linkage class of a network comprising three complexes is shown. The species í µí± í µí± is assumed to be present in complexes í µí° ¶ í µí± 1 and í µí° ¶ í µí± 2 , but nowhere else in the network.
Source publication
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation of particular steady-state prop...
Context in source publication
Context 1
... a simple example, in which some species í µí± í µí± ∈ í µí²® makes a unimolecular appearance in complexes í µí° ¶ í µí± 1 and í µí° ¶ í µí± 2 , but is absent elsewhere in the network. Assume additionally that í µí° ¶ í µí± 1 , í µí° ¶ í µí± 2 form a linkage class with another complex, namely í µí° ¶ í µí± 3 . The situation is shown in Fig. 1. A small linkage class of a network comprising three complexes is shown. The species í µí± í µí± is assumed to be present in complexes í µí° ¶ í µí± 1 and í µí° ¶ í µí± 2 , but nowhere else in the ...
Similar publications
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation of particular steady-state prop...
Genome-scale metabolic models (GEMs) have been widely used for phenotypic prediction of microorganisms. However, the lack of other constraints in the stoichiometric model often leads to a large metabolic solution space inaccessible. Inspired by previous studies that take allocation of macromolecule resources into account, we developed a simplified...
Citations
... A complex is balanced in the set of flux distributions S = {v|Nv = 0, v min ≤ v ≤ v max } if for every v ∈ S , it holds that [Av] i = 0 .This condition can be verified by determining that the minimum and maximum values of [Av] i equal to 0 for each complex i , separately. The latter can be ensured by solving two linear programs:s.t.The dependence of balanced complexes on the flux bounds is addressed in follow-up studies50 . ...
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.
