Convex Representation of Metabolic Networks with Michaelis–Menten Kinetics

Document Type

Article

Publication Date

6-1-2024

Abstract

Polyhedral models of metabolic networks are computationally tractable and can predict some cellular functions. A longstanding challenge is incorporating metabolites without losing tractability. In this paper, we do so using a new second-order cone representation of the Michaelis–Menten kinetics. The resulting model consists of linear stoichiometric constraints alongside second-order cone constraints that couple the reaction fluxes to metabolite concentrations. We formulate several new problems around this model: conic flux balance analysis, which augments flux balance analysis with metabolite concentrations; dynamic conic flux balance analysis; and finding minimal cut sets of networks with both reactions and metabolites. Solving these problems yields information about both fluxes and metabolite concentrations. They are second-order cone or mixed-integer second-order cone programs, which, while not as tractable as their linear counterparts, can nonetheless be solved at practical scales using existing software.

Identifier

85191632126 (Scopus)

Publication Title

Bulletin of Mathematical Biology

External Full Text Location

https://doi.org/10.1007/s11538-024-01293-1

e-ISSN

15229602

ISSN

00928240

PubMed ID

38671332

Issue

6

Volume

86

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