Flux exponent control predicts metabolic dynamics from network structure

Abstract

Metabolic dynamics such as stability of steady states, oscillations, lags and growth arrests in stress responses are important for microbial communities in human health, ecology, and metabolic engineering. Yet it is hard to model due to sparse data available on trajectories of metabolic fluxes. For this reason, a constraint-based approach called flux control (e.g., flux balance analysis) was invented to split metabolic systems into known stoichiometry (plant) and unknown fluxes (controller), so that data can be incorporated as refined constraints, and optimization can be used to find behaviors in scenarios of interest. However, flux control can only capture steady state fluxes well, limiting its application to scenarios with days or slower timescales. To overcome this limitation and capture dynamic fluxes, this work proposes a novel constraint-based approach, flux exponent control (FEC). FEC uses a different plant-controller split between the activities of catalytic enzymes and their regulation through binding reactions. Since binding reactions effectively regulate fluxes' exponents (from previous works), this yields the rule of FEC, that cells regulate fluxes' exponents, not the fluxes themselves as in flux control. In FEC, dynamic regulations of metabolic systems are solutions to optimal control problems that are computationally solvable via model predictive control. Glycolysis, which is known to have minute-timescale oscillations, is used as an example to demonstrate FEC can capture metabolism dynamics from network structure. More generally, FEC brings metabolic dynamics to the realm of control system analysis and design.