Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects

TL;DR

This paper develops a flux balance model to understand how macromolecular crowding influences cell metabolism, revealing an optimal cytoplasmic density that maximizes metabolic rate and aligns with observed values in E. coli.

Contribution

The study introduces a novel flux balance model that incorporates macromolecular crowding effects, explaining the optimal cytoplasmic density for cellular metabolism.

Findings

Identifies two metabolic regimes based on nutrient uptake.

Predicts an optimal cytoplasmic density matching E. coli data.

Shows crowding effects balance reaction rates and diffusion.

Abstract

Macromolecules occupy between 34 and 44% of the cell cytoplasm, about half the maximum pack- ing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental question we investigate the effect of macromolecular crowding on cell metabolism. We develop a cell scale flux balance model capturing the main features of cell metabolism at different nutrient uptakes and macromolecular densities. Using this model we show there are two metabolic regimes at low and high nutrient uptakes. The latter regime is charac- terized by an optimal cytoplasmatic density where the increase of reaction rates by confinement and the decrease by diffusion slow-down balance. More important, the predicted optimal density is in the range of the experimentally determined density of E. coli. We conclude that cells have evolved to a cytoplasmatic density resulting in the maximum metabolic rate given the nutrient availability and macromolecular crowding effects and report a flux balance model accounting for its effect.