Dynamic Constrained Allocation Flux Balance Analysis (dCAFBA)

The survival of bacteria in dynamic environments depends on their ability to coordinate metabolism and gene expression. This interplay is fundamental: metabolism provides the energy and building blocks for protein synthesis, while the proteome, in turn, catalyzes and constrains metabolic fluxes. Here, we present a practical guide to dynamic Constrained Allocation Flux Balance Analysis (dCAFBA), a computational framework that integrates proteome allocation constraints with metabolic models to simulate this coordination. We provide step-by-step instructions for model construction, simulation, and analysis. The utility of dCAFBA is demonstrated through case studies of bacterial adaptation to carbon and amino acid shifts.