Figure 2.

Schematic illustration of protein resource fluxes in bacteria. AAs inside the cell come from the uptake and metabolism of the nutritional substrate (S) via P₁ (flagella, transporters, metabolic enzymes, and their affiliated proteins) or from the degradation of aberrant proteins via P₃ (proteases and their affiliated proteins). The former is defined as AA supply flux (v₁, J₁) and the latter as the degradation flux (v₃, J₃). AAs are translated into polypeptides via R (ribosome-affiliated proteins), defined as translation flux (v₀, J₀). Unfolded polypeptides (UP) mature as native proteins via P₂ (chaperones and other proteins promoting protein maturation) or mistakenly mature as aberrant proteins (AP) because of the lack of P₂. The former is defined as normal maturation flux (v₂, J₂) and the latter as aberrant maturation flux (v₄, J₄). APs can also form protein aggregates spontaneously, defined as the aggregation flux (v₅, J₅). Here, v_i denotes the total flux rate and J_i ($\equiv v_i/M_c$, where M_c denotes total cell mass and i ∈ {0, 1, 2, 3, 4, 5}) denotes flux rate per unit cell mass. Each flux can be represented as a function of the concentration or proteome fraction of related proteins.