Figure 1.

The protein degradation model

There are a total of five types of substrate proteins, defined in Table 2. Substrate proteins (rounded rectangles, sky blue) are synthesized from mRNA molecules (blue line, top left) in the ribosome (brown, top left) and ubiquitinated by E3 ubiquitin ligases (orange ovals) with ubiquitins (yellow circles). The ubiquitinated proteins are degraded (gray ovals) or deubiquitinated by deubiquitinating enzymes (light green hexagon). The total protein concentration is represented by x(t) with symbol Σ at the center.