Table 2.
Modeling of four mechanisms of microRNA action in the non-linear protein translation model
| Observable value | Initiation(k1) | Step after initiation(k2) | Ribosome assembly (k3) | Elongation (k4) |
|---|---|---|---|---|
| Wild-type cap, inefficient initiation | ||||
| Steady-state rate | slightly decreases | decreases | no change | decreases after threshold |
| Relaxation time | no change | no change | no change | goes up and down |
| Wild-type cap, efficient initiation | ||||
| Steady-state rate | no change | slightly decreases after strong inhibition | no change | decreases |
| Relaxation time | no change | goes up and down | no change | no change |
| A-cap, inefficient initiation | ||||
| Steady-state rate | decreases | decreases | no change | slightly decreases after strong inhibition |
| Relaxation time | no change | no change | no change | goes up and down |
| A-cap, efficient initiation | ||||
| Steady-state rate | decreases after threshold | slightly decreases after strong inhibition | no change | decreases |
| Relaxation time | goes up and down | goes up and down | no change | increases |
MicroRNA action effect is described for the protein synthesis steady rate and the relaxation time (see also Fig. 8). "Efficient initiation" and "inefficient initiation" correspond to two qualitatively different solution types of Nissan and Parker's model (see the beginning of "Effect of microRNA on the translation dynamics" section). The effect of A-cap structure is modeled by making the cap-dependent initiation step very slow (by making the k1 parameter very small). It is assumed that the ribosome assembly step in protein translation, described by the k3 rate constant, is not rate limiting.