Table 1.
Values of the parameters used in the simulations compared to those in experiments. All values listed are taken from in vitro experiments except for the ones marked with (*). All simulated parameters except for K+; K−; kC+; Kd; and ρActA were chosen to match those of previous studies [13, 39]. K+ was set by the additional polymerization constraint of aligning subunit polarization vectors (see Methods and Model); we decreased K− and kC+ to compensate for the reduced polymerization rate. ρActA was chosen to cover the experimental range of ActA densities, and also to explore the full range of behaviors of our model. ε was estimated from [81] which estimates 10–40 active binding sites per bacterium and a total bacterium binding energy of 10 kcal/mol (order 10 kBT per bacterium).
| Parameter | in vitro Exp. [ref] | Simulated |
|---|---|---|
| ℓp | 0.5–17.7 µM [90–94] | 0.1 µm |
| lave | 0.1–1 µm [95, 96]* | 0.1 µm |
| typical bead diameter | 0.2–2 µm [51] | 0.1 µm |
| viscosity (η) | 2.4 cP [51] | 2.4 cP |
| D = kBT/3πηa | 36.6 µm2/s | 36.6 µm2/s |
| K+ | 11.6 µM−1s−1 [17, 97] | 50 µM−1s−1 |
| K− | 0.3 s−1 [17, 97] | 2860 s−1 |
| [G-Actin] (initial) | 7 µm [20] | 600µM |
| [G-actin] (steady state) | 8.5 µM [65]* | 370µM |
| K+[G-Actin]/K− (initial) | 270 | 11 |
| Ka | ?µM−1s−1 | ~ K+ |
| Kd | 0.002 s−1 [98] | 2860 s−1 |
| [Arp2/3] | 0.1 µM [20] | 2.1 µM |
| Ka[Arp2/3]/Kd | N/A | 0.037 |
| KC+ | 8 µM−1s−1 [79] | — |
| KC− | 4· 10−4 s−1 [79, 99] | 0 s−1 |
| [Cap] | 0.1 µM [20] | — |
| kC+ = KC+[Cap] | 0.8 s−1 | 1570 s−1 |
| ρActA | 0.3–2.1 per 100 nm2 [56, 57] | 0–2.6 per 100 nm2 |
| ε | Few kBT [81]* | 0–16 kBT |