TABLE 1: .
Overview of key parameters used in the simulation. All configuration files are available; see Material and Methods.
| Parameter | Value | Description/Reference |
|---|---|---|
| MT parameters | ||
| Polymerization speed | 0.3 µm/s | ( Hooikaas et al., 2020) |
| Depolymerization speed | 1 µm/s | ( Hooikaas et al., 2020) |
| Rigidity | 20 pN/µm | ( Gittes et al., 1993) |
| Stall force | 5 pN | Describes the modulation of growth speed and catastrophe rate by antagonistic force ( Dogterom and Yurke, 1997) |
| Catastrophe rate | 0.058 s–1, 0.15 s–1 | Matched to WT data of Hooikaas et al. (2020) |
| MT-bounding volume | ||
| Viscosity | 0.1 pN.s/µm2 | Internal viscosity of T-cells. As for most blood cells, it is usually estimated to be lower than that of somatic cells. Different values of internal viscosity for Jurkat cells have been reported ( Khakshour et al., 2015; Daza et al., 2019). |
| Elasticity | 100 pN/µm | This typical stiffness is used for the interaction of MTs with the nucleus. |
| Radius | 7 µm | ( Hooikaas et al., 2020) |
| Synapse fraction | 0.9 | This corresponds to a synapse cutting off 10% of the height of the cell (1.4 µm). |
| Interpolation distance | 1 µm | |
| Centrosome parameters | ||
| First anchoring stiffness | 500 pN/µm | Rotational stiffness on the MTs at the center of the centrosome, as proposed previously ( Letort et al., 2016). |
| Second anchoring stiffness | 500 pN/µm | Rotational stiffness on the MTs exerted at the periphery of the centrosome, as proposed previously ( Letort et al., 2016). |
| Number of MTs | 150 | ( Hooikaas et al., 2020) |
| Dynein parameters | ||
| Walking speed | 0.5 µm/s | ( Ohashi et al., 2019) |
| Number | 100 | |
| Stall force | 4 pN | ( Belyy et al., 2016) |
| Binding rate | 5 s–1 | A typical value used for modeling ( Leduc et al., 2004; Xu et al., 2012; Klumpp et al., 2015; Feng et al., 2018) |
| Unbinding rate | 0.05 s–1 | The unbinding rate of the dynein–dynactin–BicD2 complex ( McKenney et al., 2014; Ohashi et al., 2019). |
| Initialization | Random on synapse | Dynein is initialized on the synapse and part of the interpolated curve connecting the synapse to the rest of the cell. The region is defined as being within 1.6 µm of the synapse along the vertical axis. |
| Effective stiffness | 33 pN/µm | The stiffness of the dynein anchor, dynein–membrane binder, and membrane binder–synaptic membrane are all modeled as 100 pN/µm in series. This corresponds to an effective stiffness of ∼33 pN/µm. |
| Confinement to membrane | 100 pN/µm | |
| Lattice occupation | 4 nm | Width of the lattice that can only contain a single dynein |
| Site shift | 2 nm | This is lower than the measured step size of dynein in vitro ( Gennerich et al., 2007; Elshenawy et al., 2019). We consider this as a rather effective value to take backstepping and binding sites on different protofilaments into account. |
| System parameters | ||
| Dimensionality | 3D | |
| Number of repeats | 15 per condition | |