TABLE 1.
Parameter and initial condition values used in 3D simulations
| Parameter | Description | Value | Comments |
|---|---|---|---|
| IP3_basal | Basal IP3 concentration | 0.16 μm | (30) |
| k_PIP2hyd | Rate of PIP2 hydrolysis by PLC_act_PM | 1.188 s−1 | Appropriate for IP3 production |
| kBasalSynPIP | Rate of basal synthesis of PIP | 0.0015 s−1 | Similar to Xu et al. (26) |
| kBasalSynPIP2 | Rate of basal synthesis of PIP2 | 0.045 s−1 | Similar to Xu et al. (26) |
| Kf | Forward rate of PIP2 binding to sink protein | 0.003 s−1 | Appropriate for IP3 production |
| KfPLCact | Forward rate of PLC activation | 10 s−1 | Appropriate for PIP2 hydrolysis |
| kIP3deg | IP3 degradation rate | 0.14 s−1 | (30) |
| Kr | Reverse rate of PIP2 binding to sink protein | 1 s−1 | Appropriate for IP3 production |
| krPLCact | Reverse rate of PLC activation | 2 s−1 | Appropriate for PIP2 hydrolysis |
| kStimSynPIP | Rate of stimulated synthesis of PIP | 3 s−1 | Appropriate for IP3 production |
| kStimSynPIP2 | Rate of stimulated synthesis of PIP2 | 150 s−1 | Appropriate for IP3 production |
| PIP_basal | Basal PIP concentration | 2857 mol/μm2 | (26) |
| PIP2_basal | Basal PIP2 concentration | 4000 mol/μm2 | (26) |
| PIP2syndecay | Decay rate factor for PIP2 synthesis | 0.8 s | Appropriate for PIP2 synthesis |
| PIPsyndecay | Decay rate factor for PIP synthesis | 0.8 s | Appropriate for PIP synthesis |
| stimdecay | Decay rate factor for PLC_act_PM | 0.8 s | Appropriate for PIP2 hydrolysis |
| τ0 | Time at which stimulation is introduced | 0.1 s | |
| τPIP2syn | Time at which stimulation is introduced | 0.1 s | |
| τPIPsyn | Time at which stimulation is introduced | 0.1 s | |
| DAG_PM_init | Initial DAG concentration | 2000 mol/μm2 | Model from Xu et al. (26) |
| IP3_Cyt_init | Initial IP3 concentration | 0.16 μm | (30) |
| PI_PM_init | Initial PI concentration | 142,857 mol/μm2 | (30) |
| PIP_PM_init | Initial PIP concentration | 2857 mol/μm2 | (30) |
| PIP2_bound_PM_init | Initial amount of sink protein bound to PIP2 | 36,003 mol/μm2 | Appropriate for IP3 production |
| PIP2_PM_init | Initial PIP2 concentration | 4000 mol/μm2 | (26) |
| PIP2Sink_PM_init | Initial amount of PIP2 sink protein | 2997 mol/μm2 | Appropriate for IP3 production |
| PLC_act_PM_init | Initial concentration of activated PLC | 0 mol/μm2 | (26) |
| PLC_PM_init | Initial concentration of inactive PLC | 100 mol/μm2 | (26) |