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Team:ETH Zurich/modeling/parameters
From 2014.igem.org
(Difference between revisions)
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|L<sub>PLux</sub>||0.02461 nM<sup>-1</sup>min<sup>-1</sup>||Leakiness after using riboswitch for PLas||Fitted | |L<sub>PLux</sub>||0.02461 nM<sup>-1</sup>min<sup>-1</sup>||Leakiness after using riboswitch for PLas||Fitted | ||
| + | |- | ||
| + | |k<sub>DBxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of Bxb1||Fitted | ||
| + | |- | ||
| + | |k<sub>-DBxb1</sub>||10<sup>-4</sup> min<sup>-1</sup>||Dissociation rate of DBxb1||Fitted | ||
| + | |- | ||
| + | |k<sub>SABxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Rate of formation of SABxb1 from DBxb1 and SIBxb1||Fitted | ||
| + | |- | ||
| + | |k<sub>-SABxb1</sub>||10<sup>-4</sup> min<sup>-1</sup>||Dissociation rate of SABxb1||Fitted | ||
| + | |- | ||
| + | |d<sub>DBxb1</sub>||0.02 min<sup>-1</sup>||Degradation rate of DBxb1||Assumed | ||
| + | |- | ||
| + | |k<sub>ϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of ϕc31||Fitted | ||
| + | |- | ||
| + | |k<sub>-Dϕc31</sub>||10<sup>-4</sup> min<sup>-1</sup>||Rate of dissociation of Dϕc31||Fitted | ||
| + | |- | ||
| + | |k<sub>SAϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Rate of formation of SAϕc31 from Dϕc31 and SIϕc31||Fitted | ||
| + | |- | ||
| + | |k<sub>-SAϕc31</sub>||10<sup>-4</sup> min<sup>-1</sup>||Rate of dissociation of SAϕc31||Fitted | ||
| + | |- | ||
| + | |d<sub>Dϕc31</sub>||0.02 min<sup>-1</sup>||Degradation rate of Dϕc31||Assumed | ||
| + | |- | ||
| + | |k<sub>offBxb1</sub>||100 nM<sup>-2</sup>min<sup>-1</sup>||Rate of flipping of T<sub>on,i</sub> to T<sub>offBxb1</sub>||Assumed | ||
| + | |- | ||
| + | |k<sub>GFP,LuxI</sub>||10 min<sup>-1</sup>||Production rate of GFP and LuxI||Assumed | ||
| + | | | ||
| + | |k<sub>-offBxb1</sub>||100 nM<sup>-2</sup>min<sup>-1</sup>||Rate of flipping of T<sub>offBxb1</sub> to T<sub>on,f</sub>||Assumed | ||
|} | |} | ||
{{:Team:ETH Zurich/tpl/foot}} | {{:Team:ETH Zurich/tpl/foot}} | ||
Revision as of 07:54, 9 October 2014
Parameters
No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.
| Parameter | Value | Description | Reference | |||||
|---|---|---|---|---|---|---|---|---|
| αLuxR | 60 nMmin-1 | Production rate of LuxR | Estimated | |||||
| kRLux | 0.1 nM-1min-1 | Rate of formation of RLux from 30C6HSL and LuxR | Weber | |||||
| k-RLux | 10 min-1 | Dissociation rate of RLux | Weber | |||||
| kDRLux | 0.05 nM-1min-1 | Dimerization rate of RLux | Weber | |||||
| k-DRLux | 1 min-1 | Dissociation rate of DRLux | Weber | |||||
| KdPLux | 0.007652 nM | Dissociation rate constant for DRLux-PLux | Fitted | |||||
| d30C6HSL | 0.004 min-1 | Degradation rate of 30C6HSL | Estimated/Fitted | |||||
| dLuxR | 0.0174 min-1 | Degradation rate of LuxR | Weber | |||||
| dRLux | 0.0174 min-1 | Degradation rate of RLux | Weber | |||||
| dDRLux | 0.0231 min-1 | Degradation rate of DRLux | Weber | |||||
| dBxb1 | 0.01 min-1 | Degradation rate of Bxb1 | Assumed | |||||
| LPLux | 0.04458 nM-1min-1 | Leakiness after using riboswitch for PLux | Fitted | |||||
| αLasR | 60 nMmin-1 | Production rate of LasR | Estimated | |||||
| kRLas | 0.1 nM-1min-1 | Rate of formation of RLas from 30C12HSL and LasR | Weber | |||||
| k-RLas | 10 min-1 | Dissociation rate of RLas | Weber | |||||
| kDRLas | 0.05 nM-1min-1 | Dimerization rate of RLas | Weber | |||||
| k-DRLas | 1 min-1 | Dissociation rate of DRLas | Weber | |||||
| KdPLas | 1.3672 nM | Dissociation rate constant for DRLas-PLas | Fitted | |||||
| d30C12HSL | 0.004 min-1 | Degradation rate of 30C12HSL | Estimated/Fitted | |||||
| dLasR | 0.0174 min-1 | Degradation rate of LasR | Weber | |||||
| dRLas | 0.0174 min-1 | Degradation rate of RLas | Weber | |||||
| dDRLas | 0.0231 min-1 | Degradation rate of DRLas | Weber | |||||
| dϕC31 | 0.01 min-1 | Degradation rate of ϕC31 | Assumed | |||||
| LPLux | 0.02461 nM-1min-1 | Leakiness after using riboswitch for PLas | Fitted | |||||
| kDBxb1 | 1 nM-1min-1 | Dimerization rate of Bxb1 | Fitted | |||||
| k-DBxb1 | 10-4 min-1 | Dissociation rate of DBxb1 | Fitted | |||||
| kSABxb1 | 1 nM-1min-1 | Rate of formation of SABxb1 from DBxb1 and SIBxb1 | Fitted | |||||
| k-SABxb1 | 10-4 min-1 | Dissociation rate of SABxb1 | Fitted | |||||
| dDBxb1 | 0.02 min-1 | Degradation rate of DBxb1 | Assumed | |||||
| kϕc31 | 1 nM-1min-1 | Dimerization rate of ϕc31 | Fitted | |||||
| k-Dϕc31 | 10-4 min-1 | Rate of dissociation of Dϕc31 | Fitted | |||||
| kSAϕc31 | 1 nM-1min-1 | Rate of formation of SAϕc31 from Dϕc31 and SIϕc31 | Fitted | |||||
| k-SAϕc31 | 10-4 min-1 | Rate of dissociation of SAϕc31 | Fitted | |||||
| dDϕc31 | 0.02 min-1 | Degradation rate of Dϕc31 | Assumed | |||||
| koffBxb1 | 100 nM-2min-1 | Rate of flipping of Ton,i to ToffBxb1 | Assumed | |||||
| kGFP,LuxI | 10 min-1 | Production rate of GFP and LuxI | Assumed | k-offBxb1 | 100 nM-2min-1 | Rate of flipping of ToffBxb1 to Ton,f | Assumed |
