Table 1 |
|||
Parameters used in the deterministic and stochastic simulations | |||
Parameter | Description | Value | Reference |
K_{d1} | dissociation constant of LuxR to A | 100 nM | [41] |
unbinding rate of LuxR to A | 10 min^{−1} | estimated | |
K_{d2} | dissociation constant of LuxR·AI dimerization | 20 nM | fitted |
dissociation rate of dimer (LuxR·AI)_{2} | 1 min^{−1} | estimated | |
k_{A} | synthesis rate of A by LuxI | 0.04 min^{−1} | fitted |
K_{dlux} | dissociation constant of (LuxR·AI)_{2} to the lux promoter | 200 nM | fitted |
dissociation rate of (LuxR·AI)_{2} to the lux promoter | 10 min^{−1} | estimated | |
b | burst size | 20 | [38] |
k_{R} | transcription rate of luxR | 200/bmin^{−1} | fitted |
k_{I} | transcription rate of luxI | 50/bmin^{−1} | fitted |
p_{R} | translation rate of luxR mRNA | bd_{mR}min^{−1} | |
p_{I} | translation rate of luxI mRNA | bd_{mI}min^{−1} | |
α_{R} | ratio between unactivated and activated rate of expression of luxR | 0.001 | fitted |
α_{I} | ratio between unactivated and activated rate of expression of luxI | 0.01 | fitted |
d_{A} | degradation rate of A (same inside and outside the cell) | 0.001 min^{−1} | [42] |
degradation rate of (LuxR·AI)_{2} | 0.002 min^{−1} | estimated | |
d_{C} | degradation rate of LuxR·AI | 0.002 min^{−1} | estimated |
d_{R} | degradation rate of LuxR | 0.002 min^{−1} | estimated |
d_{I} | degradation rate of LuxI | 0.01 min^{−1} | estimated |
d_{mR} | degradation rate of luxR mRNA | 0.347 min^{−1} | [43] |
d_{mI} | degradation rate of luxI mRNA | 0.347 min^{−1} | [43] |
D | effective diffusion rate of A through the cell membrane | 10 min^{−1} | [44] |
τ | cell cycle duration (doubling time) in RM/succinate at 30 C | 45 min | [10] |
λ | relative weight between the det./sto. components of the cell cycle | 0.8 | [33,45] |
V_{0} | cell volume at the beginning of cell cycle | 1.5 μm^{3} | [46] |
V_{tot} | total cell culture volume | 2·10^{−4}μl |
Weber and Buceta
Weber and Buceta BMC Systems Biology 2013 7:6 doi:10.1186/1752-0509-7-6