Figure 2
From: Binary gene induction and protein expression in individual cells
Structure of the stochastic model for binary gene induction. Reactions enclosed in the box were simulated with Gillespie's exact method (see supporting material for reaction details). The reaction volume, i.e., the nucleus volume, was 100 μ m3. TA: transcription activator. Φ represents RNA and protein degradation. Simulations started with 1 copy of inactive promoter, 0 ~ 512 copies of TA (equivalent to 0 ~ 8 nM), and 0 copies of all other molecule species. k
i
, k
if
and k
ib
, for i = 1, 2, ..., 7, are stochastic reaction constants (k2fand k'2fare the TA-dependent and TA-independent activation rates of the promoter, respectively; k5 = In 2/
, k7 = In 2/
, where and are RNA and protein half-lives, respectively). s is protein detection sensitivity. Unless otherwise indicated, reaction constants k
1f
, k
1b
, k
2f
, k'
2f
, k
3f
, k
3b
, k
4
and k
6
were fixed for all simulations (k
1f
, k
3f
= 1.12 × 10-4; k
1b
, k
3b
= 1.48 × 10-2; k
2f
= 1.67 × 10-4; k'
2f
= 1 × 10-9; k
2b
= 3.33 × 10-5; k
4
= 5.56 × 10-3; k
6
= 4.17 × 10-3; unit = s-1). Background noise followed normal distribution N(10, 32) excluding values less than 1.