Figure 6.

(A) Kinetic network model for transcription regulated by “OFF”-riboswitches. (B) Dependence of protein production on the network parameters with “negative feedback” (k_f1 = 0.1 s⁻¹, k_−f1 = 0.04 s⁻¹, k_f2 = 2.5 × 10⁻³ s⁻¹, k_−f2 = 0.04 s⁻¹, k_t1 = 0.1 s⁻¹, k_t2 = 0.016 s⁻¹, k_b = 0.1 μM⁻¹ s⁻¹, k_−b = 10⁻³ s⁻¹, k_t3 = 0.01 s⁻¹, K₁ = 0.016, k₂ = 0.3 s⁻¹, k₃ = 0.064 s⁻¹, k_d1 = 2.3 × 10⁻³ s⁻¹, k_d2 = 2.7 × 10⁻⁴s⁻¹, k_d3 = 4.5 × 10⁻³s⁻¹, and μ = 5 × 10⁻⁴s⁻¹. (Top) Protein levels [P] (color (different gray shades in the print version) coded) as functions of k_t1/k_f1 and k_b). The dependence of [P] on k_t1 and k_b is categorized into three regimes. Points on the dashed line separating regime II and regime III satisfy k_b[M] = k_t1. The major pathway in the transcription process in each regime is shown on the right. The arrow indicates the data point from the value of k_t1 = 0.1 s⁻¹ and k_b = 0.1 s⁻¹. (Bottom) [P] as functions of k_t2/k_f2 and k_b. Points on the dashed line separating regime I and M/MI satisfy k_b1[M] = k_−f2. The data point corresponding to the arrow results from using the value of k_t2 = 0.016 s⁻¹ and k_b = 0.1 s⁻¹. Figure adapted from J.-C. Lin and Thirumalai (2012).