Figure 8.

Role of feedback to a spike in the DNA concentration. (A) Response of protein level $\left(\Delta P\right)$ relative to the change of steady-state level $\left(\Delta P_{st}\right)$ when the DNA level increases by 50%. The response time is 850 s with negative feedback (blue line) and 1450 s without feedback (red line). The values of folding and unfolding rates used are 10-fold larger than those given in Table 1. (B) Response of the fraction of fully transcribed RNA, $\Delta F$, when the DNA level increases by 50%. The fraction of fully transcribed RNA increases initially with negative feedback (blue line) and decreases initially without feedback (red line) before settling to a new steady state. (C) Fractional change in protein steady-state level relative to that in DNA concentration, $\delta P_{st}/\delta D$, in response to a 50% rise in DNA level, as a function of $k_{t2}/k_{-f2}$ and $k_b$ for the riboswitch network with negative feedback using parameters in Table 1. Points on the dashed line separating regime I and regime II/III satisfy $k_b\left[M\right]=k_{-f2}$. (D) Same as (C) with the overall folding and unfolding rates being 10-fold greater than those in Table 1. The arrow indicates the data point when $k_{t2}$ and $k_b$ are at the values from Table 1.