Table 1 Biochemical rates of molecular interactions involved in the curli regulation network. Reaction rates were derived according to catalytic properties of c-di-GMP regulation and protein-protein interactions identified in [7]. Since the focus was on post-translational dynamics, the protein expression levels of all DGCs and PDEs were held constant using the parameters V max1 (YegE), V max2 (YhjH), YdaMtot (YdaM) and YciRtot (YciR)
Rate function | Description of the reaction |
|---|---|
\(V_{1} = \frac {V_{\max 1}}{1 + x_{1}/K_{\mathrm {i}}^{\text {YegE}}}\) | Synthesis of c-di-GMP by YegE |
\(V_{2} = \frac {V_{\max 2} x_{1}}{x_{1} + K_{\mathrm {m}}^{\text {YhjH}}}\) | Degradation of c-di-GMP by YhjH |
\(V_{3} =(\textit {YciRtot} -x_{2})\frac {k_{\text {YciRact}} x_{1}}{x_{1} + K_{\mathrm {m}}^{\text {YciR}}}\) | Degradation of c-di-GMP by YciR |
\(V_{4} = \frac {k_{\text {YdaMact}} {x_{3}^{n}}}{\left (K_{\mathrm {d}_{\text {polymer}}}^{\text {YdaM}} \right)^{n} + {x_{3}^{n}}}\) | Synthesis of c-di-GMP by YdaM (no PI) |
\(V_{5} = k_{\text {YciRde}} x_{2} \frac {x_{1}}{x_{1} + K_{\mathrm {d}}^{\text {YciR}}}\) | Transition from YciR II (YdaM inhibiting) |
| Â | to YciR I (PDE activity) due to c-di-GMP |
| Â | binding |
V 6=c 6(Y c i R t o t−x 2) | Transition YciR I → YciR II |
\(V_{7} = k_{\text {YdaMde}} x_{3} \frac {x_{2}}{x_{2} + K_{\mathrm {d}}^{\text {YdaM}}}\) | Inhibition of YdaM due to binding of YciR II |
V 8=c 8(YdaMtot−x 3) | Re-activation of YdaM |