Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks
Figure 3
Cooperative binding and dissociation reactions can increase the efficiency and robustness of duplex formation.
(A) Reaction scheme without sRNA and target mRNA dissociation. (B) Topological representation of the cooperative reaction schemes with low, medium and high values for y3 and y4. y3 determines whether the association rate constants favor the sRNA-Hfq branch or the target mRNA-Hfq branch [y3≡((k2⋅k4)/(k1⋅k3))1/2] and it has values of 10−4, 100 and 104 (unitless) in the simulations. y4 biases the system from negative to positive cooperative association [y4≡((k3⋅k4)/(k1⋅k2))1/2] and it has values of 10−4, 100 and 104 (unitless) in the simulations. The relative magnitude of the kinetic parameters is represented graphically by the weight of the arrows. (C) As described for Figure 2C. (D) Reaction scheme for duplex formation with association and dissociation reactions that are independent. (E) Topological representation of the reaction schemes with low, medium and high values for the k5 and y5 parameters. k5 is the overall rate of duplex formation and release with values of 100, 103 and 106 time−1 in the simulations. y5 determines the overall magnitude of the dissociation rate constants for the sRNA and target mRNA [y5≡(k−1⋅k−2⋅k−3⋅k−4)1/4] and it has values of 100, 104 and 108 time−1 in the simulations. (F) As described for Figure 2C.