Inferring Biological Mechanisms by Data-Based Mathematical Modelling: Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case

Figure 3

Allosteric interactions enhance sensitivity. (a) The interactions between AB (red) and AA (blue) constitute an allosteric binding mechanism. At low AA concentrations little AA can bind to AB. As the AA concentrations increase, more AB-AA complexes form (1). Binding of AA biases the AB dimer into a different conformation (2) that binds AA with high affinity, and a second AA binds to the AB dimer (3). (b) The allosteric binding mechanism enhances the sensitivity to changes in the AA concentration. The solid line shows the fraction of AA-saturated AB dependent on the AA concentration when we use the physiological affinities. The dashed line shows the fraction of AA-saturated AB if AB had only one conformation and interacted with AA with high affinity. (c) The interactions between AB (red), AA (blue), and 𝜎^𝐹 (green) lead to a sophisticated allosteric control mechanism. At low AA concentrations 𝜎^𝐹 can bind to AB (1). As the AA concentrations increase, AB-𝜎^𝐹-AA complexes form (2). Binding of AA biases the AB dimer into a different conformation (3) that binds 𝜎^𝐹 with low and AA with high affinity. 𝜎^𝐹 thus rapidly unbinds (4) and a second AA binds to the AB dimer (5). (d) The sophisticated allosteric binding mechanism enhances the sensitivity to changes in the AA concentration. The solid line shows the fraction of unbound 𝜎^𝐹 dependent on the AA concentration when we use the physiological affinities. The dashed line shows the fraction of unbound 𝜎^𝐹 if AB had only one conformation and interacted both with 𝜎^𝐹 and AA with high affinity.