Figure 3. Predicted effect of crowding on the rRNA promoter binding affinity for two crowding scenarios.

In the transition state scenario, binding affinities initially strengthen as macromolecular crowding is increased due to increased entropic forces, while in the diffusion limited scenario binding affinities weaken as macromolecular crowding is increased due to increased diffusion times. In both cases, binding affinities weaken when macromolecular crowding is increased beyond the WT crowding state due to increased diffusion times (see also Figures S8 and S2.4 in Text S1). Quantitatively, affinities can vary by up to a factor of 5 (transition state limited scenario) to 16 (diffusion limited scenario), measured as the ratio of the maximum and minimum values of binding affinities in the range of rRNA operon copy numbers considered. Similar results are obtained for RBS binding affinities. Binding affinities were normalized to WT values. Insert: predicted macromolecular volume fraction, Φ, as a function of rRNA operon copy number per chromosome.