Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon
Figure 5
DNA loops simulated in the presence of HU and deformable LacR capture in-vivo looping properties.
The predicted ease of DNA loop formation between the headpieces of (A) a rigid V-shaped LacR complex and (B) a deformable LacR assembly mimics looping propensities deduced from the in-vivo expression of lac genes [11]–[13]. The chain-length-dependent gene-expression profiles of E. coli cells are expressed as J factors using Eqn. (4). Values of J for a strain with wild-type (WT) proteins and a mutated strain (ΔHU) that cannot express HU are depicted respectively by large and small dark symbols, with data reported in different publications for the same DNA construct [11]–[13] expressed as average values. The simulated J factors reflect the likelihood that an ideal, naturally straight DNA molecule folds along a pathway compatible with the spatial constraints imposed by the binding of LacR and the presence or absence of HU (points connected respectively by thick and thin lines).