Fig. 5: Consolidated models for ligand-specific changes in the conformational ensemble in IPTG-LacI and ONPF-LacI, as compared to DNA-LacI.

Schematics summarizing the rigidity of LacI core domain secondary structure elements in IPTG-LacI and ONPF-LacI as compared to DNA-LacI, with rigidified regions in each ligand-bound state shown in teal, de-rigidified regions shown in purple, and regions for which there is no data shown with stripes. Red circles show the positions of predicted structural water molecules, and red lines show the interactions of the predicted structural water molecules with atoms in ligands or amino acid residues. Orange lines represent hydrogen bonds uniquely formed among protein atoms in each ligand-bound state as compared to DNA-LacI. Rigidified loops in each schematic are thick for emphasis. A In IPTG-LacI, hydrogen bond formation at the ligand-binding pocket periphery promotes interactions between the N- and C-terminal subdomains of the core, which causes small structural rearrangements in the N-terminal subdomains (arrows) to increase flexibility in the hinge helix (black X). B In ONPF-LacI, the C-terminal core subdomain is not extensively perturbed as compared to DNA-LacI. However, N-terminal core subdomain loops become more structured, which may stabilize the interface of the core domain with the DNA-binding domain to bind the operator.