Fig. 3: The apo ensemble contains little active-like helix 12 conformations.
From: Definition of functionally and structurally distinct repressive states in the nuclear receptor PPARγ
a Examples of three classes of helix 4 to helix 12 bonding observed in deposited crystal structures (PDB codes 1PRG, 2PRG, and 3R5N). Almost all of the 176 active structures (chain A) available show bonding between K347 and the helix 12 backbone. Two of the 176 structures have a salt bridge between K347 and E499. None of the 176 inactive conformations (chain B) showed bonding between K347 and helix 12. b All 58 representative structures shown in Supplementary Fig. 1 were subjectively classified as having active-like or inactive-like helix 12 conformations. Prevalence of bonding between helix 12 residues and K347 calculated from 1 μs simulations of each representative structure in each class are shown. c The Boltzmann average values for interaction of the terminal side chain protons on K347 (i.e., NH3) and all other residues was calculated for PPARγ alone (apo) or bound to the indicated ligands. d Comparison of wt and K347A mutants bound to rosiglitazone or without ligand (apo) using TROSY-HSQC NMR. Source data are provided as a Source Data file (Source data_Heidari.xlsx).
