Effect of heterodimer partner RXRα on PPARγ activation function-2 helix in solution

The structural mechanism of allosteric communication between retinoid X receptor (RXR) and its heterodimer partners remains controversial. As a first step towards addressing this question, we report a nuclear magnetic resonance (NMR) study on the GW1929-bound peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domain (LBD) with and without the 9-cis-retinoic acid (9cRA)-bound RXRα LBD. Sequence-specific 13Cα, 13Cβ, and 13CO resonance assignments have been established for over 95% of the 275 residues in the PPARγ LBD monomer. The 1HN, 15N, and 13CO chemical shift perturbations induced by the RXRα LBD binding are located at not only the heterodimer interface that includes the C-terminal residue Y477 but also residues Y473 and K474 in the activation function-2 (AF-2) helix. This result suggests that 9cRA-bound RXRα can affect the PPARγ AF-2 helix in solution and demonstrates that NMR is a powerful new tool for studying the mechanism of allosteric ligand activation in RXR heterodimers.