Effect of heterodimer partner RXRalpha on PPARgamma 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 ¹³C^α, ¹³C^β, 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.