Structural and energetic differences between the human RXRα–PPARγ heterodimer with and without DNA binding

Abstract Structural data of multidomain structures of nuclear receptor complexes provides essential insights into how the quaternary complex impacts the nuclear receptor function. The heterodimeric complex between retinoic X receptor alpha (RXRα) and peroxisome proliferator-activated receptor gamma (PPARγ) is one of the most important and predominant regulatory systems, controlling lipid metabolism by binding to specific DNA promoter regions. X-ray and molecular dynamics (MD) simulations have revealed the average conformation adopted by the RXRα–PPARγ heterodimer bound to DNA, providing information about how multiple domains communicate to regulate receptor properties. However, knowledge of the energetic basis of the protein-ligand and protein-protein interactions is still lacking. Here we explore the structural and energetic mechanism of RXRα–PPARγ–DNA systems through microsecond MD simulations, molecular mechanics generalized Born surface area binding free energy calculations, principal component analysis, the free energy landscape, and correlated motion analysis. In our MD simulations, the RXRα–PPAR system was either bound or not bound to DNA and formed a complex with co-crystallized ligands (PDB entry 3DZY). Our results reveal new protein-ligand and protein-protein interactions that had not been reported in prior crystallographic studies. Binding free energy studies showed differences in protein-ligand and protein-protein affinity, whereas principal component analysis revealed differences in the conformational entropy depending on whether RXRα–PPARγ is bound or not bound to DNA. Correlated motions suggested that the allosteric communication is DNA dependent and bidirectional, impacting the protein-ligand and protein-protein interactions.