Coincident binding of synthetic and natural ligands to the nuclear receptor PPARγ

Crystal structures of peroxisome proliferator-activated receptor (PPAR) gamma have revealed overlapping binding modes for synthetic and natural ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a synthetic orthosteric ligand and a medium-chain fatty acid to a nonorthosteric alternate site forms a "ligand link" to the functionally important Ω-loop that synergistically affects PPARγ structure and function. Synthetic ligand extensions within the orthosteric pocket can "push" fatty acid cobinding modes towards the Ω-loop, and our retrospective analysis of the electron density of other PPARγ crystal structures bound to synthetic ligands identified alternate site density consistent with a cobound natural ligand. Mutagenesis studies indicate that residues contacting the cobound fatty acid may be important for basal cellular PPARγ activity and activation by synthetic ligands. These findings contribute to a growing body of evidence indicating ligand binding to nuclear receptors can be more complex than the classical one-for-one orthosteric exchange of natural and synthetic ligands.