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In vitro assays - Activity of synthetic PPAR ligands is usually measured through a binding assay (if a radioligand is available) or through a cellular transient transfection reporter gene assay. The latter assay makes use of agonist stimulated dimerization leading to expression of the reporter enzyme (e.g. secreted placental alkaline phosphatase or firefly luciferase) which can be assayed with a colorimetric or photometric plate reader (1 and references therein).

X-rav structures - The x-ray crystal structures of PPAR8 with a fatty acid or a synthetic fibrate ligand have been determined (36). The crystal structure of PPARa with a small molecule ligand and the coactivator motif from the steroid receptor coactivator 1 (SRC-1) has recently been solved (38). The structure of PPARy itself and as a PPARy/RXR dimer with the SRC-1 coactivator fragment has also been determined (39, 40). These structures show that all the receptors have a Y-shaped binding pocket in common. However PPARy and PPARa have an extra binding area that accommodate somewhat larger ligands. Most of the small molecule PPAR ligands have an acidic moiety (e.g.TZD, carboxylic acid etc.) that binds to Ser289, His323, His449 and Tyr473 using the PPARy numbering. Since these receptors all bind fatty acids of different sizes, the binding pockets are large and accommodating to a variety of ligands. The volume of the binding pocket is largest for PPARy followed by PPARa with PPAR5 being the smallest.

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