User:Adam Davis/Sandbox 1

Structural highlights

This is an X-ray crystallography structure, with a resolution of 1.95 Å, which models the region of PPARδ from Gln171 to Tyr441^[1]. It is composed of , with one small . The structure is bound to a synthetic ligand, , which contains a carboxylate group, a thiophenol, a thiazole, and a fluorine substituted phenyl ring. This ligand can be divided into a hydrophilic head group (carboxylate) and a hydrophobic tail (thiophenol, thiazole, phenyl). There is also a glycerol molecule in the structure, which is an artifact of the crystallization process and is not biologically relevant.

The ligand binding pocket (LBP) is made of (Arm I residues are green, Arm II residues are blue, Arm III residues are red), with fifteen residues that contact the ligand. interacts with the ligand through Phe246, Cys249, His287, Phe291, Ile327, His413, Leu433, and Tyr437. The of the ligand interacts via polar contacts with Arm I residues His287, His413, and Tyr437. , includes residues Val245, Val305, Val312, Leu317, and Ile 328, while includes Leu249 and Thr252. The of the ligand interacts via nonpolar contacts with residues from all three arms (Phe246, Phe291, His 413, Ile327, Leu433, Cys249, Val245, Val305, Val312, Leu317, Ile328, Thr252, and Leu294).

Using site-directed mutagenesis to replace LBP amino acids with Met, the authors found that from Arm II, Val312 and Ile328, are key to the specificity of this ligand for PPARδ.

Function

PPARs are ligand-activated transcription factors. The endogenous activators for these receptors are prostaglandins and fatty acids, but synthetic ligands have also been developed for therapeutic use^[2]. After activation, PPAR forms a heterodimer with the retinoid X receptor, and the complex binds to DNA, either stimulating or repressing transcription of genes involved in glucose or lipid metabolism.

PPARδ is found in many tissues, but is particularly prominent in muscle. It is important for fatty acid metabolism, and is known to increase insulin sensitivity^[3].

Disease

PPARδ agonists are being investigated as treatments for metabolic disorders including dyslipidemia, Type 2 Diabetes, and cardiovascular disease.

Relevance