Structural Basis for Differential Transcription Activation by Enantiomeric Agonists of PPARγ and Crystal Structure of TNF-α-Inducing Protein (Tipα) from Helicobacter pylori

Abstract

Peroxisome proliferator-activated receptor γ (PPARγ) is a member of the nuclear receptor superfamily. It functions as a ligand-activated transcription factor and plays important roles in the regulation of adipocyte differentiation, type 2 diabetes mellitus, and inflammation. Many PPARγ agonists bind to the canonical ligand-binding pocket near the helix H12. More recently, an alternate ligand-binding site of the PPARγ ligand-binding domain (LBD) was identified

it is located beside the Ω loop between the helices H2´ and H3. Previously it was reported that the chirality of two optimized enantiomeric PPARγ ligands (S35 and R35) differentiates their PPARγ transcriptional activity, binding affinity, and inhibitory activity toward Cdk5 (cyclin-dependent kinase 5)-mediated phosphorylation of PPARγ at Ser273. S35 is a PPARγ phosphorylation inhibitor with promising glucose uptake potential, while R35 behaves as a potent conventional PPARγ agonist. To provide a structural basis for understanding the differential activities of these ligands, I have determined crystal structures of the PPARγ LBD in complex with either S35 or R35. These structural data reveal a significant difference in the binding modes of these enantiomeric ligands to the PPARγ LBD. S35 occupies the alternate ligand-binding site, whereas R35 binds to the canonical ligand-binding pocket, thus explaining their different behaviors as PPARγ agonists. This finding provides a useful platform for the development of a new generation of PPARγ ligands as anti-diabetic drug candidates.

Helicobacter pylori infection is one of the highest risk factors for gastroduodenal diseases including gastric cancer. Tumor necrosis factor-α (TNF-α) is one of the essential cytokines for tumor promotion and thus a H. pylori protein that induces TNF-α is believed to play a significant role in gastric cancer development in humans. The HP0596 gene product of H. pylori strain 26695 was identified as the TNF-α inducing protein (Tipα). Tipα is secreted from H. pylori as dimers and enters the gastric cells. It was shown to have a DNA binding activity. Here I have determined the crystal structure of Tipα from H. pylori. Its monomer consists of two structural domains (mixed domain and helical domain). Tipα exists as a dimer in the crystal and the dimeric structure represents a novel scaffold for DNA binding. A positively-charged surface patch formed across the two monomers of the Tipα dimer by the loop between helices α1 and α2 may be important in DNA binding.