The effect of regulating molecules on the structure of the PPAR-RXR complex

Ortal Amber-Vitos, Navaneet Chaturvedi, Esther Nachliel, Menachem Gutman, Yossi Tsfadia

Research output: Contribution to journalArticlepeer-review


The PPAR-RXR complex is one of the most significant and prevalent regulatory systems, controlling lipid metabolism by gene expression. Both proteins are members of the nuclear hormone receptor family, consisting of a ligand-binding domain (LBD), a hinge and a DNA binding domain (DBD). The two proteins form a heterodimer in the nucleus. The ligand-free complex interacts with corepressor proteins and blocks the expression of the genes. With the activating ligands and coactivator segments of regulating proteins, the heterodimer becomes active and allows translation of the genes under its control. We implemented model-independent all-atom molecular dynamics simulations for clarifying the structure changes that the activating ligand and the regulatory peptides impose on the PPAR-RXR system, starting with an LBD up to the PPAR-RXR-DNA complex. The simulations were carried out first with an active state of the protein. Once the relaxed state was attained, it was transformed into the inactive-state, the resulting structure was simulated. As the complex alternates between the active-inactive conformations, most of the changes are noticed at the junction area between the two subunits, located on the surface of a long fused helical structure made of H10–H11 of the proteins. The significant differences between the states included enhanced rigidity of the inactive complex, enhancement of tight contacts. The main drive for the transformation is the relocation of the tip of H12 of the PPAR that drives the carboxylate of the C-terminal towards the junction between H10–H11 of the RXR, leading to rearrangement of the main contact zone of the proteins.

Original languageEnglish
Pages (from-to)1852-1863
Number of pages12
JournalBiochimica et Biophysica Acta - Molecular and Cell Biology of Lipids
Issue number11
StatePublished - 1 Nov 2016


  • All-atom molecular dynamics
  • Heterodimer-complex
  • PPAR
  • RXR
  • Regulation

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology


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