Structural mechanism underlying ligand binding and activation of PPARγ

Area of Science:

• Molecular biology
• Biochemistry
• Structural biology

Background:

• Nuclear receptors, including peroxisome proliferator-activated receptor gamma (PPARγ), possess occluded ligand-binding pockets.
• Understanding ligand binding mechanisms (induced fit vs. conformational selection) is crucial for receptor function.
• Molecular simulations suggest theoretical ligand entry pathways, but experimental validation is needed.

Purpose of the Study:

• To elucidate the mechanism by which structurally distinct agonists bind to PPARγ.
• To investigate whether PPARγ ligand binding follows an induced fit or conformational selection model.
• To characterize the kinetic and conformational changes associated with PPARγ activation by agonists.

Main Methods:

• Nuclear magnetic resonance (NMR) spectroscopy to monitor conformational changes.
• Isothermal titration calorimetry (ITC) to determine binding thermodynamics.
• Surface plasmon resonance (SPR) analysis to assess binding kinetics.

Main Results:

• Evidence supports a two-step induced fit mechanism for PPARγ agonist binding.
• An initial fast kinetic step is followed by a slow conformational change.
• Agonist binding likely involves an encounter complex at a surface pore before transitioning to the orthosteric pocket.

Conclusions:

• PPARγ activation by agonists proceeds via an induced fit mechanism.
• Ligand binding involves an initial encounter complex and subsequent transition to the orthosteric pocket.
• This process induces a transcriptionally active conformation of PPARγ.