Defining a conformational ensemble that directs activation of PPARγ

Nat Commun. 2018 May 4;9(1):1794. doi: 10.1038/s41467-018-04176-x.

Abstract

The nuclear receptor ligand-binding domain (LBD) is a highly dynamic entity. Crystal structures have defined multiple low-energy LBD structural conformations of the activation function-2 (AF-2) co-regulator-binding surface, yet it remains unclear how ligand binding influences the number and population of conformations within the AF-2 structural ensemble. Here, we present a nuclear receptor co-regulator-binding surface structural ensemble in solution, viewed through the lens of fluorine-19 (19F) nuclear magnetic resonance (NMR) and molecular simulations, and the response of this ensemble to ligands, co-regulator peptides and heterodimerization. We correlate the composition of this ensemble with function in peroxisome proliferator-activated receptor-γ (PPARγ) utilizing ligands of diverse efficacy in co-regulator recruitment. While the co-regulator surface of apo PPARγ and partial-agonist-bound PPARγ is characterized by multiple thermodynamically accessible conformations, the full and inverse-agonist-bound PPARγ co-regulator surface is restricted to a few conformations which favor coactivator or corepressor binding, respectively.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Humans
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Molecular Dynamics Simulation*
  • PPAR gamma / agonists
  • PPAR gamma / chemistry*
  • PPAR gamma / metabolism
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Binding
  • Protein Conformation*
  • Protein Multimerization
  • Thermodynamics

Substances

  • Ligands
  • PPAR gamma
  • Peptides