Defining a conformational ensemble that directs activation of PPARγ

Ian M. Chrisman, Michelle D. Nemetchek, Ian Mitchelle S. De Vera, Jinsai Shang, Zahra Heidari, Yanan Long, Hermes Reyes-Caballero, Rodrigo Galindo-Murillo, Thomas E. Cheatham, Anne Laure Blayo, Youseung Shin, Jakob Fuhrmann, Patrick R. Griffin, Theodore M. Kamenecka, Douglas J. Kojetin, Travis S. Hughes

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number1794
JournalNature Communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018
Externally publishedYes

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Peroxisome Proliferator-Activated Receptors
regulators
Chemical activation
activation
Conformations
Ligands
ligands
Cytoplasmic and Nuclear Receptors
Co-Repressor Proteins
Fluorine
Lenses
Magnetic Resonance Spectroscopy
Crystal structure
peptides
fluorine
Nuclear magnetic resonance
Peptides
lenses
nuclear magnetic resonance
crystal structure

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Chrisman, I. M., Nemetchek, M. D., De Vera, I. M. S., Shang, J., Heidari, Z., Long, Y., ... Hughes, T. S. (2018). Defining a conformational ensemble that directs activation of PPARγ. Nature Communications, 9(1), [1794]. https://doi.org/10.1038/s41467-018-04176-x

Defining a conformational ensemble that directs activation of PPARγ. / Chrisman, Ian M.; Nemetchek, Michelle D.; De Vera, Ian Mitchelle S.; Shang, Jinsai; Heidari, Zahra; Long, Yanan; Reyes-Caballero, Hermes; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.; Blayo, Anne Laure; Shin, Youseung; Fuhrmann, Jakob; Griffin, Patrick R.; Kamenecka, Theodore M.; Kojetin, Douglas J.; Hughes, Travis S.

In: Nature Communications, Vol. 9, No. 1, 1794, 01.12.2018.

Research output: Contribution to journalArticle

Chrisman, IM, Nemetchek, MD, De Vera, IMS, Shang, J, Heidari, Z, Long, Y, Reyes-Caballero, H, Galindo-Murillo, R, Cheatham, TE, Blayo, AL, Shin, Y, Fuhrmann, J, Griffin, PR, Kamenecka, TM, Kojetin, DJ & Hughes, TS 2018, 'Defining a conformational ensemble that directs activation of PPARγ', Nature Communications, vol. 9, no. 1, 1794. https://doi.org/10.1038/s41467-018-04176-x
Chrisman IM, Nemetchek MD, De Vera IMS, Shang J, Heidari Z, Long Y et al. Defining a conformational ensemble that directs activation of PPARγ. Nature Communications. 2018 Dec 1;9(1). 1794. https://doi.org/10.1038/s41467-018-04176-x
Chrisman, Ian M. ; Nemetchek, Michelle D. ; De Vera, Ian Mitchelle S. ; Shang, Jinsai ; Heidari, Zahra ; Long, Yanan ; Reyes-Caballero, Hermes ; Galindo-Murillo, Rodrigo ; Cheatham, Thomas E. ; Blayo, Anne Laure ; Shin, Youseung ; Fuhrmann, Jakob ; Griffin, Patrick R. ; Kamenecka, Theodore M. ; Kojetin, Douglas J. ; Hughes, Travis S. / Defining a conformational ensemble that directs activation of PPARγ. In: Nature Communications. 2018 ; Vol. 9, No. 1.
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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.",
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