Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ

Abstract
Data availability
Article and author information
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Abstract

Crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) have revealed overlapping binding modes for synthetic and natural/endogenous ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a synthetic ligand to the orthosteric pocket can push natural and endogenous PPARγ ligands (fatty acids) out of the orthosteric pocket towards an alternate ligand-binding site near the functionally important omega (Ω) loop. X-ray crystallography, NMR spectroscopy, all-atom molecular dynamics simulations, and mutagenesis coupled to quantitative biochemical functional and cellular assays reveal that synthetic ligand and fatty acid cobinding can form a 'ligand link' to the Ω loop and synergistically affect the structure and function of PPARγ. These findings contribute to a growing body of evidence indicating ligand binding to nuclear receptors can be more complex than the classical one-for-one orthosteric exchange of a natural or endogenous ligand with a synthetic ligand.

Data availability

Crystal structures and diffraction data have been deposited in the PDB under accession codes 5UGM, 6AVI, 6AUG, 6MCZ, 6MD0, 6MD1, 6MD2, and 6MD4.

The following data sets were generated

1. Shang J
2. Kojetin DJ
(2017) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Edaglitazone
Protein Data Bank, 5UGM.

http://www.rcsb.org/structure/5UGM
1. Shang J
2. Kojetin DJ
(2017) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and Nonanoic acid
Protein Data Bank, 6AVI.

http://www.rcsb.org/structure/6AVI
1. Shang J
2. Kojetin DJ
(2017) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with SR16832
Protein Data Bank, 6AUG.

http://www.rcsb.org/structure/6AUG
1. Shang J
2. Kojetin DJ
(2018) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Arachidonic Acid
Protein Data Bank, 6MCZ.

http://www.rcsb.org/structure/6MCZ
1. Shang J
2. Kojetin DJ
(2018) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Oleic Acid
Protein Data Bank, 6MD0.

http://www.rcsb.org/structure/6MD0
1. Shang J
2. Kojetin DJ
(2018) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and Oleic acid
Protein Data Bank, 6MD1.

http://www.rcsb.org/structure/6MD1
1. Shang J
2. Kojetin DJ
(2018) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and Arachidonic acid
Protein Data Bank, 6MD2.

http://www.rcsb.org/structure/6MD2
1. Shang J
2. Kojetin DJ
(2018) Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Rosiglitazone and Oleic acid
Protein Data Bank, 6MD4.

http://www.rcsb.org/structure/6MD4

The following previously published data sets were used

1. Kojetin D
2. Johnson B
(2012) PPARgamma LBD complexed with rosiglitazone
Biological Magnetic Resonance Bank, 17975.

https://doi.org/10.13018/BMR17975
(2012) Human PPAR gamma in complex with nonanoic acids
Protein Data Bank, 4EM9.

https://www.rcsb.org/structure/4EM9
(2012) Human peroxisome proliferator-activated receptor gamma in complex with rosiglitazone
Protein Data Bank, 4EMA.

https://www.rcsb.org/structure/4EMA
1. Wang Z
(2009) Crystal Structure of PPARg in complex with T2384
Protein Data Bank, 3K8S.

https://www.rcsb.org/structure/3K8S
(1998) LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
Protein Data Bank, 2PRG.

https://www.rcsb.org/structure/2PRG
1. Gampe Jr RT
2. Montana VG
3. Lambert MH
4. Miller AB
5. Bledsoe RK
6. Milburn MV
7. Kliewer SA
8. Willson TM
9. Xu HE
(2000) THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND ROSIGLITAZONE AND CO-ACTIVATOR PEPTIDES.
Protein Data Bank, 1FM6.

https://www.rcsb.org/structure/1FM6
(2011) Human PPAR gamma ligand binding domain in complex with MCC555
Protein Data Bank, 3B0Q.

https://www.rcsb.org/structure/3B0Q
(2011) Crystal structure of PPAR gamma ligand binding domain in complex with a novel partial agonist GQ-16
Protein Data Bank, 3T03.

https://www.rcsb.org/structure/3T03
1. Bruning JB
2. Nettles KW
(2007) Crystal Structure of PPARgamma ligand binding domain bound to partial agonist SR145
Protein Data Bank, 2Q61.

https://www.rcsb.org/structure/2Q61
(2011) Human PPAR gamma ligand binding dmain complexed with GW9662 in a covalent bonded form
Protein Data Bank, 3B0R.

https://www.rcsb.org/structure/3B0R
(1998) LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
Protein Data Bank, 1PRG.

https://www.rcsb.org/structure/1PRG

Article and author information

Author details

Jinsai Shang

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8164-1544
Richard Brust

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9200-1101
Sarah A Mosure

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.
Jared Bass

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.
Paola Munoz-Tello

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.
Hua Lin

Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.
Travis S Hughes

Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5764-5884
Miru Tang

Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States

Competing interests
The authors declare that no competing interests exist.
Qingfeng Ge

Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States

Competing interests
The authors declare that no competing interests exist.
Theodore M Kamekencka

Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States

Competing interests
The authors declare that no competing interests exist.
Douglas J Kojetin

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States

For correspondence
dkojetin@scripps.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8058-6168

Funding

National Institute of Diabetes and Digestive and Kidney Diseases (R01DK101871)

Douglas J Kojetin

American Heart Association (16- POST27780018)

Richard Brust

National Science Foundation (1659594)

Sarah A Mosure

The Scripps Research Institute

Sarah A Mosure

National Institute of Diabetes and Digestive and Kidney Diseases (R00DK103116)

Travis S Hughes

National Institute of Diabetes and Digestive and Kidney Diseases (F32DK108442)

Richard Brust

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.