Structural modeling of the AhR:ARNT complex in the bHLH–PASA–PASB region elucidates the key determinants of dimerization
Open accessAbstract
Elucidation of the dimerization process of the aryl hydrocarbon receptor (AhR) with the AhR nuclear translocator (ARNT) is crucial for understanding the mechanisms underlying the functional activity of AhR, including mediation of the toxicity of environmental contaminants. In this work, for the first time a structural model of the AhR:ARNT dimer encompassing the entire bHLH–PASA–PASB domain region is proposed. It is developed by using a template-based modeling approach, relying on the recently available crystallographic structures of two dimers of homologous systems in the bHLH–PAS family of proteins: the CLOCK:BMAL1 and the HIF2α:ARNT heterodimers. The structural and energetic characteristics of the modeled AhR:ARNT protein–protein interface are determined by evaluating the variations in solvent accessible surface area, the total binding free energy and the per-residue free energy contributions obtained by the MM-GBSA method and the Energy Decomposition Analysis. The analyses of the intricate network of inter-domain interactions at the dimerization interfaces provide insights into the key determinants of dimerization. These are confirmed by comparison of the computational findings with the available experimental mutagenesis and functional analysis data. The results presented here on the AhR:ARNT dimer structure and interactions provide a framework to start analyzing the mechanism of AhR transformation into its functional DNA binding form.
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Modeling studies on the AhR:ARNT dimer, based on the HIF-2α:ARNT template, predicted that the Fα/Gβ site may be involved in the dimerization interface.
“our modeling studies on the AhR:ARNT dimer, based on the HIF-2α:ARNT template, predicted that the Fα/Gβ site may be involved in the dimerization interface47,48.”
From Modeling the binding of diverse ligands within the Ah receptor ligand binding domain (2019) · cites this paper as [48]
The Structural templates and homology models and Dimerization interfaces sections (pages unavailable) describe an AhR:ARNT model based on the HIF-2α:ARNT template and identify a PAS-B dimerization interface involving the F helix. Our copy does not identify an Fα/Gβ site or establish that this particular site is part of the predicted interface. (LLM, conf=0.78)
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- Authors
- Corrada, D., Denison, M. S., & Bonati, L.
- Affiliations
- University of Milano-Bicocca (IT)
- University of California System (US)
- Corresponding author
- Bonati, Laura
- Venue
- Molecular BioSystems
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-03-30
- Volume
- 13
- Issue
- 5
- Pages
- 981-990
- ISSN
- 1742-2051 (ISSN-L)
- 1742-206X
- PMC
- PMC5576476
- OpenAlex
- W2599603428
- Cited by
- 24
- References
- 69
- Citations by year
- 2025: 2 · 2024: 2 · 2023: 4 · 2022: 2 · 2021: 4 · 2020: 4 · 2019: 3 · 2018: 2 · 2017: 1
- FWCI
- 1.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Molecular BioSystems (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of Environmental Health Sciences (R01ES07685)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Toxic Organic Pollutants Impact
- Keywords
- aryl hydrocarbon receptor, ARNT, protein dimerization, protein-protein interfaces, binding free energy, MM-GBSA, energy decomposition analysis, solvent accessible surface area, domain-domain interactions, Clock/BMAL1
- MeSH terms
- Protein Domains, Animals, Binding Sites, Models, Molecular, Protein Binding, Mutagenesis, Protein Structure, Tertiary, Receptors, Aryl Hydrocarbon, Crystallography, X-Ray, Structural Homology, Protein, Mice, Aryl Hydrocarbon Receptor Nuclear Translocator, Basic Helix-Loop-Helix Proteins, Protein Multimerization
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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