Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms

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 AhR functional activity, 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 HIF-2α: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 here presented 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.

show abstract

“…17 Therefore, the use of computational modeling is essential for the molecular understanding of the AhR structure and interactions. 18 …”

Section: Introductionmentioning

confidence: 99%

Structural modeling of the AhR:ARNT complex in the bHLH–PASA–PASB region elucidates the key determinants of dimerization

2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Similarly, we found no changes in transcription before or during the first three months of our experiment. However, once animals emerged from winter dormancy the following spring (222 days post experiment), we found that exposed and infected (diseased) tortoises had decreased transcription for four genes responding to defenses against microbial pathogens (Mx1, Kibenge et al, ; ATF; Zhou et al, ), cellular and oxidative stress (SOD; Walsh et al, ; Sarma & Sharma, ), and cell differentiation, growth, and renewal as well as ligand proliferation and activation of protein chaperones (AHR; Stanford et al, 2016; Bonati et al, ). General patterns of downregulated transcript profiles have been previously observed in adult tortoises characterized as diseased and ill (Drake et al, ) and juvenile tortoises malnourished from invasive plant diets (Drake et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…A domino effect of molecular signaling and pathway interruption may impede reactions from reaching their desired target. For example, AHR is well known to respond to a diversity of ligands with the induction of expression of many genes and production of different biological and toxic effects (Bonati, Corrada, Tagliabue, & Motta, 2017;Schmidt & Bradfield, 1996). AHR also plays key regulatory roles in a variety of endogenous developmental and immune response processes (Esser & Rannug, 2015) that can affect the binding and activation of targeted proteins such as heat shock proteins.…”

Section: Pathogen and Host Dynamics In Immunomodulationmentioning

confidence: 99%

Complex immune responses and molecular reactions to pathogens and disease in a desert reptile (Gopherus agassizii)

Drake

Aiello

Bowen

et al. 2019

Ecology and Evolution

View full text Add to dashboard Cite

Immune function plays an important role in an animal's defense against infectious disease. In reptiles, immune responses may be complex and counterintuitive, and diagnostic tools used to identify infection, such as induced antibody responses are limited. Recent studies using gene transcription profiling in tortoises have proven useful in identifying immune responses to various intrinsic and extrinsic stressors. As part of a larger experiment with Mojave desert tortoises ( Gopherus agassizii ), we facilitated the transmission of the pathogenic bacteria, Mycoplasma agassizii (Myag), to naïve adults and measured innate and induced immune reactions over time. Specifically, we evaluated clinical condition, presence of Myag in the nasal/oral cavity, induced antibody responses specific to Myag, and measured molecular reactions (gene transcript profiles) in 15 captive tortoises classified as naïve, exposed, or infected and 14 wild tortoises for comparison. Myag was confirmed inside the nasal/oral cavity in exposed tortoises within 30–60 days of introduction to infected animals, yet we did not detect Myag specific induced antibody responses in these individuals until 420–595 days post exposure. Surprisingly, we found no overall differences in the gene transcript profiles between our experimental treatment groups throughout this study. This work highlights the complexities in assessing immune function and diagnosing pathogen related infections in tortoises and other reptiles.

show abstract

“…While the exact mechanism(s) by which TCDD and IR bind to and activate the AhR remain to be elucidated, the results presented here demonstrate that the differential interactions of these ligands with residues within the LBD of the hAhR are responsible for the enhanced signaling potency of IR. One avenue in which to gain additional insights into similarities and differences in the interaction of TCDD and IR with residues inside the binding cavities of the hAhR and mAhR is by performing molecular docking of these ligands into the homology models of their LBDs [ 45 ]. Docking analysis of TCDD within both the AhR LBDs has been previously reported by our laboratory [ 35 ], and the docking simulations of IR binding presented here have allowed prediction of the binding geometries and direct comparison with those of TCDD.…”

Section: Discussionmentioning

confidence: 99%

Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist

Faber

Soshilov

Tagliabue

et al. 2018

IJMS

Self Cite

View full text Add to dashboard Cite

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that modulates gene expression following its binding and activation by structurally diverse chemicals. Species differences in AhR functionality have been observed, with the mouse AhR (mAhR) and human AhR (hAhR) exhibiting significant differences in ligand binding, coactivator recruitment, gene expression and response. While the AhR agonist indirubin (IR) is a more potent activator of hAhR-dependent gene expression than the prototypical ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), it is a significantly less potent activator of the mAhR. DNA binding analysis confirmed the greater potency/efficacy of IR in stimulating transformation/DNA binding of the hAhR in vitro and domain-swapping experiments demonstrated that the enhanced response to IR was primarily due to the hAhR ligand binding domain (LBD). Site-directed mutagenesis and functional analysis studies revealed that mutation of H326 and A349 in the mAhR LBD to the corresponding residues in the hAhR LBD significantly increased the potency of IR. Since these mutations had no significant effect on ligand binding, these residues likely contribute to an enhanced efficiency of transformation/DNA binding by IR-bound hAhR. Molecular docking to mAhR LBD homology models further elucidated the different roles of the A375V mutation in TCDD and IR binding, as revealed by [3H]TCDD competitive binding results. These results demonstrate the differential binding of structurally diverse ligands within the LBD of a given AhR and confirm that amino acid differences within the LBD of AhRs contribute to significant species differences in ligand response.

show abstract

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms

Cited by 26 publications

References 83 publications

Structural modeling of the AhR:ARNT complex in the bHLH–PASA–PASB region elucidates the key determinants of dimerization

Structural modeling of the AhR:ARNT complex in the bHLH–PASA–PASB region elucidates the key determinants of dimerization

Complex immune responses and molecular reactions to pathogens and disease in a desert reptile (Gopherus agassizii)

Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist

Contact Info

Product

Resources

About