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Title: Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor.

Authors: Fraccalvieri, Domenico; Soshilov, Anatoly A; Karchner, Sibel I; Franks, Diana G; Pandini, Alessandro; Bonati, Laura; Hahn, Mark E; Denison, Michael S

Published In Biochemistry, (2013 Jan 29)

Abstract: The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness.

PubMed ID: 23286227 Exiting the NIEHS site

MeSH Terms: Amino Acid Motifs; Amino Acid Sequence; Amino Acid Substitution*; Animals; Avian Proteins/chemistry*; Avian Proteins/genetics; Avian Proteins/physiology; Binding Sites; COS Cells; Cercopithecus aethiops; Environmental Pollutants/chemistry; Humans; Ligands; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed; Polychlorinated Dibenzodioxins/chemistry; Protein Binding; Protein Structure, Tertiary; Receptors, Aryl Hydrocarbon/chemistry*; Receptors, Aryl Hydrocarbon/genetics; Receptors, Aryl Hydrocarbon/physiology; Structural Homology, Protein; Transcriptional Activation; Zebrafish Proteins/chemistry*; Zebrafish Proteins/genetics; Zebrafish Proteins/physiology

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