Binding affinity between AhR and exogenous/endogenous ligands: molecular simulations and biological experiment

References

• SchmidtJV, BradfieldCA. Ah receptor signaling pathways. Annu Rev Cell Dev Biol. 1996;12:55–89.
   PubMed Web of Science ®Google Scholar
• FukunagaBN, ProbstMR, Reisz-PorszaszS, HankinsonO. Identification of functional domains of the aryl hydrocarbon receptor. J Biol Chem. 1995;49:29270–29278.
   Google Scholar
• MaQ. Induction of CYP1A1: the AhR/DRE paradigm transcription, receptor regulation, and expanding biological roles. Curr Drug Metab. 2001;21:149–164.
   Web of Science ®Google Scholar
• KewleyRJ, WhitelawML, Chapman-SmithA. The mammalian basic helix–loop–helix/PAS family of transcriptional regulators. Int J Biochem Cell Biol. 2004;36:189–204.
   PubMed Web of Science ®Google Scholar
• WilhelmssonA, CuthillS, DenisM, WikstomAC, GustafssonJA, PoellingerL. The specific DNA binding activity of the dioxin receptor is modulated by the 90 kd heat shock protein. EMBO J. 1990;1:69–76.
   Google Scholar
• PetrulisJR, PerdewGH. The role of chaperone proteins in the aryl hydrocarbon receptor core complex. Chem Biol Interact. 2002;141:25–40.
   PubMed Web of Science ®Google Scholar
• EmaM, SogawaK, WatanabeN, ChujohY, MatsushitaN, GotohO, FunaeY, Fujii-KuriyamaY. cDNA cloning and structure of mouse putative Ah receptor. Biochem Biophys Res Commun. 1992;184:246–253.
   PubMed Web of Science ®Google Scholar
• WhitlockJPJr. Introduction of cytochrome P4501A1. Annu Rev Pharmacol Toxicol. 1999;39:103–125.
   PubMed Web of Science ®Google Scholar
• SafeS. Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and related compounds: environmental and mechanistic considerations which support the development of toxic equivalency factors (TEFs). Crit Rev Toxicol. 1990;21:51–88.
   PubMed Web of Science ®Google Scholar
• BonnesenC, EgglestonIM, HayesJD. Dietary indoles and isothiocyanates that are generated from cruciferous vegetables can both stimulate apoptosis and confer protection against DNA damage in human colon cell lines. Cancer Res. 2001;61:6120–6130.
   PubMed Web of Science ®Google Scholar
• FletcherN, HanbergA, HakanssonH. Hepatic vitamin A depletion is a sensitive marker of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure in four rodent species. Toxicol Sci. 2001;62:166–175.
   PubMed Web of Science ®Google Scholar
• SafeS. Molecular biology of the Ah receptor and its role in carcinogenesis. Toxicol Lett. 2001;120:1–7.
   PubMed Web of Science ®Google Scholar
• VeldhoenM, HirotaK, WestendorfAM, BuerJ, DumoutierL, RenauldJC, StockingerB. The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins. Nature. 2008;453:106–109.
   PubMed Web of Science ®Google Scholar
• QuintanaFJ, BassoAS, IglesiasAH, KornT, FerezMF, BettelliE, CaccamoM, OukkaM, WeinerHL. Control of T(reg) and T(H)17 cell differentiation by the aryl hydrocarbon receptor. Nature. 2008;453:65–71.
   PubMed Web of Science ®Google Scholar
• NguyenLP, BradfieldCA. The search for endogenous activators of the aryl hydrocarbon receptor. Chem Res Toxicol. 2008;21:102–116.
   PubMed Web of Science ®Google Scholar
• YoshikawaE, MiyagiS, DedachiK, Ishihara-SuganoM, ItohS, KuritaN. Specific interactions between aryl hydrocarbon receptor and dioxin congeners: ab initio fragment molecular orbital calculations. J Mol Graph Model. 2010;29:197–205.
   PubMed Web of Science ®Google Scholar
• MiyagiS, SawamuraS, YoshikawaE, DedachiK, Ishihara-SuganoM, ItohS, KuritaN. Ab initio fragment molecular orbital calculations on Specific interactions between aryl hydrocarbon receptor and dioxin. Int J Quantaum Chem. 2012;112:289–299.
   Web of Science ®Google Scholar
• KitauraK, IkeoE, AsadaT, NakanoT, UebayasiM. Fragment molecular orbital method: an approximate computational method for large molecules. Chem Phys Lett. 1999;313:701–706.
   Web of Science ®Google Scholar
• NakanoT, KaminumaT, SatoT, AkiyamaY, UebayasiM, KitauraK. Fragment molecular orbital method: application to polypeptides. Chem Phys Lett. 2000;318:614–618.
   Web of Science ®Google Scholar
• AkahoshiE, YoshimuraS, UrunoS, ItohS, Ishihara-SuganoM. Tyrosine hydroxylase assay: a bioassay for aryl hydrocarbon receptor-active compounds based on tyrosine hydroxylase promoter activation. Toxicol Mech Methods. 2012;22:458–460.
   PubMed Web of Science ®Google Scholar
• PandiniA, SoshilovAA, SongY, ZhaoJ, BonatiL, DenisonMS. Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis. Biochemistry. 2009;48:5972–5983.
   PubMed Web of Science ®Google Scholar
• SaliA, BlundellTL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234:779–815.
   PubMed Web of Science ®Google Scholar
• MottoI, BordognaA, SoshilovAA, DenisonMS, BonatiL. New aryl hydrocarbon receptor homology model targeted to improve docking reliability. J Chem Inf Model. 2011;51:2868–2881.
   PubMed Web of Science ®Google Scholar
• KeyJ, ScheuermannTH, AndersonPC, DaggettV, GardnerKH. Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B. J Am Chem Soc. 2009;131:17647–17654.
   PubMed Web of Science ®Google Scholar
• MorrisGM, HueyR, LindstromW, SannerMF, BelewRK, GoodsellDS, OlsonAJ. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;16:2785–2791.
   Web of Science ®Google Scholar
• CaseDA, CheathamTE3rd, DardenT, GohlkeH, LuoR, MerzKMJr., OnufrievA, SimmerlingC, WangB, WoodsRJ. The Amber biomolecular simulation programs. J Comput Chem. 2005;26:1668–1688.
   PubMed Web of Science ®Google Scholar
• HornakV, AbelR, OkurA, StockbineB, RoitbergA, SimmerlingC. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006;65:712–725.
   PubMed Web of Science ®Google Scholar
• JorgensenWL, ChandrasekharJ, MaduraJ, ImpeyRW, KleinML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.
   Web of Science ®Google Scholar
• BeslerBH, MerzKMJr., KollmanPA. Atomic charges derived from semiempirical methods. J Comput Chem. 1990;11:431–439.
   Web of Science ®Google Scholar
• FrischMJ, TrucksGW, SchlegelHB, ScuseriaGE, RobbMA, CheesemanJR, MontgomeryJA, VrevenT, KudinKN, BurantJC, MillamJM, IyengarSS, TomasiJ, BaroneV, MennucciB, CossiM, ScalmaniG, RegaN, PeterssonGA, NakatsujiH, HadaM, EharaM, ToyotaK, FukudaR, HasegawaJ, IshidaM, NakajimaT, HondaY, KitaoO, NakaiH, KleneM, LiX, KnoxJE, HratchianHP, CrossJB, AdamoC, JaramilloJ, GompertsR, StratmannRE, YazyevO, AustinAJ, CammiR, PomelliC, OchterskiJW, AyalaPY, MorokumaK, VothGA, SalvadorP, DannenbergJJ, ZakrzewskiVG, DapprichS, DanielsAD, StrainMC, FarkasO, MalickDK, RabuckAD, RaghavachariK, ForesmanJB, OrtizJV, CuiQ, BaboulAG, CliffordS, CioslowskiJ, StefanovBB, LiuG, LiashenkoA, PiskorzP, KomaromiI, MartinRL, FoxDJ, KeithT, Al-LahamMA, PengCY, NanayakkaraA, ChallacombeM, GillPMW, JohnsonB, ChenW, WongMW, GonzalezC, and PopleJA. Gaussian 03, revision D.01. Pittsburgh (PA): Gaussian; 2003.
   Google Scholar
• NakanoT, KaminumaT, SatoT, FukuzawaK, AkiyamaY, UebayasiM, KitauraK. Fragment molecular orbital method: use of approximate electrostatic potential. Chem Phys Lett. 2002;351:475–480.
   Web of Science ®Google Scholar
• ItoM, FukuzawaK, IshikawaT, MochizukiY, NakanoT, TanakaS. Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: specification of residues associated with ligand inducible information transmission. J Phys Chem. 2008;B112:12081–12094.
   Web of Science ®Google Scholar
• KomejiY, IshidaT, FedorovDG, KitauraK. Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin. J Comput Chem. 2007;28:1750–1762.
   PubMed Web of Science ®Google Scholar
• LovellSC, DavisIW, Arendall IIIWB, de BakkerPIW, WordJM, PrisantJS, RichardsonJS, RichardsonDC. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins Struct Funct Genet. 2003;50:437–450.
   PubMed Web of Science ®Google Scholar
• WiedersteinM, SipplMJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007;35:407–410.
   PubMed Web of Science ®Google Scholar
• HuiL, RobertsonAD, JensenJH. Very fast empirical prediction and interpretation of protein pKa values. Proteins. 2005;61:704–721.
   PubMed Web of Science ®Google Scholar
• WatanabeC, WatanabeH, TanakaS. An interpretation of positional displacement of the helix12 in nuclear receptors: preexistent swing-up motion triggered by ligand binding. Biochim Biophys Acta. 2010;1804:1832–1840.
   PubMed Web of Science ®Google Scholar
• AmariS, AizawaM, ZhangJ, FukuzawaK, MochizukiY, IwasawaY, NakataK, ChumanH, NakanoT. VISCANA: visualized cluster analysis of protein–ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening. J Chem Inf Model. 2006;46:221–230.
   PubMed Web of Science ®Google Scholar