Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR.
  • Metaadatok
Tartalom: http://real.mtak.hu/34675/
Archívum: MTA Könyvtár
Gyűjtemény: Status = Published

Type = Article
Cím:
Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR.
Létrehozó:
Szöllősi, Dániel
Erdei, Áron
Gyimesi, Gergely
Magyar, Csaba
HegedĹąs, TamĂĄs
Kiadó:
Public Library of Science
Dátum:
2016
Téma:
QH3020 Biophysics / biofizika
Tartalmi leírás:
Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2alpha and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.
Nyelv:
angol
Típus:
Article
PeerReviewed
info:eu-repo/semantics/article
Formátum:
text
Azonosító:
Szöllősi, Dániel and Erdei, Áron and Gyimesi, Gergely and Magyar, Csaba and Hegedűs, Tamás (2016) Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR. PLoS ONE, 11 (1). pp. 1-22. ISSN 1932-6203
Kapcsolat:
https://dx.doi.org/10.1371/journal.pone.0146066
MTMT:2994492; doi:10.1371/journal.pone.0146066