Journal Title
Title of Journal: J Mol Model
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Abbravation: Journal of Molecular Modeling
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Publisher
Springer-Verlag
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Authors: Neil J Harrison Sarah CR Lummis
Publish Date: 2005/10/26
Volume: 12, Issue: 3, Pages: 317-324
Abstract
We have constructed a molecular model of the ligandbinding domain of the GABAC receptor which is a member of the Cysloop ligandgated ion channel family The extracellular domains of these receptors share similar sequence homology 20 with Limnaea acetylcholinebinding protein for which an Xray crystal structure is available We used this structure as a template for homology modeling of the GABAC receptor extracellular domain using FUGUE and MODELLER software FlexX was then used to dock GABA into the receptor ligandbinding site resulting in three alternative energetically favorable orientations Residues located no more than 5 Å from the docked GABA were identified for each model of these three were found to be common to all models with 14 others present only in certain models Using data from experimental studies we propose that the most likely orientation of GABA is with its amine close to Y198 and its carboxylate close to R104 These studies have therefore provided a model of the ligandbinding domain which will be useful for both GABAC and GABAA receptor studies and have also yielded an experimentally testable hypothesis of the location of GABA in the binding pocketWe thank the Wellcome Trust SCRL and the MRC NLH for funding SCRL is a Wellcome Trust Senior Research Fellow in Basic Biomedical Studies We also thank Dr David Burke for his contributions in running MODELLER and Dr Andy Thompson for his assistance in creation of the figures
Keywords:
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