Molecular dynamics simulations of GABA binding to the GABAC receptor: The role of Arg104

Abstract

GABA is the major inhibitory neurotransmitter in the nervous system and acts at a variety of receptors including GABAC receptors, which are a subclass of GABAA receptors. Here we have used molecular dynamics simulations of GABA docked into the extracellular domain of the GABAC receptor to explain the molecular interactions of the neurotransmitter with the residues that contribute to the binding site; in particular, we have explored the interaction of GABA with Arg104. The simulations suggest that the amine group of GABA forms cation-π interactions with Tyr102 and Tyr198, and hydrogen-bonds with Gln83, Glu220, Ser243, and Ser168, and, most prominently, with Arg 104. Substituting Arg104 with Ala, Glu, or Lys, which experimentally disrupt GABAC receptor function, and repeating the simulation revealed fewer and different bonding patterns with GABA, or the rapid exit of GABA from the binding pocket. The simulations therefore unveil interactions of GABA within the binding pocket, and explain experimental data, which indicate that Arg104 is critical for the efficient functioning of the receptor. © 2008 by the Biophysical Society.