TY - JOUR T1 - Structural Features of the Glutamate Binding Site in Recombinant NR1/NR2A <em>N</em>-Methyl-<span class="sc">d</span>-aspartate Receptors Determined by Site-Directed Mutagenesis and Molecular Modeling JF - Molecular Pharmacology JO - Mol Pharmacol SP - 1470 LP - 1484 DO - 10.1124/mol.104.008185 VL - 67 IS - 5 AU - Philip E. Chen AU - Matthew T. Geballe AU - Phillip J. Stansfeld AU - Alexander R. Johnston AU - Hongjie Yuan AU - Amanda L. Jacob AU - James P. Snyder AU - Stephen F. Traynelis AU - David J. A. Wyllie Y1 - 2005/05/01 UR - http://molpharm.aspetjournals.org/content/67/5/1470.abstract N2 - We have used site-directed mutagenesis of amino acids located within the S1 and S2 ligand binding domains of the NR2A N-methyl-d-aspartate (NMDA) receptor subunit to explore the nature of ligand binding. Wild-type or mutated NR1/NR2A NMDA receptors were expressed in Xenopus laevis oocytes and studied using two electrode voltage clamp. We investigated the effects of mutations in the S1 and S2 regions on the potencies of the agonists l-glutamate, l-aspartate, (R,S)-tetrazol-5yl-glycine, and NMDA. Mutation of each of the corresponding residues found in the NR2A receptor subunit, suggested to be contact residues in the GluR2 α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit, caused a rightward shift in the concentration-response curve for each agonist examined. None of the mutations examined altered the efficacy of glutamate as assessed by methanethiosulfonate ethylammonium potentiation of agonist-evoked currents. In addition, none of the mutations altered the potency of glycine. Homology modeling and molecular dynamics were used to evaluate molecular details of ligand binding of both wild-type and mutant receptors, as well as to explore potential explanations for agonist selectivity between glutamate receptor subtypes. The modeling studies support our interpretation of the mutagenesis data and indicate a similar binding strategy for l-glutamate and NMDA when they occupy the binding site in NMDA receptors, as has been proposed for glutamate binding to the GluR2 AMPA receptor subunit. Furthermore, we offer an explanation as to why “charge conserving” mutations of two residues in the binding pocket result in nonfunctional receptor channels and suggest a contributing molecular determinant for why NMDA is not an agonist at AMPA receptors. ER -