title: Structural dynamics of the glycine-binding domain of the N-methyl-D-aspartate receptor.
abstract: N-Methyl-D-aspartate receptors mediate the slow component of excitatory neurotransmission in the central nervous system. These receptors are obligate heteromers containing glycine- and glutamate-binding subunits. The ligands bind to a bilobed agonist-binding domain of the receptor. Previous x-ray structures of the glycine-binding domain of NMDA receptors showed no significant changes between the partial and full agonist-bound structures. Here we have used single molecule fluorescence resonance energy transfer (smFRET) to investigate the cleft closure conformational states that the glycine-binding domain of the receptor adopts in the presence of the antagonist 5,7-dichlorokynurenic acid (DCKA), the partial agonists 1-amino-1-cyclobutanecarboxylic acid (ACBC) and L-alanine, and full agonists glycine and D-serine. For these studies, we have incorporated the unnatural amino acid p-acetyl-L-phenylalanine for specific labeling of the protein with hydrazide derivatives of fluorophores. The single molecule fluorescence resonance energy transfer data show that the agonist-binding domain can adopt a wide range of cleft closure states with significant overlap in the states occupied by ligands of varying efficacy. The difference lies in the fraction of the protein in a more closed-cleft form, with full agonists having a larger fraction in the closed-cleft form, suggesting that the ability of ligands to select for these states could dictate the extent of activation.
authors.affiliation: From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030 and.
authors.forename: Drew M
authors.initials: DM
authors.lastname: Dolino
authors.affiliation: the Departments of Chemistry and.
authors.forename: David
authors.initials: D
authors.lastname: Cooper
authors.affiliation: From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030 and.
authors.forename: Swarna
authors.initials: S
authors.lastname: Ramaswamy
authors.affiliation: the Departments of Chemistry and.
authors.forename: Henriette
authors.initials: H
authors.lastname: Jaurich
authors.affiliation: the Departments of Chemistry and Electrical and Computer Engineering, Rice University, Houston, Texas 77251 cflandes@rice.edu.
authors.forename: Christy F
authors.initials: CF
authors.lastname: Landes
authors.affiliation: From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030 and vasanthi.jayaraman@uth.tmc.edu.
authors.forename: Vasanthi
authors.initials: V
authors.lastname: Jayaraman
mesh_terms: D000409:Alanine / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D031541:Fluorescence Resonance Energy Transfer; D005998:Glycine / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D051381:Rats; D016194:Receptors, N-Methyl-D-Aspartate / Q000819:agonists / Q000737:chemistry* / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D016194:Receptors, N-Methyl-D-Aspartate; D000409:Alanine; D005998:Glycine
keywords: Fluorescence Resonance Energy Transfer (FRET); Glutamate Receptor; Ion Channel; Ionotropic Glutamate Receptor; LRET; Ligand-binding Protein; NMDA Receptor; Protein Dynamics; Receptor Structure-Function