Conformational Selection and Submillisecond Dynamics of the Ligand-binding Domain of the N-Methyl-d-aspartate Receptor

J Biol Chem. 2016 Jul 29;291(31):16175-85. doi: 10.1074/jbc.M116.721274. Epub 2016 May 21.


The N-methyl-d-aspartate (NMDA) receptors are heteromeric non-selective cation channels that require the binding of glycine and glutamate for gating. Based on crystal structures, the mechanism of partial agonism at the glycine-binding site is thought to be mediated by a shift in the conformational equilibrium between an open clamshell and a closed clamshell-like structure of the bilobed ligand-binding domain (LBD). Using single-molecule Förster resonance energy transfer (smFRET) and multiparameter fluorescence detection, which allows us to study the conformational states and dynamics in the submillisecond time scale, we show that there are at least three conformational states explored by the LBD: the low FRET, medium FRET, and high FRET states. The distance of the medium and low FRET states corresponds to what has been observed in crystallography structures. We show that the high FRET state, which would represent a more closed clamshell conformation than that observed in the crystal structure, is most likely the state initiating activation, as evidenced by the fact that the fraction of the protein in this state correlates well with the extent of activation. Furthermore, full agonist bound LBDs show faster dynamic motions between the medium and high FRET states, whereas they show slower dynamics when bound to weaker agonists or to antagonists.

Keywords: N-methyl-d-aspartate receptor (NMDA receptor, NMDAR); biophysics; fluorescence resonance energy transfer (FRET); glutamate receptor; ion channel; ionotropic glutamate receptor; protein conformation; single-molecule biophysics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Fluorescence Resonance Energy Transfer*
  • Humans
  • Protein Domains
  • Rats
  • Receptors, N-Methyl-D-Aspartate / chemistry*


  • Receptors, N-Methyl-D-Aspartate

Associated data

  • PDB/1PB7
  • PDB/1PBQ