Configurational Preference of the Glutamate Receptor Ligand Binding Domain Dimers

Biophys J. 2017 Jun 6;112(11):2291-2300. doi: 10.1016/j.bpj.2017.04.042.


Ionotropic glutamate receptors are a family of tetrameric ion channels with functional states consisting of nonconducting, conducting, and desensitized states that are starting to become well characterized by electrophysiological and biophysical studies. However, the structure and relative energetics of these states beyond the general structure of the receptor are still not well understood. It is known that the interface between monomeric subunits of the tetramer plays a major role in distinguishing these functional states. We have used umbrella sampling and multimicrosecond molecular dynamics simulations of the GluA2 AMPA subtype glutamate receptor ligand-binding domain (LBD) dimers to characterize a natural propensity of the LBD dimers for various configurational states. Our results show a proposed desensitized conformation of the LBD dimer is a highly preferable conformation of the LBD dimer without the influence of other receptor domains or crystallographic conditions. This has been demonstrated by both free protein simulations of 5 μs duration, as well as by computed free energy difference between the active and desensitized states. At the same time, the simulations performed using the same protocols revealed that for the LBD mutant L483Y, known to lack desensitization, the postulated active state of the LBD dimer is indeed the preferred configurational state, which remained stable in the simulations. Our findings pave the path for developing more detailed hypotheses of the full receptor activation mechanism. Combined with the energetics of glutamate binding to the LBD and the energy required to open the transmembrane pore helices, our results strongly support a hypothesis that the low absolute free-energy state is the desensitized state of the intact AMPA receptor.

MeSH terms

  • Glutamic Acid / chemistry
  • Glutamic Acid / metabolism
  • Molecular Dynamics Simulation
  • Mutation
  • Protein Binding
  • Protein Domains
  • Protein Multimerization
  • Protein Stability
  • Receptors, AMPA / chemistry
  • Receptors, AMPA / genetics
  • Receptors, AMPA / metabolism*
  • Solutions
  • Water / chemistry


  • Receptors, AMPA
  • Solutions
  • Water
  • Glutamic Acid
  • glutamate receptor ionotropic, AMPA 2