Theoretical Investigation of Structure and Gating Mechanisms in Glutamate Receptor Ion Channels

Abstract

The ionotropic glutamate receptors (iGluRs) are excitatory synaptic transmitters found in the fore-brain. Together with potassium, sodium, and calcium channels they form a tetrameric ligand gated ion channel class of P-loop receptors. The structures of iGluRs are currently not resolved, while functional mechanisms are not well understood. To gain insight into the structure of the iGluR channel region, the KcsA potassium channel pore is used as a working model for its known structural homology with iGluR transmembrane regions. A conserved hydrophobic patch among all P-loop receptors is located along the pore lining M3 helix which spans the lipid-water interface. This patch creates a helical bundle crossing where single residue mutations produce constitutive open channels in mice, suggesting its role in the control of ion conduction. Molecular dynamics simulations and umbrella sampling methods were used to examine the opening of the KcsA M3 bundle crossing starting from the closed KcsA crystal structure (PDB ID: 1k4c). The potential of mean force defining the free energy landscape obtained from the structures of KcsA is then used to abstract the unknown closed and open forms of iGluR transmembrane regions. Assuming the P-loop region comprising the selectivity filter changes little between functional states, energetically defined conformations provide points of refinement for unknown structures of transmembrane regions for proteins such as iGluRs. In order to describe a mechanistic model of iGluR, Ca2+/Mg2+ selectivity is currently under investigation for an NMDA type iGluR. Homology modeling of the transmembrane region based on potassium channels is being used to infer structure; and Ca2+/Mg2+ interactions with organic caging agents are used to parameterize divalent ion selectivity. Understanding how iGluRs control ion conduction together with monovalent versus divalent ion selectivity will aid in describing ion channel structure-function relation.