Abstract
N-methyl-d-aspartate receptors (NMDARs) are members of the ionotropic glutamate receptor family that mediate excitatory synaptic transmission in the central nervous system. The channels of NMDARs are permeable to Ca2+ but blocked by Mg2+, distinctive properties that underlie essential brain processes such as induction of synaptic plasticity. However, due to limited structural information about the NMDAR transmembrane ion channel forming domain, the mechanism of divalent cation permeation and block is understood poorly. In this paper we developed an atomistic model of the transmembrane domain (TMD) of NMDARs composed of GluN1 and GluN2A subunits (GluN1/2A receptors). The model was generated using (a) a homology model based on the structure of the NaK channel and a partially resolved structure of an AMPA receptor (AMPAR), and (b) a partially resolved X-ray structure of GluN1/2B NMDARs. Refinement and extensive Molecular Dynamics (MD) simulations of the NMDAR TMD model were performed in explicit lipid bilayer membrane and water. Targeted MD with simulated annealing was introduced to promote structure refinement. Putative positions of the Mg2+ and Ca2+ ions in the ion channel divalent cation binding site are proposed. Differences in the structural and dynamic behavior of the channel protein in the presence of Mg2+ or Ca2+ are analyzed. NMDAR protein conformational flexibility was similar with no ion bound to the divalent cation binding site and with Ca2+ bound, whereas Mg2+ binding reduced protein fluctuations. While bound at the binding site both ions retained their preferred ligand coordination numbers: 6 for Mg2+, and 7–8 for Ca2+. Four asparagine side chain oxygens, a back-bone oxygen, and a water molecule participated in binding a Mg2+ ion. The Ca2+ ion first coordination shell ligands typically included four to five side-chain oxygen atoms of the binding site asparagine residues, two water molecules and zero to two backbone oxygens of the GluN2B subunits. These results demonstrate the importance of high-resolution channel structures for elucidation of mechanisms of NMDAR permeation and block.
Highlights
N-methyl-D-aspartate receptors (NMDARs) are glutamate- and glycine-gated ionotropic glutamate receptors found mainly in postsynaptic membranes in the central nervous system [1, 2]
NMDAR transmembrane domain (TMD) homology model refinement using molecular dynamics (MD) simulations in membrane and water we present results of MD simulations used to develop, refine and simulate the MD-optimized NMDAR TMD model in membrane and water
Using NMDAR TMD homology model slightly refined in MD simulations we performed two independent MD simulations with either Mg2+ or Ca2+ bound in the divalent cation binding site
Summary
N-methyl-D-aspartate receptors (NMDARs) are glutamate- and glycine-gated ionotropic glutamate receptors (iGluRs) found mainly in postsynaptic membranes in the central nervous system [1, 2]. Dysfunction of NMDARs has been associated with multiple nervous system disorders such as schizophrenia, Alzheimer’s disease, bipolar disorder, post-traumatic stress disorder, cerebral ischemia-induced neuronal injury, and epilepsy [3,4,5,6,7,8]. Because of their broad involvement in brain function and disorders, NMDARs are targets of therapeutic interest [5, 9].
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