All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water

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.

A structurally derived model of subunit‐dependent NMDA receptor function

“…; Mesbahi‐Vasey et al . ; Zhou & Wollmuth, ) allowing conceptualization of models of receptor function that can be constrained to be consistent with both the physical structure of the receptor and with functional data from both single channel and macroscopic current recordings.…”

“…; Mesbahi‐Vasey et al . ) have yielded insight into the functional contributions of multiple domains within each subunit. The structural evidence emerging from these studies are complementary to many functional studies (Gielen et al., , ; Yuan et al .…”

Ethanol-induced conformational fluctuations of NMDA receptors

“…In agreement with experimental studies, the results suggest that single binding of glutamate or glycine induces an intermediate pore size enhancement within the TMDs. While a full transformation of the receptor into an open conformational state cannot be observed in the time-scales of our simulation (see also [25][26][27]), our simulations demonstrate the affinity of both co-agonists to their known binding sites as well as enhancements in pore volume that are significantly larger than the volume changes induced by a single agonist.…”

“…In the present in silico study, we utilise molecular dynamics (MD) simulations to analyse the global binding properties of alcohol and conformational dynamics of the NMDA receptor based on the recently identified crystal structure of the intact heterotetrameric GluN1-GluN2B ion channel of rat at 4 Å [21]. While a number of recent studies have investigated the general binding properties of mostly homological models of this receptor [25][26][27][28], to our knowledge, this is the first investigation of ethanol-induced effects on a native NMDA receptor; thereby overcoming the intrinsic bias of site directed hypothesis-driven approaches and homology modelling. In total, eight configurations were simulated (100 ns/configuration), which represent all combinatorial ensembles of physiological concentrations of ethanol, glycine and glutamate in a close extracellular environment of the receptor.…”

Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors

“…To the best of our knowledge, these are the first reported simulations of a full NMDAR under physiological conditions. Previously, only parts of NMDARs, [10][11][12][13][14][15][16] or an NMDAR without glycans and with a bound xenobiotic, 17 were simulated. On the other hand, computer simulations of biomolecules at atomic resolution have been successfully employed in the past to study much smaller proteins (with hundreds of amino acid residues, vs. ~3,000 residues in an NMDAR), resulting in detailed understanding of various metastable conformations and the dynamics of transitions between them.…”