NMDAR
September 2024
The N-methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels that mediate most of the excitatory neurotransmission in the mammalian brains. They are essential for learning and memory, making them important therapeutic targets for treating neurological and psychiatric disorders.
Anti-NMDAR antibodies produced by the immune system are often found in people with autoimmune encephalitis (AE), an autoimmune disease that causes severe symptoms such as memory deficits and neurological issues. These anti-NMDAR autoantibodies disrupt the association between NMDARs and cell adhesion proteins, leading to the removal of NMDARs from the cell surface and reduced brain function.
Currently, clinical treatments for AE involve only non-specific immunotherapies. The lack of precise characterization of patient-derived anti-NMDAR monoclonal antibodies (mAbs) and their molecular action has prevented the development of NMDAR-targeted therapies for AE.
In a recent study, scientists isolated anti-NMDAR autoantibodies and elucidated the structural basis of mAb binding to NMDAR using cryo-EM analysis. They discovered two distinct auto-mAb-binding epitopes on NMDARs and elucidated the key molecular interactions for binding, opening new opportunities for AE treatment.
After identifying two anti-NMDARs autoantibodies from patients (5F6, 2G7), the scientists solved the 3D structure of the corresponding antibody fragments (Fab5F6 and Fab2G7) in complex with NMDAR. NMDARs are tetrameric protein assemblies composed of two obligate GluN1 subunits and two of either GluN2 or GluN3 subunits. The structural analysis revealed that both autoantibodies interacted with the surface exposed area (R1 lobe) of the extracellular N-terminal domain (NTD) of the GluN1 subunit of NMDAR (Image 1A-B), but bound distinct epitopes (Image 1C): Fab5F6 interacted with the side of the NTD, while Fab2G7 bound to the top of the NTD.
Image 1. 3D structures of NMDAR-Fab complexes with distinct epitope binding: Fab2G7 interacts with the top, while Fab5F6 with the side of NMDAR N-terminal domain. A) NMDAR-Fab2G7 complex (PDB: 8JJ2; Fab2GT in blue, NMDAR is colored by chain: GluN1 in green and purple, GluN2 in orange and red). The NTD domain and its R1 lobe are indicated by green labels, the binding region is highlighted in the blue circle. B) NMDAR-Fab5F6 complex (PDB: 8JJ0; Fab5F6 in white, NMDAR is colored by chain: GluN1 in green and purple, GluN2 in orange and red). The NTD domain and its R1 lobe are indicated by green labels, the binding region is highlighted in the white circle. C) Overlay of the NMDAR-Fab2G7 complex (PDB: 8JJ2, blue) and NMDAR-Fab5F6 complex (PDB: 8JJ0, white). The pictures are produced with the 3decision® software.
By analyzing the protein-protein interactions (PPIs) at the antibody-antigen interface, scientists identified key molecular interactions for both Fabs.
Fab5F6 forms polar interactions with Arg36 and Lys37 on GluN1 (Image 2A). Functional studies revealed that mutating these GluN1 residues completely suppressed Fab5F6 binding, highlighting their essential role.
Fab2G7 interacts with a different portion of GluN1, establishing hydrogen bonds with Lys51 and Gln48 on GluN1 (Image 2B). Mutation of these residues abolished Fab2G7 binding, functionally validating their importance.
Image 2. Analysis of the PPIs of NMDAR-Fab complexes and different interaction pattern. A) Interface between GluN1-NTD and Fab5F6 (PDB:8JIZ; Fab5F6 in white, GluN1 in green). The GluN1 residues Arg36 and Lys37 are labeled in green. B) Interface between GluN1-NTD and Fab2G7 (PDB:8JJ1; Fab2G7 in blue, GluN1 in green). Dashed lines represent the PPIs network: polar interactions are in yellow, hydrogen bonds in blue, cation-pi interactions in red. The GluN1 residues Gln48 and Lys51 are labeled green.). The pictures are produced with the 3decision® software.
This study offered new insights into the molecular mechanism by which anti-NMDAR autoantibodies contribute to AE. These findings provide a structural foundation for the development of targeted therapies for AE treatment.
Reference: Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S. Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Nat Struct Mol Biol. 2024 Sep 3. doi: 10.1038/s41594-024-01387-3. Epub ahead of print. PMID: 39227720.