Role of D-serine Binding to the NMDA Receptor Ligand-Binding Domain

Abstract

The N-methyl-D-aspartate receptor (NMDAR) is a ligand-gated ion channel that promotes synaptic plasticity critical for learning and memory. NMDAR activation is initiated by binding of two different neurotransmitter agonists to the ligand-binding domains (LBDs). Specifically, the GluN2 subunit binds glutamate, while the GluN1 subunit binds either glycine or D-serine. While the mechanisms of glycine and glutamate binding to NMDAR LBDs have already been determined, little is known about the mechanisms by which D-serine can bind to and activate the receptor. To probe binding mechanisms, we performed multi-microsecond molecular dynamics simulations of the GluN1/GluN2A LBD dimer in the presence of freely diffusing D-serine and glutamate and observed multiple binding and unbinding events. While D-serine is primarily a GluN1 agonist, we surprisingly observed that D-serine binds to both GluN1 and GluN2A NMDAR subunits. Computing interaction frequencies between LBD residues and D-serine revealed residues important for agonist binding. However, we observed that binding pathways are made up of sequences of interactions that guide D-serine into the binding site. To identify properties of these pathways, we developed a framework for analyzing binding pathways by geometric and spatial similarity, which allowed us to cluster them according to the region of the LBD with which D-serine interacts. This allowed us to identify groups of residues that work together to contribute to particular binding pathways. We determined that D-serine and glutamate bind by similar pathways and found that D-serine is able to stabilize the active LBD conformation. Lastly, we determined that N-linked glycans at physiologically relevant glycosylation sites generally do not interfere with agonist-binding pathways to modulate LBD activity. These insights highlight the versatility of D-serine as an NMDAR agonist and its unique role in receptor activation.