Dynamics and Interplay of the Binding Pockets in the Glycine Receptor

Abstract

The glycine receptor, a pentameric ligand-gated ion channel, plays a vital role in inhibitory neurotransmission, reflexes, and neuronal excitability. It is crucial to maintaining the balance and responsiveness of the nervous system to sensory input. The binding of ligands, in this case, glycines, in the extracellular domain (ECD) of the receptor initiates a series of conformational rearrangements that culminate in the opening of the ion channel in the transmembrane domain. There are five binding sites for orthosteric ligands at the interface among the five subunits of the receptor. Experiments suggest that two or three bound glycines are sufficient to activate the receptor and that the occupancy of binding sites affects (un)binding rates. Here, we evaluated the dynamics and interplay of empty and occupied binding pockets and their potential cooperativity. We investigated ECD models for the glycine receptor, built from cryo-EM data, by performing molecular dynamics simulations for different combinations of ligand occupancies. We highlighted the role of glycine in contracting the binding site, optimizing the water content to the amount necessary to mediate crucial interactions and dragging Loop C to cover the pocket. Each subunit participates in two adjacent binding pockets acting, in turn, as the principal and complementary subunit, with structures such as Loop B and Loop F being directly connected. This suggests a combination of push–pull mechanisms mediated by ligands in a potentially frustrated system, which may favor specific occupancy patterns or alternation of binding sites with different levels of contraction.