Simulation data for “Dynamics and Interplay of the Binding Pockets in the Glycine Receptor”

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 re-arrangements that culminate in the opening of the ion channel in the transmembrane domain. There are five binding sites for orthosteric ligands at the interface between 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 evaluate the dynamics and interplay of empty and occupied binding pockets and their potential cooperativity. We investigate an ECD model for the glycine receptor, built from cryo-EM data, by performing molecular dynamics simulations for different combination of ligand occupancies. Molecular dynamics trajectories and data are provided.