Characterizing the Energetic States of a Glutamate Receptor using Umbrella Sampling and Microsecond Molecular Dynamics Simulations

Abstract

Ionotropic glutamate receptor functional states consist of: non-conducting, conducting, and desensitized states that are well characterized by electrophysiological studies. However, the energetics of these states is not well understood. It is known that the interface between monomeric subunits of the tetramer plays a major role in distinguishing these functional states. We have used umbrella sampling and microsecond molecular dynamics simulations of receptor dimers to calculate several free-energetic states of AMPA subtype glutamate receptor ligand-binding domains in the absence of its transmembrane region. Our results show the desensitized conformation as a highly probable conformation during simulations thus characterizing it as a low free-energetic state. We have also developed a model of a transmembrane region of AMPA based on what is known from crystallography of AMPA and potassium channels. Umbrella sampling of this model transmembrane region in the lipid bilayer is being conducted complementary to the ligand-binding domain. We hypothesize that in the full receptor the low absolute free-energetic state is the desensitized state.