Effects of Isoflurane Binding in the Pore of a Ligand-Gated Ion Channel

Abstract

A high resolution homologue of the eukaryotic nicotinic acetylcholine receptor has been recently crystallized in an apparently open state from the bacteria Gloeobacter violaceus (Bocquet et al., Nature, 2008). Using the crystal structure of Gloeobacter violaceus' ligand-gated ion channel (GLIC) as a starting configuration, extensive molecular dynamics (MD) simulations were performed on the microsecond time scale for both a control and isoflurane-flooded system. This MD data reveal that isoflurane may diffuse from random positions within the water until it binds tightly in the pore to the M2 helices of GLIC. A similar result has also been observed in analogous simulations of the nicotinic receptor. The binding of isoflurane to the M2 helices in GLIC proceeds along a path into the channel via the large opening of the pore on the extracellular domain side. Analysis of the MD trajectory following isoflurane binding shows noticeable dehydration and decreased flexibility of the pore's solvent compared to the control system. Moreover, a close examination of the protein's backbone motions from both MD simulations suggests that presence of isoflurane dramatically increases the dynamics of the protein, in particular the dynamics of the individual residues in the M2-M3 loop. This combined data present a two-fold effect of isoflurane binding in the pore of GLIC: i) a statistically significant change in the dynamics occurs at nearby pore residues, and ii) ion conductance across the membrane decreases due to a change in the dynamical properties of the water in the pore.