Anesthetic Binding Induced Motion of GABA_A Receptors Revealed by Coarse-Grained Molecular Dynamics Simulations

Abstract

General anesthetics are indispensable in modern medicine because they induce a reversible loss of consciousness and sensation in humans. On the other hand, their molecular mechanisms of action have not yet been elucidated. Several studies have identified the main targets of some general anesthetics. The structures of γ-aminobutyric acid A (GABA A ) receptors with the intravenous anesthetics such as propofol and etomidate have recently been determined. Although these anesthetic binding structures provide essential insights into the mechanism of action of anesthetics, the detailed molecular mechanism of how the anesthetic binding affects the Cl − permeability of GABA A receptors remains to be elucidated. In this study, we performed coarse-grained molecular dynamics simulations for GABA A receptors and analyzed the resulting simulation trajectories to investigate the effects of anesthetic binding on the motion of GABA A receptors. The results showed large structural fluctuations in GABA A receptors, correlations of motion between the amino acid residues, large amplitude motion, and autocorrelated slow motion, which were obtained by advanced statistical analyses. In addition, a comparison of the resulting trajectories in the presence or absence of the anesthetic molecules revealed a characteristic pore motion related to the gate-opening motion of GABA A receptors.

Substituted Cysteine Modification and Protection with n-Alkyl-MTS Reagents Quantifies Steric Changes Induced by a Mutation in Anesthetic Binding Sites on GABA Type A Receptors

“…These distances may represent extremes that occur with low probability. However, they are reasonably consistent with recent course-grained molecular dynamics simulations (Nakata et al, 2023) based on cryo-EM structures of α1β2γ2L GABA A receptors with anesthetics bound (Kim et al, 2020). Our present results also indicate that steric relationships between βM286 or αL232 and etomidate vs. propofol are similar at 1.3 Å resolution, yet different.…”