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

Nakata, S.; Mori, Y.; Tanaka, S.

doi:10.1101/2023.03.10.530555

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bioRxiv · 10.1101/2023.03.10.530555

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

Nakata, S.·Mori, Y.·Tanaka, S.

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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 {gamma}-aminobutyric acid A (GABAA) 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 GABAA receptors remains to be elucidated. In this study, we performed coarse-grained molecular dynamics simulations for GABAA receptors and analyzed the resulting simulation trajectories to investigate the effects of anesthetic binding on the motion of GABAA receptors. The results showed large structural fluctuations in GABAA 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, 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 GABAA receptors.

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Nakata, S., Mori, Y., Tanaka, S.. 2023-03-12. Anesthetic-Binding Induced Motion of GABA A Receptors Revealed by Coarse-Grained Molecular Dynamics Simulations. https://doi.org/10.1101/2023.03.10.530555

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