The free energy landscape of GABA binding to a pentameric ligand-gated ion channel and its disruption by mutations

TL;DR

This study uses advanced simulations to elucidate the GABA binding process to a pLGIC receptor, revealing how mutations disrupt binding and receptor function, providing insights into ligand-receptor interactions at the atomic level.

Contribution

It introduces a novel simulation protocol to study ligand binding in pLGICs, capturing the binding sequence and effects of mutations on free energy landscapes.

Findings

GABA binds between Arg111 and Glu204 in the receptor.

Mutations to Ala reduce ligand affinity and disrupt binding.

Loop C dynamics regulate ligand access and locking.

Abstract

Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are important neuroreceptors that mediate fast synaptic transmission. They are activated by the binding of a neurotransmitter, but the details of this process are still not fully understood. As a prototypical pLGIC, here we choose the insect resistance to dieldrin (RDL) receptor, involved in the resistance to insecticides, and investigate the binding of the neurotransmitter GABA to its extracellular domain at the atomistic level. We achieve this by means of $\mu$-sec funnel-metadynamics simulations, which efficiently enhance the sampling of bound and unbound states by using a funnel-shaped restraining potential to limit the exploration in the solvent. We reveal the sequence of events in the binding process, from the capture of GABA from the solvent to its pinning between the charged residues Arg111 and Glu204 in the binding pocket. We characterize the associated free energy landscapes in the wild-type RDL receptor and in two mutant forms, where the key residues Arg111 and Glu204 are mutated to Ala. Experimentally these mutations produce non-functional channels, which is reflected in the reduced ligand binding affinities, due to the loss of essential interactions. We also analyze the dynamical behaviour of the crucial loop C, whose opening allows the access of GABA to the binding site, while its closure locks the ligand into the protein. The RDL receptor shares structural and functional features with other pLGICs, hence our work outlines a valuable protocol to study the binding of ligands to pLGICs beyond conventional docking and molecular dynamics techniques.