Asymmetric opening of the homopentameric 5-HT3A serotonin receptor in lipid bilayers

Abstract

Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. We report three structures of the Cys-loop 5-HT3A serotonin receptor (5HT3R) reconstituted into saposin-based lipid bilayer discs: a symmetric and an asymmetric apo state, and an asymmetric agonist-bound state. In comparison to previously published 5HT3R conformations in detergent, the lipid bilayer stabilises the receptor in a more tightly packed, ‘coupled’ state, involving a cluster of highly conserved residues. In consequence, the agonist-bound receptor conformation adopts a wide-open pore capable of conducting sodium ions in unbiased molecular dynamics (MD) simulations. Taken together, we provide a structural basis for the modulation of 5HT3R by the membrane environment, and a model for asymmetric activation of the receptor.

Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel

“…Although most structures derived from X-ray crystallography and cryo-EM are symmetric, partly due to the use of symmetric restraints during model building, there are a few examples of pLGICs with asymmetric structures. Recent cryo-EM structures of the 5-HT 3A receptor in lipid nanodiscs revealed an asymmetric closed state, whereas a symmetrized open state was stabilized by serotonin molecules bound at all five ECD sites (Zhang et al, 2021). Additionally, a cryo-EM structure of the resting state Torpedo nAChR with toxins bound to two of the five subunits displayed asymmetries in both the ECD and TMD (Rahman et al, 2020), and cryo-EM structures of the GABA A receptor displayed ECD asymmetry in the resting state compared to the desensitized where ligands were bound (Masiulis et al, 2019).…”

Mg2+-dependent conformational equilibria in CorA: an integrated view on transport regulation

“…Intriguingly, the existence of asymmetric conformations has been observed in the absence of ligand for the serotonine receptor 5HT3R, revealing conformational plasticity also in the resting state. Such conformations are more energetically favorable when the agonist is bound, suggesting an asymmetric activation where resting asymmetric states are possible intermediates of the gating 45 . Asymmetric activation was proposed also for the nicotinic receptor nAChR, where the movement of pore lining helices was shown to induce the asymmetry in the ligand-bound form 46 .…”

Comprehensive strategies of machine-learning-based quantitative structure-activity relationship models

“…Yasushi Okuno's group at Kyoto University proposed an interdisciplinary framework called DEFMap, which combines experimental data, MD simulation, and DL to extract protein dynamic information from cryo-EM density maps ( Matsumoto et al., 2021 ). Shuguang Yuan's group used part of the framework to prove that the frozen structure analyzed in the traditional artificial cell membrane environment is very different from the real cell membrane environment ( Zhang et al, 2021 ), subverting the traditional understanding that the 3D structure of the membrane protein is the same as its physiological state in the artificial cell membrane or precipitant environment.…”