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

Abstract

Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.

Conformational decoupling in acid-sensing ion channels uncovers mechanism and stoichiometry of PcTx1-mediated inhibition

“…In addition, PcTx1 induces a long-lived conformational state in the ASIC1a ECD that is uncoupled from the pore but alters ASIC1a pharmacology. Lastly, the work presented here, to our knowledge, constitutes the first use of concatemeric multisubunit protein assemblies engineered for VCF recordings, thus offering the possibility to label a defined subset of subunits to unveil potential asymmetric gating and binding events, such as those proposed for a variety of ligand-gated ion channels ( Jasti et al, 2007 ; Baconguis and Gouaux, 2012 ; Mowrey et al, 2013 ; Zhu et al, 2018 ; Guros et al, 2020 ; Zhang et al, 2021 ; Bergh et al, 2021 ).…”

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

“…In our computational work, we used molecular simulations of GLIC conducted under either resting or activating conditions [24] to quantify occupancy and duration of lipid interactions. Simulation frames previously identified as either closed or open (Fig.…”

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

“…In particular, it has been shown that receptor activation or gating is mediated by two major quaternary transitions involving a radial contraction or (un)-blooming of the extracellular domain to increase the affinity for the neurotransmitter and a global (un)-twisting to initiate pore opening [42] , [114] . These molecular motions provide meaningful reaction coordinates to monitor receptor activation [115] .…”