Functional Annotation of Ion Channel Structures by Molecular Simulation

Abstract

SummaryIon channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT3R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT3R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor.

The dual‐gate model for pentameric ligand‐gated ion channels activation and desensitization

“…Importantly, recent structural and modelling work suggests that the bona fide open structure of pLGICs most likely resembles the open structures of GLIC and GluCl, rather than the much larger pore conformation of the cryo-EM structure of the zebrafish α1 GlyR bound to glycine alone (Gonzalez-Gutierrez et al 2017). A contrario, recent MD simulations suggest that the wide open zebrafish α1 GlyR structure is conductive, while the ivermectin-and glycine-bound α1 GlyR structure should not conduct ions (Trick et al 2016). In these simulations, however, it is unclear whether the simulated conduction properties of the wide-open zebrafish α1 GlyR match the experimentally derived values, nor is it possible to infer how much structural change is required to convert the ivermectinand glycine-bound α1 GlyR structure into a conductive conformation.…”

“…A contrari o, recent MD simulations suggest that the wide open zebrafish α1 GlyR structure is conductive, while the ivermectin‐ and glycine‐bound α1 GlyR structure should not conduct ions (Trick et al . ). In these simulations, however, it is unclear whether the simulated conduction properties of the wide‐open zebrafish α1 GlyR match the experimentally derived values, nor is it possible to infer how much structural change is required to convert the ivermectin‐ and glycine‐bound α1 GlyR structure into a conductive conformation.…”

CHAP: A versatile tool for the structural and functional annotation of ion channel pores

“…However, if these profiles suggest the channel may contain a hydrophobic gate or any other interesting features then a more in-depth analysis based on equilibrium MD simulation of the structure can be performed. Figure 2 is a crystal structure of a mammalian 5-HT 3 receptor (PDB ID: 4PIR) in which the existence of a hydrophobic gate has been demonstrated by previous studies (Trick et al, 2016;Yuan et al, 2016) . Initial structural analysis with CHAP (i.e.…”

“…In a previous study we have shown how molecular dynamics (MD) simulations of water behaviour within these nanoscale structures can be used to aid this process (Trick et al, 2016) . Here we now present a new and highly versatile computational tool that implements this methodology to predict the conductive status of new ion channel structures.…”

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport

“…Toolkits such as IBiSA_tools [247] may provide more detailed, centralized analyses of ion conduction, though they rely on at least brief independently generated molecular dynamics simulations. Automated simulation methods based on water permeation (as recently proposed by Sansom and colleagues [248]) may provide more accessible analyses, though the appropriate constraints and range of simulation models remain to be validated. All-atom molecular dynamics simulations of full conformational transitions associated with activation, permeation, desensitization, etc.…”