Desensitization in pentameric ligand-gated ion channels plays an important role in regulating neuronal excitability. Here, we show that docosahexaenoic acid (DHA), a key ω−3 polyunsaturated fatty acid in synaptic membranes, enhances the agonist-induced transition to the desensitized state in the prokaryotic channel GLIC. We determined a 3.25 Å crystal structure of the GLIC-DHA complex in a potentially desensitized conformation. The DHA molecule is bound at the channel-periphery near the M4 helix and exerts a long-range allosteric effect on the pore across domain-interfaces. In this previously unobserved conformation, the extracellular-half of the pore-lining M2 is splayed open, reminiscent of the open conformation, while the intracellular-half is constricted, leading to a loss of both water and permeant ions. These findings, in combination with spin-labeling/EPR spectroscopic measurements in reconstituted-membranes, provide novel mechanistic details of desensitization in pentameric channels.DOI: http://dx.doi.org/10.7554/eLife.23886.001

Markov chains provide realistic models of numerous stochastic processes in nature. We demonstrate that in any Markov chain, the change in occupation number in state A is correlated to the change in occupation number in state B if and only if A and B are directly connected. This implies that if we are only interested in state A, fluctuations in B may be replaced with their mean if state B is not directly connected to A, which shortens computing time considerably. We show the accuracy and efficacy of our approximation theoretically and in simulations of stochastic ion-channel gating in neurons.

Thiol- and thiophene-functionalized SWNTs prepared via the reaction of a substituted amine with fluoronanotubes show similar levels of sidewall functionalization, however, the use of Au nanoparticles as chemical markers for AFM gives misleading results for substituent distribution since STM shows the thiol substituents grouped in bands while the thiophene substituents uniformly distributed along the SWNTs.

CorA, a divalent-selective channel in the metal ion transport superfamily, is the major Mg2+-influx pathway in prokaryotes. CorA structures in closed (Mg2+-bound), and open (Mg2+-free) states, together with functional data showed that Mg2+-influx inhibits further Mg2+-uptake completing a regulatory feedback loop. While the closed state structure is a symmetric pentamer, the open state displayed unexpected asymmetric architectures. Using high-speed atomic force microscopy (HS-AFM), we explored the Mg2+-dependent gating transition of single CorA channels: HS-AFM movies during Mg2+-depletion experiments revealed the channel’s transition from a stable Mg2+-bound state over a highly mobile and dynamic state with fluctuating subunits to asymmetric structures with varying degree of protrusion heights from the membrane. Our data shows that at Mg2+-concentration below Kd, CorA adopts a dynamic (putatively open) state of multiple conformations that imply structural rearrangements through hinge-bending in TM1. We discuss how these structural dynamics define the functional behavior of this ligand-dependent channel.

A chimeric ligand–gated channel is activated by the ligands that activate both parent channels, which gate it through two distinct mechanisms.

Pentameric ligand-gated ion channels (pLGICs) play essential roles in the transmission and interpretation of synaptic signals. The recent solution of multiple X-ray structures of pLGICs has allowed detailed examination of the molecular mechanisms of synaptic transduction at the atomic level. We have described the mechanism of activation for the proton-gated ion channel GLIC, shedding light on the allosteric mechanisms for the entire family of pLGICs. Using a large-scale string method to explore pathways connecting open and the closed state structures, we have described the conformational changes in the agonist-binding extracellular domain, the ion-conducting trans-membrane domain, and the gating interface that communicates the change. We have observed switching of key interactions, allowing for the sensing of agonist/proton binding, leading to a discrete change in the channel pore. These changes involve several residues conserved across the pLGIC family. We have employed transition analysis of data, collected during millions of short path sampling simulations, to compute free energy surfaces that suggest multiple possible pathways, quantitatively reproduce allosteric stabilization of the open state at low pH, and reveal intermediates that are promising as target states for new drugs and anesthetics.

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