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- W2913825247 abstract "Pentameric ligand gated ion channels (pLGICs) are important in neuronal communication between synapses. Endogenous ligands are known to mediate both the opening and closing of pLGICs and these proteins are also the target for a number of neurotoxins, animal venoms, as well as pharmacological agents. In the past decade a number of crystal structures have elucidated gating mechanisms as well as open, closed, and desensitized states, often in the presence of agonists or antagonists. More recently, cryo-electron microscopy (cryo-EM) has also produced high resolution structures of channels in the pLGIC family and has shed further light on ligand mediated activation. Given the importance of these proteins to pharmaceutical intervention, a method to understand how ligands bind to pLGICs could have important clinical impacts. We have recently implemented a tool that allows inclusion of cryo-EM densities as an input to the popular molecular dynamics package GROMACS. Using a fitting procedure that uses successively higher resolution density maps derived from experimental cryo-EM data, we demonstrate the ability to drive a simulation to a conformation corresponding to EM density. Here we use recently solved cryo-EM structures of members of the pLGIC family to demonstrate the use of this procedure to give insight into modes of ligand binding in this important class of molecules. The atomic structures derived from this method are then compared to the models built directly from the EM density as well as to available crystal structures. We believe this novel technique has much promise to help elucidate mechanisms of drug binding in the increasing number of systems that have been characterized in a ligand bound state via cryo-EM." @default.
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- W2913825247 date "2019-02-01" @default.
- W2913825247 modified "2023-09-30" @default.
- W2913825247 title "Combining Cryo-EM and Simulation to Understand Ligand Binding in Pentameric Ligand Gated Ion Channels" @default.
- W2913825247 doi "https://doi.org/10.1016/j.bpj.2018.11.3061" @default.
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