Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution

Abstract

One contribution of 15 to a theme issue 'Multi-resolution simulations of intracellular processes'. ion channels ( pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.

Photopharmacology of Ion Channels through the Light of the Computational Microscope

“…MD models the physical movements of the system as a function of time by solving Newton’s equations of motion, whereas MC generates an ensemble of configurations according to the corresponding Boltzmann distribution. Such simulations allow one to further characterize the conformational rearrangements occurring upon ligand binding and their connection with ion conduction [ 38 , 39 , 40 , 41 , 42 , 43 , 44 ]. In combination with enhanced sampling methods and/or free energy calculations, MD can also provide an estimate of the ligand affinity (e.g., binding energy differences between the two forms of the photoswitch or between two photoswitchable ligands), as well as molecular insights into the energetic determinants of binding (e.g., to identify the most suitable position for introducing a reactive Cys for PTL covalent attachment).…”

A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism

“…While the transmission of the mechanical signal triggered by agonist binding that culminates in channel opening is not yet fully understood, significant advances can be achieved by means of mutagenesis experiments to pinpoint key residues/mechanisms as well as molecular simulations (Crnjar et al, 2019b), especially because an increasing number of high-resolution structures are now available in a variety of states (Hilf and Dutzler, 2008;Bocquet et al, 2009;Althoff et al, 2014;Hassaine et al, 2014;Miller and Aricescu, 2014;Sauguet et al, 2014;Du et al, 2015;Huang et al, 2015;Kudryashev et al, 2016;Nys et al, 2016;Basak et al, 2018a,b;Polovinkin et al, 2018;Zhu et al, 2018).…”

Electrophysiological Studies of GABAA Receptors Using QPatch II, the Next Generation of Automated Patch‐Clamp Instruments

“…Upon ligand binding, the ion channel opens and current flows. The gating of the channels can play a critical role in fast synaptic, and sometimes extrasynaptic, communications (see Barbaris, 2019; Crnjar, Comitani, Melis, & Molteni, 2019; Solomon, Tallapragada, Chebib, Johnston, & Hanrahan, 2019). LGICs are widely expressed in the CNS and PNS, can be modulated positively or negatively by small molecules, and are well‐pursued drug targets in the pharmaceutical industry and academic research.…”