Recent Advancements in Modeling and Simulations of Ion Channels

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Background

Ion channels are specialized membrane proteins that provide energetically favorable pathways for ion flow in and out of the cells. By selectively controlling ion fluxes, they play a primary role in the generation of membrane potential, and they are involved in the regulation of a number of physiological processes that are of fundamental importance for both excitable and non-excitable cells. The activity of ion channels is in turn regulated by stimuli of various kinds, including changes in membrane potential (voltage-gated ion channels), ligand binding (ligand-gated ion channels), and structural deformations of the membrane (mechanosensitive channels). Ion channels are also an important class of drug targets, as their dysfunction is related to a wide spectrum of diseases. Deciphering the molecular mechanisms underlying conduction, selectivity, and gating of ion channels is therefore of pivotal importance for a deeper understanding of their functionality and pharmacological modulation. The complexity of these aspects calls for a multidisciplinary approach involving computational modeling and simulations at various scales of resolution.

Recent advances in experimental methods, including cryo-microscopy, NMR, and other spectroscopic techniques, are disclosing novel 3D structures of ion channels at an unprecedented pace. By complementing experiments, computational modeling and simulations have traditionally played a leading role in the field of ion channel research. For example, molecular dynamics simulations have been instrumental to elucidate the mechanistic features of ion conduction and selectivity in individual channels at an atomic level of detail, providing a direct link with experimentally resolved structures and single-channel electrophysiology measurements. On the other hand, reduced resolution models (ranging from Brownian dynamics to mean-field continuum models) provide a viable means for studying ion currents and their interplay at the relevant time- and length-scales scales of cells, tissues, and even organs.

The increasing availability of experimental structures, coupled with the constantly increasing performances of computational resources, poses novel challenges to the field of ion channel simulations, as it is now finally possible to investigate the mechanisms of conduction, selectivity, gating, and drug-modulation in quantitative terms, and to compare the finest functional details among different channel families. These quantitative analyses imply the adoption of computational setups closer to experimental conditions, which among others, will require larger simulated systems, improved force fields, and better representations of the protein-lipid interactions and of the surrounding environment. The aim of this Research Topic is to promote discussions about the recent advancements, current bottlenecks, and future directions in these themes in order to strengthen the consistency between simulation setups and results and the functioning of ion channels under physiological and pathophysiological conditions.

We encourage the submission of Original Research, Reviews, Mini Reviews, and Perspective articles that cover, but are not limited to, the following topics:

• Simulation of recently characterized ion channels
• Investigation of the mechanism of ion conduction through conventional or enhanced molecular dynamics simulations
• Investigation of the gating and polymodular regulation of ion channels through conventional or enhanced molecular dynamics simulations
• Simulation of drug-channels interactions
• Comparison of force fields for studying ion conduction or related properties
• Development of methods and algorithms for simulating events taking place at different time- and length-scales

Keywords: Molecular Dynamics, Brownian Dynamics, Multiscale Modeling, Enhanced Sampling, Markov-State Models, Ion conduction, Ion selectivity, Channel gating, Protein-lipid interactions

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