Combining Computational and Experimental Approaches to Characterize Ion Channels and Transporters

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About this Research Topic

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Background

Electrical signals in living cells arise from ion channels, which cause rapid changes of the membrane potential by the selective passage of certain ions across the membrane, and transporters, which generate ion gradients on a slower time scale and thus provide the energetic basis for the passive ion flux through channels. Ion channels and transporters are expressed in almost every living cell and fulfil a plethora of distinct cellular functions. An increasing number of human diseases are caused by dysfunctional ion channels or transporters makes these proteins important targets for pharmaceutical interventions. Understanding the structural dynamics of ion channels and transporters at atomic resolution will provide new insight into their function and represents an important step towards designing blockers or activators to specifically modulate their function as therapeutic option in diseases.

Ion channels and transporters have been extensively studied using electrophysiological, biochemical and genetic experiments. X-ray crystallography and cryo-electron microscopy have provided high-resolution structures for most of the known ion channel and transporter families. Moreover, molecular dynamics (MD) simulations of the conformational fluctuations and changes of comprehensive molecular systems, encompassing whole channels or transporter proteins together with a lipid bilayer, aqueous salt solutions and ligands in the presence of realistic transmembrane potential gradients have become possible in recent years. Advances in both computer hardware and theoretical methods have made all-atom simulations accessible on the microsecond time scale. However, force fields and simulation parameters are still imperfect, and certain processes of high physiological importance such as protonation or Ca2+ permeation can be currently described in atomistic simulations only imperfectly.

Atomistic MD simulations are still challenging for slow conformational changes associated with the gating of ion channels and or translocation of transporters. Such processes can be often described with simple kinetic equations that describe transitions between different conformations. Kinetic modeling permits prediction of time courses or voltage and [substrate] concentrations that are immediately testable by experiments. It thus constitutes an extremely useful intermediate step between experiment and its comprehensive interpretation with an atomistic model.

The accuracy with which membrane transport processes can be experimentally quantified makes ion channels and transporters well suited for advancing and testing computational approaches. This Research Topic intends to bring experimental and computational analyses of ion channels and transporters together. It is not restricted to certain transport protein families or physiological processes. We invite contributions on (i) novel approaches to computationally describe membrane transport, (ii) the combination of experimental and computational approaches to study ion channels or transporters, or (iii) novel functional properties of selected ion channels or transporters with experiments, kinetic modelling, or molecular dynamics simulations.

Keywords: Physiology, Electrical signals, cells, ion channels, transporters

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