Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation

Emelie Flood, Céline Boiteux, Bogdan Lev, Igor Vorobyov, Toby W. Allen

Research output: Contribution to journalReview article

2 Citations (Scopus)

Abstract

Membrane ion channels are the fundamental electrical components in the nervous system. Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what these proteins look like in atomic detail but do not tell us how they function. Molecular dynamics simulations have progressed to the point that we can now simulate realistic molecular assemblies to produce quantitative calculations of the thermodynamic and kinetic quantities that control function. In this review, we summarize the state of atomistic simulation methods for ion channels to understand their conduction, activation, and drug modulation mechanisms. We are at a crossroads in atomistic simulation, where long time scale observation can provide unbiased exploration of mechanisms, supplemented by biased free energy methodologies. We illustrate the use of these approaches to describe ion conduction and selectivity in voltage-gated sodium and acid-sensing ion channels. Studies of channel gating present a significant challenge, as activation occurs on longer time scales. Enhanced sampling approaches can ensure convergence on minimum free energy pathways for activation, as illustrated here for pentameric ligand-gated ion channels that are principal to nervous system function and the actions of general anesthetics. We also examine recent studies of local anesthetic and antiepileptic drug binding to a sodium channel, revealing sites and pathways that may offer new targets for drug development. Modern simulations thus offer a range of molecular-level insights into ion channel function and modulation as a learning platform for mechanistic discovery and drug development.

Original languageEnglish (US)
JournalChemical Reviews
DOIs
StatePublished - Jan 1 2019

Fingerprint

Ion Channels
Chemical activation
Modulation
Neurology
Membranes
Free energy
Acid Sensing Ion Channels
Pharmaceutical Preparations
Ligand-Gated Ion Channels
General Anesthetics
Sodium Channels
X ray crystallography
Local Anesthetics
Anticonvulsants
Anesthetics
Molecular dynamics
Microscopic examination
Sodium
Thermodynamics
Ions

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. / Flood, Emelie; Boiteux, Céline; Lev, Bogdan; Vorobyov, Igor; Allen, Toby W.

In: Chemical Reviews, 01.01.2019.

Research output: Contribution to journalReview article

Flood, Emelie ; Boiteux, Céline ; Lev, Bogdan ; Vorobyov, Igor ; Allen, Toby W. / Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. In: Chemical Reviews. 2019.
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