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Related Concept Videos

Ion Channels01:19

Ion Channels

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The movement of ions like sodium, potassium, and calcium into and out of the cell is essential to maintain the electrochemical gradient in living cells. The ion channels—a class of membrane transport proteins—help maintain this ionic gradient for the smooth functioning of physiological activities such as maintaining cell size and volume, conducting nerve impulses, and gas and nutrient exchange.
Ion channels are specialized integral membrane proteins on the plasma membrane that allow...
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Ligand-gated Ion Channels01:19

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Ligand-gated ion channels are transmembrane proteins with a channel for ions to pass through and a binding site for a ligand. The channel opens only when a ligand attaches to the binding site.
Three Subfamilies of Ligand-gated Ion Channels
Ligand-gated ion channels fall into three subfamilies. The 'Cys-loop' includes the nicotinic acetylcholine receptors, γ-aminobutyric acid (GABA), glycine, and 5-hydroxytryptamine receptors. The second one is the 'Pore-loop' channels that...
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Mechanically-gated ion channels are proteins found in eukaryotic and prokaryotic cell membranes that open in response to mechanical stress. Tension, compression, swelling, and shear stress can alter the conformation of the protein, opening a transmembrane channel that allows the passage of ions for signal transmission. In eukaryotes, mechanically-gated channels are distributed in several regions like the neurons, lungs, skin, bladder, and heart, where they play critical roles in numerous...
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Ligand-Gated Ion Channel Receptor: Gating Mechanism01:30

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Ligand-gated ion channels are transmembrane proteins that play a vital role in intercellular communication and functions of the nervous system. They allow the influx of ions across the membrane once the neurotransmitter binds, allowing the subsequent transmission of electrical excitation across the neurons. Other ligand-gated ion channels, like the γ-aminobutyric acid (GABA) receptor, permit anions like chloride into the cells on the binding of the GABA molecule. Their entry into the cell...
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Mutagenesis and Functional Analysis of Ion Channels Heterologously Expressed in Mammalian Cells
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Functional Annotation of Ion Channel Structures by Molecular Simulation.

Jemma L Trick1, Sivapalan Chelvaniththilan2, Gianni Klesse2

  • 1Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Structure (London, England : 1993)
|November 22, 2016
PubMed
Summary

Molecular dynamics simulations help understand ion channel function. These methods predict if structures like the serotonin receptor (5-HT3R) are closed or open, aiding functional annotation.

Keywords:
annotationhydrophobic gatingion channelmembrane proteinmolecular dynamics

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Ion channels are crucial membrane proteins with many newly resolved structures.
  • Functional annotation of these channel structures remains challenging.
  • Hydrophobic gating can induce pore dewetting, leading to a non-conductive state in ion channels.

Purpose of the Study:

  • To demonstrate the utility of molecular dynamics (MD) simulations for functional annotation of ion channel structures.
  • To apply MD simulations to predict the conductive state of the serotonin receptor (5-HT3R) and glycine receptor.

Main Methods:

  • Utilized molecular dynamics simulations to analyze water behavior within ion channel pores.
  • Employed three simulation analyses: water equilibrium densities, single-ion free-energy profiles, and computational electrophysiology.
  • Applied water equilibrium density simulations to different conformational states of a glycine receptor.

Main Results:

  • All three MD simulation approaches accurately predicted the 5-HT3R crystal structure as a functionally closed state.
  • Demonstrated the successful application of water density simulations for annotating glycine receptor conformational states.
  • Hydrophobic gating's role in pore dewetting and channel closure was computationally supported.

Conclusions:

  • Molecular dynamics simulations provide valuable insights into ion channel function and gating mechanisms.
  • MD-based functional annotation tools can accurately predict channel states from structural data.
  • These computational approaches enhance the understanding of ion channel biology and drug discovery.