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Related Concept Videos

Voltage-gated Ion Channels01:26

Voltage-gated Ion Channels

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Voltage-gated ion channels are transmembrane proteins that open and close in response to changes in the membrane potential. They are present on the membranes of all electrically excitable cells such as neurons, heart, and muscle cells.
Generally, all voltage-gated ion channels have a 'voltage-sensing domain' that spans the lipid bilayer. The charged residues in the sensor move in response to the membrane potential changes that open the channel allowing ions movement. There are several...
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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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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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Facilitated Transport01:19

Facilitated Transport

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The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a...
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Ligand-Gated Ion Channel Receptor: Gating Mechanism01:30

Ligand-Gated Ion Channel Receptor: Gating Mechanism

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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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Patch Clamp01:18

Patch Clamp

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Many fundamental cell functions such as muscle contraction and nerve transmission rely on the electrical signals produced by the movement of positively and negatively charged ions across the cell membrane. One competent method to record current flowing across the whole cell or single ion channel is the patch-clamp technique.
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Author Spotlight: Functional Site-Directed Fluorometry in Native Cells to Study Skeletal Muscle Excitability
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ChanFAD: A Functional Annotation Database for Ion Channels.

Elizabeth V Castro1,2, John W Shepherd1, Ryan S Guggenheim1,2

  • 1Department of Neuroscience, Baldwin Wallace University, Berea, OH, United States.

Frontiers in Bioinformatics
|October 28, 2022
PubMed
Summary
This summary is machine-generated.

ChanFAD is a new database that centralizes ion channel structure and functional data. It links primary sequence, 2D interactions, and 3D protein structures for researchers studying these critical membrane proteins.

Keywords:
databasefunctional annotationion channelsprotein structureproteomics

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Ion channels are vital membrane proteins regulating cellular functions.
  • Existing resources lack integrated data on ion channel sequence, interactions, and 3D structures.
  • A unified platform is needed to connect diverse ion channel information.

Purpose of the Study:

  • To introduce ChanFAD, a novel database for ion channel functional annotation.
  • To provide a centralized resource linking primary sequence, 2D interactions, and 3D protein structures.
  • To facilitate research on ion channel function, drug interactions, and mutation effects.

Main Methods:

  • Developed ChanFAD, a database integrating ion channel data.
  • Utilized the NCBI iCn3D structure viewing tool for PDB structure annotation.
  • Included primary sequence, organism, and external database links.

Main Results:

  • ChanFAD offers functional annotation of PDB structures for ion channels.
  • The database links structural data with primary sequence and interaction information.
  • Example use cases demonstrate applications in drug-channel interactions and mutation analysis.

Conclusions:

  • ChanFAD serves as a valuable, centralized resource for the ion channel research community.
  • The database enhances understanding of ion channel structure-function relationships.
  • ChanFAD is freely accessible at https://www.chanfad.org/.