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Calmodulin-dependent Signaling01:16

Calmodulin-dependent Signaling

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Calmodulin (CaM) is a calcium-binding protein in eukaryotes that controls various calcium-regulated cellular processes. It has four calcium-binding sites that bind calcium to form the calcium-calmodulin ( Ca2+-CaM) complex. GPCR stimulation increases the calcium levels in the cells that bind to CaM and induces a conformational change.
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Calcium is an essential signaling molecule required for various cellular functions. Calcium pumps and ion channels on cell and organellar membranes, such as those on the endoplasmic reticulum (ER), regulate calcium concentrations inside the cell. They remain closed, keeping the cytosolic calcium levels low at a resting state.
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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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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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Pull-down of Calmodulin-binding Proteins
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Dynamics of AKAP/Calmodulin complex is largely driven by ionic occupancy state.

Gauri Thapa1, Akash Bhattacharya2, Swati Bhattacharya1

  • 1Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.

Journal of Molecular Graphics & Modelling
|November 15, 2024
PubMed
Summary
This summary is machine-generated.

The ionic state of Calmodulin (CaM) significantly impacts the dynamics of its complex with the AKAP79/150 peptide. Molecular dynamics simulations reveal Ca2+ stabilization via hydrogen bonds, suggesting further structural studies are warranted.

Keywords:
AKAPCalmodulinLigand bindingMolecular dynamics simulations

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Area of Science:

  • Neuroscience
  • Structural Biology
  • Biochemistry

Background:

  • AKAP79/150 is a neuronal scaffold protein regulating kinase activity.
  • Calmodulin (CaM) binding to AKAP79/150 is regulated by Ca2+.
  • Previous studies identified the CaM-AKAP79/150 binding site and solved an X-ray structure.

Purpose of the Study:

  • To explore the motional dynamics of the CaM-AKAP79/150 helix complex.
  • To investigate the influence of different ionic occupancy states (Ca2+, Mg2+, apo) on CaM dynamics.
  • To understand the energetic and structural basis of CaM-AKAP79/150 interaction.

Main Methods:

  • Molecular dynamics (MD) simulations.
  • Analysis of CaM backbone dynamics under varying ionic conditions.
  • Energetic analysis and hydrogen bond analysis.

Main Results:

  • CaM backbone dynamics are predominantly governed by the ionic occupancy state.
  • AKAP79/150 peptide binding is not energetically favored in the Ca2+ state over apo-CaM.
  • The Mg2+ state is energetically destabilized compared to the apo state.
  • The Ca2+ state shows preferential stabilization of the AKAP79/150 peptide via additional hydrogen bonds.

Conclusions:

  • Ionic occupancy state is a critical determinant of CaM-AKAP79/150 complex dynamics.
  • Further structural biology studies should aim to achieve full Ca2+ occupancy.
  • NMR studies may reveal conformational states not observed in crystal structures.