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ATP Driven Pumps II: P-type Pumps01:34

ATP Driven Pumps II: P-type Pumps

The P-type pumps are a large family of integral membrane transporter ATPases. They are divided into five major types based on substrate specificity, from I to V.
A typical P-type pump has three cytosolic domains: nucleotide-binding (N), phosphorylation (P), and activator (A) domains. These domains are connected to the membrane-spanning helices by short amino acid segments. ATP hydrolysis and covalent phosphoenzyme intermediate formation are crucial parts of the catalytic cycle. At the highly...
ATP Driven Pumps III: V-type Pumps01:30

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V-type pumps are ATP-driven pumps found in the vacuolar membranes of plants, yeast, endosomal and lysosomal membranes of animal cells, plasma membranes of a few specialized eukaryotic cells, and some prokaryotes. They are also known as the V1Vo-ATPase, that couple ATP hydrolysis to transport protons against a concentration gradient.
The peripheral or cytosolic V1 domain with eight subunits is involved in ATP hydrolysis. The integral or transmembrane V0 domain containing at least five subunits...
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ATP-driven pumps, also known as transport ATPases, are integral membrane proteins. They have binding sites for ATP located on the membrane's cytosolic side and the ion-conducting domain in the transmembrane region. These pumps use the free energy released from ATP hydrolysis to move the solutes across cell membranes against an electrochemical gradient.
There are four main types of ATP-driven pumps - P-type, V-type, F-type, and ABC transporter. All these pumps are of varying complexities and are...

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Molecular dynamics simulations of the Ca2+-pump: a structural analysis.

Anders Lervik1, Fernando Bresme, Signe Kjelstrup

  • 1Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway. anders.lervik@chem.ntnu.no

Physical Chemistry Chemical Physics : PCCP
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PubMed
Summary

Molecular dynamics simulations reveal how the Ca(2+)-ATPase ion pump affects surrounding lipid bilayers. Protonation of residues enhances Ca(2+) binding, while membrane thinning near the protein may explain increased activity.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Membrane Protein Dynamics

Background:

  • The Ca(2+)-ATPase ion pump plays a crucial role in cellular calcium homeostasis.
  • Understanding its interaction with the lipid bilayer is key to elucidating its function.
  • Previous studies suggest Ca(2+) binding is sensitive to the protonation state of amino acid residues.

Purpose of the Study:

  • To investigate the effects of the Ca(2+)-ATPase in its E1 conformation on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer using large-scale molecular dynamics simulations.
  • To analyze the influence of protein structure on membrane properties like thickness and area per lipid.
  • To correlate observed membrane perturbations with experimental findings on protein activity.

Main Methods:

  • Large-scale molecular dynamics (MD) simulations (∼100 ns) of Ca(2+)-ATPase (E1 conformation) within a POPC bilayer.
  • Analysis of ion-residue interactions, focusing on the role of protonated residues.
  • Quantification of membrane structural changes, including bilayer thickness and projected area per lipid near the protein.
  • Application of an analytical model to interpret changes in lipid area and membrane curvature.

Main Results:

  • Simulations confirm that protonated residues strengthen Ca(2+)-residue interactions, consistent with experimental observations.
  • The POPC bilayer exhibits a local thinning of approximately 12% near the protein surface, with this effect decaying exponentially (0.8 nm decay length).
  • Projected area per lipid decreases near the protein, but an analytical model suggests this is an apparent effect due to local curvature, with the real area per lipid remaining largely unchanged.

Conclusions:

  • The protonation state of binding sites significantly influences Ca(2+) ion interactions within the Ca(2+)-ATPase.
  • Local membrane thinning and deformation around the Ca(2+)-ATPase are significant.
  • These membrane perturbations are potentially linked to the enhanced protein activity observed experimentally within specific membrane thickness ranges.