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Related Concept Videos

Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

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In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
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Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
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Mitochondria, chloroplasts, and gram-negative bacteria have transmembrane, beta-barrel proteins called porins to mediate the free diffusion of ions and metabolites across the membrane. Mitochondrial porin precursors contain conserved amino acid sequences called beta signals at their C-terminal. Beta signals have a  motif of PoXGXXHyXHy (Po-Polar, X-Any amino acid, G-Glycine, Hy-LargeHydrophobic), which are crucial for precursor recognition to initiate precursor assembly. Beta-barrel...
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The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
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ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
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Plasma membranes have integral transmembrane proteins involved in facilitated transport. These proteins are collectively referred to as transport proteins, and they function as either channels for the material or as carriers themselves. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids and a hydrophilic channel through their core that provides a hydrated opening for solutes to pass through the membrane layers. Passage through the channel allows...
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Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
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Comparing transmembrane protein structures with ATOLL.

Célien Jacquemard1, Guillaume Bret1, Thomas Grutter2

  • 1UMR7200 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, Faculté de Pharmacie, 67400 Illkirch-Graffenstaden, France.

Bioinformatics (Oxford, England)
|December 26, 2021
PubMed
Summary
This summary is machine-generated.

ATOLL simplifies visualizing complex transmembrane helix bundles by projecting them onto a 2D plane. This tool aids in comparing membrane protein structures for functional insights.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Transmembrane helices are crucial for membrane protein function.
  • Representing 3D helix bundle structures in 2D for comparison is challenging.

Purpose of the Study:

  • To develop a method for flattening helix bundles of membrane proteins.
  • To facilitate the comparison of membrane protein structures.

Main Methods:

  • ATOLL (Aligned Transmembrane dOmains Layout fLattening) projects helix bundles onto the lipid bilayer plane.
  • The program is implemented in Python3.

Main Results:

  • ATOLL provides a simplified 2D representation of 3D helix bundles.
  • Enables easier comparison of different structures of the same or different membrane proteins.

Conclusions:

  • ATOLL is a valuable tool for analyzing and comparing membrane protein structures.
  • The program is accessible via a web server and open-source code.