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Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

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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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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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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Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
08:14

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Published on: April 20, 2015

Rapid membrane protein topology prediction.

Aron Hennerdal1, Arne Elofsson

  • 1Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish e-science Research Center, Stockholm University, Stockholm, Sweden.

Bioinformatics (Oxford, England)
|April 16, 2011
PubMed
Summary

This study evaluates TOPCONS-single for predicting alpha-helical membrane protein topology. While effective, it shows slightly lower accuracy than methods using multiple sequence alignments.

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Area of Science:

  • * Bioinformatics
  • * Computational Biology
  • * Structural Biology

Background:

  • * Predicting the topology of alpha-helical membrane proteins is crucial for understanding their function.
  • * Current state-of-the-art methods rely on time-consuming multiple sequence alignments (MSAs).
  • * There is a need for faster topology prediction methods with comparable accuracy.

Purpose of the Study:

  • * To investigate the feasibility of using consensus topology prediction from single sequences.
  • * To assess if single-sequence-based methods can achieve accuracy similar to MSA-based methods.
  • * To evaluate the performance of TOPCONS-single against other topology prediction tools.

Main Methods:

  • * Development and evaluation of TOPCONS-single, a consensus-based topology prediction method utilizing single protein sequences.
  • * Comparison of TOPCONS-single's performance against other topology prediction methods.
  • * Benchmarking against established methods that employ multiple sequence alignments.

Main Results:

  • * TOPCONS-single demonstrates superior performance compared to other single-sequence-based topology prediction methods evaluated.
  • * The accuracy of TOPCONS-single is approximately 6% lower than the top-performing multiple sequence alignment-based methods.
  • * The study confirms that single-sequence approaches can yield high accuracy in topology prediction.

Conclusions:

  • * TOPCONS-single offers a viable and efficient alternative for predicting alpha-helical membrane protein topology.
  • * While slightly less accurate than MSA-based methods, its speed and accessibility make it a valuable tool.
  • * Further development may bridge the accuracy gap between single-sequence and MSA-based prediction methods.