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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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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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Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
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Correction: Cserző et al. The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method. <i>Int. J. Mol. Sci.</i> 2023, <i>24</i>, 14016.

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Determining Membrane Protein Topology Using Fluorescence Protease Protection FPP
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The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method.

Miklós Cserző1,2, Birgit Eisenhaber3,4,5, Frank Eisenhaber3,4,5,6

  • 1Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary.

International Journal of Molecular Sciences
|September 28, 2023
PubMed
Summary

The Dense Alignment Surface (DAS) transmembrane (TM) prediction method remains highly accurate for identifying TM helices in proteins. Despite advancements, its core algorithm effectively solves TM helix prediction using sequence data.

Keywords:
dot-plotsmultiple sequence alignmenttransmembrane predictiontransmembrane proteins

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • The Dense Alignment Surface (DAS) transmembrane (TM) prediction method, introduced over 25 years ago, was a pioneering tool for distinguishing TM proteins and predicting TM helix positions.
  • DAS-TMfilter (2002) represented an algorithmic improvement, establishing it as a top-performing method for TM prediction based on local sequence information.

Purpose of the Study:

  • To report a new implementation of the DAS-TMfilter prediction web server.
  • To reevaluate the performance of the DAS-TMfilter method with an updated and expanded dataset.

Main Methods:

  • Reimplementation of the DAS-TMfilter web server.
  • Performance evaluation using a significantly larger, updated test dataset (five times the original size).

Main Results:

  • The reevaluated DAS-TMfilter method demonstrated essentially the same high accuracy as the original implementation.
  • Performance remained consistent despite the substantially larger dataset and without changes to the program's parametrization.

Conclusions:

  • The DAS-TMfilter approach robustly captures the physico-chemical properties of TM helices.
  • The method is considered to have effectively solved the scientific problem of TM helix prediction from amino acid sequences.