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Related Concept Videos

Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

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The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
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Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

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Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
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Translocation of Proteins into the Mitochondria01:19

Translocation of Proteins into the Mitochondria

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Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
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Overview of Protein Sorting and Transport01:45

Overview of Protein Sorting and Transport

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Eukaryotic cells have different membrane-bound organelles with distinct protein requirements. The process by which proteins are targeted to a specific organelle is called protein sorting.
Protein sorting can be of two types: signal-based sorting and vesicle-based trafficking. In signal-based sorting, specific amino acid sequences called sorting signals target proteins to the proper location inside the cell either via gated transport or by protein translocation.  In gated transport, folded...
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Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

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Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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Protein Transport to the Stroma01:24

Protein Transport to the Stroma

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Chloroplasts are triple membrane structures with an outer membrane, an inner membrane, and a thylakoid membrane, each containing distinct metabolite transporters, membrane translocons, and enzymes. Appropriate sorting and translocating these proteins to their correct membrane systems is essential for chloroplast function.
Protein complexes called the translocon of the outer chloroplast membrane or TOC complex, and the translocon of the inner chloroplast membrane or TIC complex mediate the...
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Related Experiment Video

Updated: Jul 1, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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TransGCN: a semi-supervised graph convolution network-based framework to infer protein translocations in

Bing Wang1,2, Xiangzheng Zhang1, Xudong Han1,2

  • 1Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China.

Briefings in Bioinformatics
|March 1, 2024
PubMed
Summary

TransGCN, a novel semi-supervised graph convolution network (GCN), accurately identifies protein translocation events from spatio-temporal proteomics data. This method improves upon existing techniques, especially in handling batch effects and predicting protein subcellular localization (PSL).

Keywords:
graph convolution networkmass spectrometryprotein subcellular localizationprotein translocationsemi-supervised learningspatio-temporal proteomics

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Area of Science:

  • Proteomics
  • Computational Biology
  • Cell Biology

Background:

  • Protein subcellular localization (PSL) is crucial for understanding protein function and biological regulation.
  • Spatio-temporal proteomics offers insights into protein movement but faces challenges with data noise and mining.
  • Accurate identification of protein translocation events is essential for biological process understanding.

Purpose of the Study:

  • To develop a computational framework for inferring protein translocation events from spatio-temporal proteomics data.
  • To improve the accuracy of protein subcellular localization (PSL) prediction.
  • To address challenges in identifying reliable protein translocation events, including noise interference and batch effects.

Main Methods:

  • Proposed TransGCN, a semi-supervised graph convolution network (GCN) framework.
  • Utilized expanded multiple distance features and joint graph representations of proteins.
  • Employed semi-supervised GCN for knowledge transfer from proteins with known PSLs.

Main Results:

  • TransGCN demonstrated superior performance in identifying protein translocations compared to state-of-the-art methods.
  • The framework effectively handled batch effects in spatio-temporal proteomics data.
  • TransGCN achieved excellent predictive accuracy in protein subcellular localization (PSL) prediction.

Conclusions:

  • TransGCN provides a robust and accurate method for inferring protein translocation events.
  • The framework enhances the reliability of spatio-temporal proteomics data analysis.
  • TransGCN offers a valuable tool for advancing research in protein function and biological regulation.