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Related Concept Videos

Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
Overview of Protein Sorting and Transport01:45

Overview of Protein Sorting and Transport

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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Post-translational Translocation of Proteins to the RER01:27

Post-translational Translocation of Proteins to the RER

A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...

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Updated: Jun 6, 2026

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
04:25

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach

Published on: August 8, 2025

TESTLoc: protein subcellular localization prediction from EST data.

Yao-Qing Shen1, Gertraud Burger

  • 1Robert-Cedergren Center for Bioinformatics and Genomics; Biochemistry Department, Université de Montréal, 2900 Edouard-Montpetit, Montreal, QC, H3T 1J4, Canada. yaoqing.shen@umontreal.ca

BMC Bioinformatics
|November 17, 2010
PubMed
Summary
This summary is machine-generated.

We developed TESTLoc, a new computational tool for predicting protein subcellular localization using partial sequences from expressed sequence tags (ESTs). This method achieves high accuracy, especially for plant data, enabling better use of EST sequence information.

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Related Experiment Videos

Last Updated: Jun 6, 2026

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
04:25

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach

Published on: August 8, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Assessment of Submitochondrial Protein Localization in Budding Yeast Saccharomyces cerevisiae
08:55

Assessment of Submitochondrial Protein Localization in Budding Yeast Saccharomyces cerevisiae

Published on: July 19, 2021

Area of Science:

  • Cellular Biology
  • Bioinformatics
  • Proteomics

Background:

  • Eukaryotic cells feature complex organization with specialized compartments for biological processes.
  • Understanding protein subcellular localization is crucial for elucidating bio-process organization and protein function.
  • Existing computational prediction tools struggle with partial protein sequences from sources like Expressed Sequence Tags (ESTs).

Purpose of the Study:

  • To develop a novel computational tool for predicting protein subcellular localization from partial sequences derived from ESTs (EST-peptides).
  • To improve the utilization of extensive eukaryotic sequence data available from ESTs.

Main Methods:

  • Development of TESTLoc, a predictor utilizing Support Vector Machine (SVM) algorithms.
  • Representation of EST-peptides using features like amino acid composition and physicochemical properties.
  • Validation on challenging datasets, including plant data.

Main Results:

  • TESTLoc demonstrates high accuracy in predicting subcellular localization for EST-peptides, achieving approximately 85% accuracy on plant data.
  • The predictor is specifically designed to handle the limitations of partial protein sequences.

Conclusions:

  • TESTLoc is an effective localization prediction tool optimized for EST data.
  • The tool offers multiple models for user selection and is publicly available for download.
  • Facilitates deeper analysis of protein localization from ESTs, expanding genomic research capabilities.