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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...
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...
Nuclear Protein Sorting01:34

Nuclear Protein Sorting

Nuclear protein sorting is the selective trafficking of histones, polymerases, gene regulatory proteins into the nucleus and exporting RNAs and ribosomes to the cytosol. It is a tightly controlled process that regulates gene expression within a cell.
Proteins targeted to the nucleus carry nuclear localization signals or NLS recognized by import receptors in the cytosol. Similarly, proteins with nuclear export signals are recognized by export receptors. Import and export receptors are...
Eukaryotic Compartmentalization01:37

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
For example, lysosomes in the animal cells...
Eukaryotic Compartmentalization01:46

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
For example, lysosomes in the animal cells...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: Jun 18, 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

Protein subcellular localization prediction of eukaryotes using a knowledge-based approach.

Hsin-Nan Lin1, Ching-Tai Chen, Ting-Yi Sung

  • 1Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, Republic of China. arith@iis.sinica.edu.tw

BMC Bioinformatics
|December 5, 2009
PubMed
Summary
This summary is machine-generated.

A new computational method, KnowPredsite, accurately predicts protein subcellular localization (PSL) for both single and multiple sites. This knowledge-based approach improves accuracy, especially for multi-localized proteins, overcoming limitations of traditional methods.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Proteomics

Background:

  • Protein subcellular localization (PSL) is crucial for understanding protein functions and cellular processes.
  • Experimental determination of PSL is laborious; computational methods are highly desirable.
  • Existing computational methods often focus on single-localized proteins, neglecting multi-localized proteins.

Purpose of the Study:

  • To develop a knowledge-based computational method, KnowPredsite, for predicting protein subcellular localization.
  • To accurately predict localization sites for both single- and multi-localized proteins.
  • To improve upon existing prediction methods like ngLOC and Blast-hit.

Main Methods:

  • KnowPredsite utilizes local sequence similarity to identify related sequences for prediction.
  • A knowledge base stores possible protein sequence variations.
  • A scoring mechanism predicts localization sites by searching the knowledge base.

Main Results:

  • KnowPredsite achieved 91.7% accuracy for single-localized proteins and 72.1% for multi-localized proteins.
  • Multi-localized protein prediction accuracy was 12.4% higher than ngLOC.
  • KnowPredsite successfully predicted proteins lacking significant BLAST hits.

Conclusions:

  • KnowPredsite effectively leverages local similarity from a knowledge base for accurate PSL prediction.
  • The method demonstrates high accuracy for both single- and multi-localized proteins.
  • KnowPredsite offers a transparent, biologically interpretable prediction process.