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Related Concept Videos

Subcellular Fractionation01:32

Subcellular Fractionation

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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.
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Nuclear Protein Sorting01:34

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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.
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Nuclear Localization Signals and Import01:46

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Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
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Overview of Protein Sorting and Transport01:45

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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.
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Conserved Binding Sites01:49

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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.
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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...
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Updated: Jun 27, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
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Protein subcellular localization prediction tools.

Maryam Gillani1, Gianluca Pollastri1

  • 1School of Computer Science, University College Dublin (UCD), Dublin, D04 V1W8, Ireland.

Computational and Structural Biotechnology Journal
|May 6, 2024
PubMed
Summary
This summary is machine-generated.

This review surveys recent computational tools for predicting protein subcellular localization, crucial for understanding protein function. It categorizes and analyzes these predictors, aiding researchers in selecting appropriate methods for biological research.

Keywords:
BioinformaticsMachine learning/deep learningProtein predictionsSubcellular localization predictions

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Protein subcellular localization is vital for understanding protein function and cellular processes.
  • Experimental determination of protein localization is often unavailable, necessitating computational methods.
  • Computational prediction of protein localization has been an active research area for over two decades.

Purpose of the Study:

  • To review and analyze recent computational tools for protein subcellular localization prediction.
  • To categorize predictors for Eukaryotic, Prokaryotic, and Virus-based systems.
  • To provide a guide for researchers to identify and utilize relevant prediction tools.

Main Methods:

  • Literature review of recent subcellular localization prediction tools.
  • Detailed analysis of predictors based on features, strengths, weaknesses, algorithms, and techniques.
  • Development of taxonomies for tool categorization and understandability.

Main Results:

  • Identification and discussion of various recent prediction tools across different categories.
  • Analysis of the performance and characteristics of different prediction methods.
  • Highlighting research gaps and challenges in the field.

Conclusions:

  • Recent advancements have led to numerous protein subcellular localization prediction tools.
  • Taxonomies aid users in selecting appropriate tools for their specific research needs.
  • Further research is needed to address identified gaps and challenges in prediction accuracy and scope.