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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

An algorithm for finding functional modules and protein complexes in protein-protein interaction networks.

Guangyu Cui1, Yu Chen, De-Shuang Huang

  • 1School of Computer Science and Engineering, Inha University, Incheon 402-751, South Korea.

Journal of Biomedicine & Biotechnology
|April 4, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces an efficient algorithm for identifying protein groups in protein-protein interaction networks. The findings help predict protein functions and complexes, improving biological understanding.

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Area of Science:

  • * Computational Biology
  • * Bioinformatics
  • * Systems Biology

Background:

  • * Biological functions are executed by protein groups, not isolated proteins.
  • * Proteins within a biological group form densely connected subgraphs in protein-protein interaction networks.
  • * Identifying these subgraphs aids in predicting functions of unknown proteins.

Purpose of the Study:

  • * To develop an efficient algorithm and program for detecting cliques and near-cliques in protein-protein interaction networks.
  • * To analyze yeast protein interaction networks using the developed algorithm.
  • * To assess the biological relevance of identified near-cliques in terms of shared function and agreement with known protein complexes.

Main Methods:

  • * Development of an efficient algorithm for clique and near-clique detection.
  • * Application of the algorithm to a protein-protein interaction network dataset (yeast proteins).
  • * Analysis of identified near-cliques for shared functions and comparison with curated protein complex databases (MIPS).

Main Results:

  • * The algorithm efficiently identifies cliques and near-cliques in protein-protein interaction networks.
  • * 59% of identified near-cliques exhibited at least one shared function among all constituent proteins.
  • * 56% of near-cliques showed strong agreement with experimentally determined protein complexes from MIPS.

Conclusions:

  • * The developed algorithm is effective for finding biologically relevant protein groups (near-cliques) in interaction networks.
  • * Near-cliques identified by the algorithm are enriched for shared functions and correspond well to known protein complexes.
  • * This approach offers a valuable tool for predicting protein function and identifying protein complexes in uncharacterized proteins.