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Related Concept Videos

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 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 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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

IRView: a database and viewer for protein interacting regions.

Shigeo Fujimori1, Naoya Hirai, Kazuyo Masuoka

  • 1Division of Interactome Medical Sciences, Institute of Medical Science, The University of Tokyo, Tokyo 108-8039, Japan.

Bioinformatics (Oxford, England)
|May 18, 2012
PubMed
Summary

IRView is a database that maps protein interacting regions (IRs) in human and mouse proteins. It aids in understanding how these regions relate within protein-protein interaction networks.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Specific regions on proteins mediate these interactions.
  • Some proteins utilize multiple or competitively used interacting regions (IRs).

Purpose of the Study:

  • To present IRView, a comprehensive database of protein interacting regions.
  • To facilitate the analysis of positional relationships between IRs.
  • To support research into the underlying mechanisms of PPI networks.

Main Methods:

  • Compiled data for 3417 IRs in human and mouse proteins from diverse sources.
  • Integrated annotated region data from InterPro.
  • Included information on single nucleotide polymorphism sites and alternative mRNA splicing variants.

Main Results:

  • IRView provides a centralized repository for IR data.
  • The web interface visualizes IRs on reference sequences, enabling positional analysis.
  • Data includes information on genetic variations affecting IRs.

Conclusions:

  • IRView offers a valuable resource for studying protein-protein interactions.
  • The database aids in understanding the structural and functional context of IRs.
  • It supports the analysis of complex PPI networks and their associated variations.