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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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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Related Experiment Video

Updated: Jun 23, 2026

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

Finding common protein interaction patterns across organisms.

Mirco Gerke1, Erich Bornberg-Bauer, Xiaoyi Jiang

  • 1Division of Bioinformatics, Biology Department, Schlossplatz 4, D-48149 Münster, Germany.

Evolutionary Bioinformatics Online
|May 21, 2009
PubMed
Summary

This study introduces PINA, a fast method for comparing protein interaction networks by first finding interesting network structures and then identifying homologous proteins. This approach aids in understanding cell function and network evolution across organisms.

Keywords:
protein interactionmolecular evolutionnetwork analysisorthology

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Protein interactions are crucial for understanding cellular functions.
  • Comparing interaction networks helps elucidate evolutionary processes.
  • Existing methods often infer homologs before comparing network structures.

Purpose of the Study:

  • To present a novel computational method for analyzing and comparing protein interaction networks.
  • To develop a faster approach for identifying homologous subnetworks between organisms.

Main Methods:

  • The PINA (protein interaction network analysis) tool was developed.
  • It scans protein interaction networks of two organisms for interesting subnetworks (e.g., hubs, clusters).
  • Orthology investigations are then performed specifically on these identified subnetworks.

Main Results:

  • PINA prioritizes topology searching before orthology detection, improving efficiency.
  • The method restricts orthology investigations to specific subnetworks, significantly speeding up the analysis.
  • Identified homologous subnetworks can be visualized and analyzed using protein annotations.

Conclusions:

  • The PINA method offers a computationally efficient way to compare protein interaction networks.
  • This approach facilitates the study of network evolution and conserved functional modules.
  • It enables rapid identification and analysis of related subnetworks across different species.