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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...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 9, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Evolutionary analysis reveals low coverage as the major challenge for protein interaction network alignment.

Waqar Ali1, Charlotte M Deane

  • 1Department of Statistics, 1 South Parks Road, Oxford, UKOX1 3TG. ali@stats.ox.ac.uk

Molecular Biosystems
|August 27, 2010
PubMed
Summary

Network evolution alone does not explain the lack of conservation in protein interaction networks. Incompleteness in data, not errors, is the main challenge for comparing interactomes.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Protein interaction networks show limited conservation across species, possibly due to data incompleteness or evolutionary processes.
  • The hypothesis that network evolution erases conservation evidence needs rigorous testing.

Purpose of the Study:

  • To test if network evolution alone can explain the poor conservation observed in protein interaction network alignments.
  • To investigate the impact of data errors, specifically false negatives and false positives, on network alignment quality.

Main Methods:

  • Developed a distance metric using summary statistics to compare experimental and simulated network alignments.
  • Utilized computational models of network evolution.
  • Assessed various error models, including false negatives and false positives, and incomplete proteome sampling.

Main Results:

  • Network evolution alone is insufficient to account for the low quality of real network alignments; simulated alignments were 4-5 times larger.
  • False negative rates were estimated between 20% and 60%, depending on proteome sampling.
  • False positives had a minimal impact compared to false negatives in network alignments.

Conclusions:

  • Network evolution is unlikely to be the sole reason for the lack of conserved protein interactions.
  • Data incompleteness, characterized by high false negative rates, is the primary obstacle in comparative interactome analysis.
  • Reducing false negatives is crucial for improving the accuracy of cross-species network comparisons.