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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,...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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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Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Categorizing biases in high-confidence high-throughput protein-protein interaction data sets.

Xueping Yu1, Joseph Ivanic, Vesna Memisević

  • 1Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA.

Molecular & Cellular Proteomics : MCP
|August 31, 2011
PubMed
Summary

Different experimental methods yield distinct yeast protein-protein interaction data. Understanding these technology-driven biases is key to accurately interpreting biological insights and resolving conflicting findings.

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Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
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Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Area of Science:

  • Proteomics
  • Systems Biology
  • Yeast Genetics

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • High-confidence PPI datasets are crucial for understanding biological networks.
  • Diverse experimental techniques generate PPI data with varying characteristics.

Purpose of the Study:

  • To characterize and evaluate functional attributes of three yeast PPI datasets.
  • To compare PPI data derived from affinity purification/mass spectrometry (AP/MS), protein-fragment complementation assay (PCA), and yeast two-hybrid (Y2H) methods.
  • To understand how experimental technology biases influence biological interpretations.

Main Methods:

  • Analysis of three high-confidence yeast PPI datasets.
  • Comparison of protein interaction characteristics across datasets.
  • Evaluation of functional biases in recovered interactions.
  • Quantification of methodological differences in detecting interactions, protein abundance correlation, and essential protein connectivity.

Main Results:

  • Datasets showed distinct, partially overlapping protein sets with differing interaction characteristics.
  • Y2H data exhibited less functional bias compared to AP/MS and PCA.
  • AP/MS and PCA datasets showed over- and under-representation of specific functional categories.
  • Methodological biases influenced conclusions on protein complex organization, essentiality, and connectivity.

Conclusions:

  • Discrepancies in biological insights from different PPI datasets often reflect inherent methodological biases.
  • No single detection methodology is universally superior; context is critical.
  • Interpreting PPI data within its experimental or cellular context is essential for overcoming biases and inferring reliable biological knowledge.