Related Experiment Video
Updated: May 12, 2026
08:38
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
Published on: March 3, 2015
Bridging structural biology and genomics: assessing protein interaction data with known complexes.
Aled M Edwards1, Bart Kus, Ronald Jansen
1Banting and Best Dept of Medical Research, University of Toronto C.H. Best Institute, 112 College St, Toronto, Ontario M5G 1L6, Canada.
Drug Discovery Today
|April 12, 2013
Summary
Genome-wide protein-protein interaction datasets contain errors inconsistent with known 3D structures. Integrating multiple noisy datasets using Bayesian methods improves accuracy and reliability of protein interaction networks.
Area of Science:
- Molecular Biology
- Structural Biology
- Bioinformatics
Background:
- Genome-wide studies aim to map protein-protein interactions (PPIs).
- The reliability and coverage of experimental methods are crucial for the utility of PPI networks.
- Known macromolecular complexes offer a benchmark for validating PPI data.
Purpose of the Study:
- To assess the consistency of genome-wide PPI datasets with known 3D structures.
- To evaluate the reliability of individual and integrated PPI data.
- To develop methods for improving the accuracy of PPI network construction.
Main Methods:
- Comparison of PPIs from genome-wide datasets against 3D structures of RNA polymerase II, Arp2/3, and the proteasome.
- Analysis of inconsistencies among different genome-wide PPI datasets.
- Evaluation of 174 additional macromolecular complexes.
- Application of Bayesian approaches to integrate multiple PPI datasets.
Main Results:
- A significant fraction of PPIs in genome-wide datasets and literature are inconsistent with known 3D structures.
- Marked inconsistencies exist among various genome-wide PPI datasets and with a larger set of complexes.
- Integrating individual, noisy PPI datasets using Bayesian methods significantly reduces the error rate.
Conclusions:
- Current genome-wide PPI data and literature-reported interactions exhibit structural inconsistencies.
- Independent PPI datasets are noisy and require integration for improved reliability.
- Bayesian integration offers a robust strategy to enhance the accuracy of protein interaction networks.
Related Concept Videos
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
02:04Protein-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...
02:04Protein-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...
01:57Protein 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...
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...
01:57Protein 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...
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...