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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,...
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 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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Related Experiment Video

Updated: Jun 25, 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

Reverse engineering the evolution of protein interaction networks.

Todd A Gibson1, Debra S Goldberg

  • 1Computational Bioscience Program, University of Colorado Denver, CO, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|February 13, 2009
PubMed
Summary
This summary is machine-generated.

We developed a new method to reconstruct the evolution of protein interaction networks using gene trees and interaction data. This approach provides a biologically faithful evolutionary history for yeast protein networks.

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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

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Systems Biology

Background:

  • Protein interaction network analysis has advanced to functional and evolutionary inferences.
  • Current evolutionary studies often rely on limited network comparisons or theoretical models lacking organism-specific gene context.

Purpose of the Study:

  • To introduce a novel framework for reverse engineering the evolution of protein interaction networks.
  • To reconstruct biologically faithful evolutionary histories of protein networks tied to specific organismal genes.

Main Methods:

  • Utilized phylogenetic gene trees and protein interaction data.
  • Developed a novel framework for reverse engineering network evolution.
  • Applied the framework to Saccharomyces cerevisiae (yeast) data.

Main Results:

  • Successfully reconstructed the evolutionary history of protein interaction networks.
  • Identified topological trends in the evolutionary lineage of yeast.
  • Demonstrated a method to fill evolutionary gaps in gene network data.

Conclusions:

  • The novel framework enables biologically faithful reconstruction of protein network evolution.
  • The approach provides insights into the evolutionary trajectory of protein interaction networks.
  • This method enhances our understanding of gene network evolution across species.