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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,...
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...
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

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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

Interface-resolved network of protein-protein interactions.

Margaret E Johnson1, Gerhard Hummer

  • 1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA. JohnsonME@niddk.nih.gov

Plos Computational Biology
|May 23, 2013
PubMed
Summary

We introduce interface-interaction networks (IINs) to detail protein-protein interactions (PPIs), revealing network modules and predicting mutation effects. This approach enhances understanding of binding specificity and competition in biological systems.

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Last Updated: May 11, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Identifying Protein-protein Interaction Sites Using Peptide Arrays
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Area of Science:

  • Systems biology
  • Structural biology
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Existing PPI networks lack detail on interaction specificity and competition.
  • Understanding these finer details is key to deciphering complex biological processes.

Purpose of the Study:

  • To develop a novel network framework, the interface-interaction network (IIN), to capture PPI specificity and competition.
  • To establish a general method for constructing IINs by integrating computational and literature-based data.
  • To analyze the topological properties and biological implications of IINs, using clathrin-mediated endocytosis (CME) proteins as a case study.

Main Methods:

  • Developed a framework merging computational structure-based interface assignment with literature curation.
  • Integrated biochemical data to enhance accuracy and completeness of interaction data.
  • Constructed an IIN for proteins involved in clathrin-mediated endocytosis (CME).
  • Analyzed the topological features and modularity of the CME IIN.

Main Results:

  • The IIN framework successfully captures specificity and competition between protein interactions.
  • The CME IIN exhibits distinctive modularity, contrasting with dense PPI networks.
  • Large modules in the IIN are characterized by interfaces with shared domain specificities (e.g., SH3 domains).
  • The network format allows prediction of mutation effects and inhibitor impacts on binding pathways.

Conclusions:

  • IINs provide a detailed view of protein association, revealing complexities masked in PPI networks.
  • The modular organization of IINs suggests distinct evolutionary pressures on interaction topology.
  • IINs offer a powerful tool for understanding binding specificity, competition, and designing targeted interventions.