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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 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...
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,...

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Related Experiment Video

Updated: May 19, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Alternative protein-protein interfaces are frequent exceptions.

Tobias Hamp1, Burkhard Rost

  • 1TUM, Bioinformatik - I12, Informatik, Garching, Germany.

Plos Computational Biology
|August 10, 2012
PubMed
Summary
This summary is machine-generated.

Protein-protein interactions (PPIs) show surprising variability. Even identical or homologous protein pairs can have different interaction interfaces across experiments, suggesting multiple solutions for essential biological functions.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • Understanding the precise molecular details of PPIs is crucial for deciphering biological functions.
  • Consistency in experimental measurements of PPIs is generally expected.

Purpose of the Study:

  • To quantify the similarity in molecular interaction details for identical and homologous protein pairs across different experimental observations.
  • To investigate the extent of variability in protein-protein interaction interfaces.
  • To identify potential reasons for observed differences in PPI interfaces.

Main Methods:

  • Comparative analysis of protein-protein interaction interfaces from multiple experiments.
  • Assessment of interface similarity for sequence-identical and homologous protein pairs.
  • Redundancy reduction of data prior to analysis.
  • Examination of factors influencing interface variability, such as copy number within complexes.

Main Results:

  • Significant variability was observed in PPI interfaces, even for identical protein pairs (up to 22% differences).
  • Homologous protein pairs exhibited even higher interface divergence (up to 68% differences).
  • Complete differences in interaction interfaces occurred in 12-29% of comparisons.
  • Variability was linked to factors like the number of interaction copies within a complex.

Conclusions:

  • The molecular details of protein-protein interactions are not fixed and can exhibit substantial variability.
  • Multiple alternative binding modes can achieve the same functional protein-protein interaction.
  • This plasticity suggests a greater flexibility in biological systems than previously assumed.