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Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Networks

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 Networks

Protein Networks

Protein Complexes with Interchangeable Parts

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: Apr 29, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Evolution of protein interactions: from interactomes to interfaces.

Jessica Andreani¹, Raphael Guerois¹

¹CEA, iBiTecS, F-91191 Gif sur Yvette, France; Université Paris-Sud & CNRS, UMR 8221, F-91191 Gif sur Yvette, France.

Archives of Biochemistry and Biophysics

|May 24, 2014

Summary

This summary is machine-generated.

Understanding protein-protein interactions is key to cellular processes. Evolutionary analysis reveals conserved interaction patterns and pressures, aiding in predicting these vital biological connections.

Keywords:

Bioinformatics Co-evolution Computational methods Docking Interactome Interface Prediction Protein–protein interaction

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Published on: October 24, 2025

Area of Science:

Molecular Biology
Evolutionary Biology
Bioinformatics

Background:

Protein-protein interactions (PPIs) are fundamental to cellular functions.
Predicting PPIs is crucial for understanding biological processes.
Evolutionary perspectives offer unique insights into PPIs.

Purpose of the Study:

To review recent research on the evolution of PPIs.
To explore the use of evolutionary information for predicting PPIs.
To analyze conservation patterns and evolutionary pressures on protein interfaces.

Main Methods:

Literature review of recent studies on PPI evolution.
Analysis of conservation patterns in interactomes.
Investigation of evolutionary and co-evolutionary pressures on protein interfaces.
Description of computational methods for interface prediction using evolutionary data.

Main Results:

PPIs exhibit varying degrees of conservation across species.
Specific properties influence the conservation of PPIs.
Evolutionary and co-evolutionary pressures shape protein-protein interfaces.
Evolutionary information significantly enhances the prediction of PPIs and interfaces.

Conclusions:

Evolutionary analysis is a powerful tool for understanding PPIs.
Conservation patterns and pressures provide predictive signals for PPIs.
Integrating evolutionary insights improves computational prediction of protein interactions and interfaces.