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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 polypeptide...

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 polypeptide...

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 to...

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 to...

Protein and Protein Structures

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Related Experiment Video

Updated: May 27, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

InterEvol database: exploring the structure and evolution of protein complex interfaces.

Guilhem Faure¹, Jessica Andreani, Raphaël Guerois

¹CEA, iBiTecS, F-91191 Gif sur Yvette and CNRS, F-91191 Gif sur Yvette, France.

Nucleic Acids Research

|November 5, 2011

Summary

This summary is machine-generated.

The InterEvol database tracks protein complex evolution by analyzing homologous binding interfaces. It provides tools to visualize and download structural and sequence data for interactome evolution studies.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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Last Updated: May 27, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Structural biology
Bioinformatics
Evolutionary biology

Background:

Understanding the evolution of protein-protein interactions is crucial for deciphering interactome dynamics.
Analyzing changes in binding interfaces provides insights into evolutionary mechanisms.

Purpose of the Study:

To introduce the InterEvol database, a resource for exploring the evolution of protein complex structures.
To facilitate the study of homologous interfaces across diverse species.

Main Methods:

Identification of close and remote structural interologs from the Protein Data Bank (PDB).
Development of tools for retrieving, visualizing, and downloading structural and sequence data.
Implementation of online recomputation of multiple sequence alignments using InterEvolAlign.
Creation of an InterEvol PyMol plugin for integrated structure-sequence exploration.

Main Results:

The InterEvol database offers a comprehensive collection of homologous protein complex interfaces.
Pre-computed and downloadable multiple sequence alignments are available for evolutionary analysis.
The database supports querying by PDB code, keywords, or partner sequences.

Conclusions:

InterEvol provides a valuable resource for researchers studying the evolutionary history of protein interactions.
The integrated tools and data facilitate in-depth analysis of interface evolution.
Monthly updates ensure the database remains current with new structural and sequence information.