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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 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 Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jun 10, 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

A comparative analysis of protein interfaces.

Jing Hu1, Changhui Yan

  • 1Department of Mathematics and Computer Science, Franklin & Marshall College, Lancaster, PA 17604, USA.

Protein and Peptide Letters
|July 30, 2010
PubMed
Summary
This summary is machine-generated.

Analyzing protein interaction interfaces reveals distinct residue compositions across protein-protein, protein-DNA, protein-RNA, protein-carbohydrate, and protein-ligand interactions. These interfaces are more conserved than non-interface surfaces, highlighting the importance of solvent accessibility in protein interactions.

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Last Updated: Jun 10, 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

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
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Published on: July 18, 2013

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Proteins interact with diverse molecules to perform essential biological functions.
  • Understanding the molecular basis of these interactions is crucial for deciphering biological mechanisms.
  • Protein interaction interfaces are key sites that dictate binding specificity and affinity.

Purpose of the Study:

  • To characterize and compare the residue composition of five distinct types of protein interaction interfaces.
  • To investigate the evolutionary conservation patterns at these interfaces.
  • To assess the influence of solvent accessibility on residue properties within interaction interfaces.

Main Methods:

  • Comparative analysis of residue composition across five interface types: protein-protein, protein-DNA, protein-RNA, protein-carbohydrate, and protein-ligand.
  • Evaluation of evolutionary conservation by comparing interface residues with non-interface surface residues.
  • Inclusion of solvent accessibility as a factor in analyzing residue propensities.

Main Results:

  • Significant differences in residue composition were observed among the five interface types, reflecting distinct interaction mechanisms.
  • All analyzed interface types exhibited higher evolutionary conservation compared to non-interface protein surfaces.
  • Solvent accessibility was identified as a critical factor influencing residue characteristics at protein interaction sites.

Conclusions:

  • The distinct residue compositions of protein interaction interfaces are indicative of specialized interaction mechanisms.
  • Protein interaction interfaces are under greater evolutionary constraint than general protein surfaces.
  • Considering solvent accessibility is essential for a comprehensive understanding of residue behavior and propensities at protein interaction interfaces.