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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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: Jul 4, 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

Contextual specificity in peptide-mediated protein interactions.

Amelie Stein1, Patrick Aloy

  • 1Institute for Research in Biomedicine, Barcelona Supercomputing Center, Barcelona, Spain.

Plos One
|July 4, 2008
PubMed
Summary
This summary is machine-generated.

Protein interaction context significantly enhances binding specificity and affinity, contributing about 20% to binding energy. This context also diversifies interaction interfaces, increasing cellular network robustness.

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Last Updated: Jul 4, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Peptide-based Identification of Functional Motifs and their Binding Partners
14:28

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Biological processes rely on transient protein interactions involving globular domains and linear motifs.
  • Linear motifs alone often lack the specificity for high-affinity protein binding.
  • Residues surrounding the motif, termed context, contribute to interaction specificity and affinity.

Purpose of the Study:

  • To systematically identify peptide-mediated protein interactions from known 3D structures.
  • To investigate the individual contributions of motif and context to binding energy.
  • To analyze the role of context in determining interaction specificity and robustness of cellular networks.

Main Methods:

  • Systematic identification of peptide-mediated protein interactions in structures with known 3D coordinates.
  • Analysis of binding energy contributions from linear motifs and surrounding context residues.
  • Quantification of topological and energetic variability in interaction interfaces.

Main Results:

  • Context residues contribute approximately 20% to the global binding energy.
  • Context plays a critical role in enhancing native partner affinity and preventing non-native interactions.
  • Interaction interfaces exhibit higher heterogeneity in context residues compared to consensus binding motifs.

Conclusions:

  • Context is crucial for achieving high specificity in peptide-mediated protein interactions.
  • The dynamic nature of interfaces and evolutionary mechanisms favor maximized binding specificity.
  • Non-native interactions and potential cross-reactions enhance cellular network robustness and resilience.