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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

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Related Experiment Video

Updated: Jun 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

Evolution of protein binding modes in homooligomers.

Judith E Dayhoff1, Benjamin A Shoemaker, Stephen H Bryant

  • 1Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA.

Journal of Molecular Biology
|November 3, 2009
PubMed
Summary

Protein interaction evolution is revealed by analyzing binding modes and interfaces. Ancient interactions often use symmetrical homodimers, while newer ones show asymmetrical arrangements.

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Area of Science:

  • Biochemistry
  • Evolutionary Biology
  • Structural Biology

Background:

  • Understanding protein interaction evolution requires analyzing interfaces and binding modes.
  • Protein homooligomers play crucial roles in biological processes.

Purpose of the Study:

  • To investigate the evolution of protein binding modes and oligomerization states in homooligomers.
  • To map binding mode conservation onto phylogenetic trees and identify evolutionary trends.

Main Methods:

  • Large-scale analysis of protein homooligomers focusing on symmetry, interface size, and binding mode conservation.
  • Mapping of 60 distinct binding modes and oligomerization states onto phylogenetic trees for nine homooligomer families.

Main Results:

  • Binding modes are conserved within phylogenetic clades, particularly among close homologs (>70% sequence identity).
  • Ancient binding modes often involve symmetrical (isologous) homodimers with larger interfaces.
  • Recently evolved binding modes tend to be asymmetrical with smaller interfaces.

Conclusions:

  • Protein binding mode evolution shows a strong correlation with phylogenetic relationships.
  • Symmetrical homodimerization appears to be an ancestral trait, with diversification towards asymmetrical arrangements in more recent evolution.