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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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...

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Related Experiment Video

Updated: Jun 20, 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

Neutral evolution on mammalian protein surfaces.

Gavin C Conant1

  • 1Division of Animal Sciences, University of Missouri, Columbia, MO, USA. conantg@missouri.edu

Trends in Genetics : TIG
|September 1, 2009
PubMed
Summary

Natural selection

Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Mammalian genetics

Background:

  • Organisms with small populations, like mammals, may experience weaker natural selection.
  • Protein evolution is influenced by factors like population size and functional constraints.

Purpose of the Study:

  • To investigate the effectiveness of natural selection on protein surface residues in mammals.
  • To determine if reduced selection on surface residues impacts protein interactions.

Main Methods:

  • Comparative analysis of amino acid substitution rates.
  • Distinguishing between protein surface and interior residues.
  • Statistical testing of neutral evolution hypothesis.

Main Results:

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  • Approximately one-third of surveyed mammalian proteins showed evidence of neutral evolution at surface residues.
  • Proteins with neutral surface evolution maintained a comparable number of interactions to other proteins.
  • This suggests a decoupling of residue-level conservation and interaction stability.

Conclusions:

  • Natural selection may preserve protein interactions indirectly, not solely through strict residue conservation.
  • Protein surface evolution in mammals can accommodate neutral changes without compromising interaction networks.
  • This finding offers a new perspective on the mechanisms maintaining protein function in evolving populations.