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Related Concept Videos

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...
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...
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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

Evolutionary conservation in multiple faces of protein interaction.

Yoon Sup Choi1, Jae-Seong Yang, Yonghwan Choi

  • 1School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea.

Proteins
|April 8, 2009
PubMed
Summary

Protein interfaces are more evolutionarily conserved than other protein surfaces. Considering multiple interfaces enhances this conservation, aiding in protein interaction prediction and structure identification.

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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

Area of Science:

  • Structural biology
  • Bioinformatics
  • Evolutionary biology

Background:

  • Protein interfaces are crucial for protein-protein interactions (PPIs).
  • Previous studies suggested higher evolutionary conservation of interfaces, but lacked large-scale verification and consideration of multiple interfaces per protein.

Purpose of the Study:

  • To systematically investigate the evolutionary conservation of protein interfaces using a large dataset.
  • To assess the impact of multiple interfaces on conservation analysis.
  • To evaluate the utility of interface conservation in PPI prediction and structure refinement.

Main Methods:

  • Analysis of a large-scale dataset comprising 2646 protein interfaces.
  • Classification of interfaces based on homodimeric/heterodimeric and obligatory/transient interactions.
  • Inclusion of all known multiple interfaces for each protein.
  • Application of conservation analysis to filter protein docking decoys.

Main Results:

  • Protein interfaces are significantly more conserved than non-interface protein surfaces.
  • Conservation levels increase when multiple interfaces are accounted for.
  • Interface conservation effectively filters docking decoys, identifying near-native structures.
  • A strong correlation was found between protein interface size and its evolutionary conservation.

Conclusions:

  • Evolutionary conservation is a robust feature for identifying protein interfaces and predicting PPIs.
  • Accounting for multiple interfaces refines conservation analysis and improves PPI prediction accuracy.
  • Interface conservation and size serve as valuable filters for computational structure prediction and PPI studies.