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Related Concept Videos

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...
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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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...

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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
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Published on: October 3, 2018

Generation of a consensus protein domain dictionary.

R Dustin Schaeffer1, Amanda L Jonsson, Andrew M Simms

  • 1Biomolecular Structure and Design Program, University of Washington, Seattle, WA 98195-5013, USA.

Bioinformatics (Oxford, England)
|November 12, 2010
PubMed
Summary

Protein domain dictionaries reveal that 40% of metafolds are not autonomous folding units. This impacts bioinformatics and protein folding simulations, necessitating updated resources for studying protein structure and function.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Protein fold discovery is rare, suggesting folds are reusable structural units.
  • Protein folding mechanisms may be dictated by topology, implying limited folding pathways for existing folds.
  • Understanding protein domain organization is crucial for predicting structure and function.

Purpose of the Study:

  • To create a consensus domain dictionary (CDD) from SCOP, CATH, and Dali.
  • To identify representative protein targets for molecular dynamics (MD) simulations within the dynameomics project.
  • To analyze the composition and autonomy of protein structural domains.

Main Methods:

  • Consolidated data from SCOP, CATH, and Dali protein domain dictionaries.
  • Generated a consensus domain dictionary (CDD).
  • Identified representative protein targets for each metafold.

Main Results:

  • A surprising 40% of metafolds in the CDD lack autonomous structural domains.
  • This finding challenges assumptions in bioinformatics studies using domain dictionaries.
  • A comprehensive list of representative protein targets for each metafold was compiled.

Conclusions:

  • Many protein metafolds are not independent folding units, impacting their study.
  • The generated CDD and target list are valuable for molecular dynamics simulations and dynameomics research.
  • Further investigation into the folding properties of non-autonomous domains is warranted.