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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...
The Proteasome02:18

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
The Proteasome01:13

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin...
The Proteasome02:18

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: May 31, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Reductive evolution of proteomes and protein structures.

Minglei Wang1, Charles G Kurland, Gustavo Caetano-Anollés

  • 1Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.

Proceedings of the National Academy of Sciences of the United States of America
|July 7, 2011
PubMed
Summary
This summary is machine-generated.

Protein linker sequences in eukaryotes are significantly longer than those in prokaryotes. This difference, not due to protein domains, suggests reductive evolution in prokaryotic linker lengths correlated with genome coding capacity.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Orthologous protein families are notably longer in Eukarya compared to Bacteria and Archaea.
  • Protein length disparities between superkingdoms have been observed but not fully explained.

Purpose of the Study:

  • To investigate the structural basis for protein length differences across superkingdoms.
  • To determine the evolutionary dynamics of protein linker and domain sequences in relation to proteome diversity.

Main Methods:

  • Analysis of protein structures across 745 genomes.
  • Comparison of linker and domain sequence lengths in Eukaryotes, Bacteria, and Archaea.
  • Correlation of linker lengths with genome coding sequence (CDS) as a measure of proteome diversity.

Main Results:

  • Prokaryotic (Bacteria and Archaea) linker sequences are substantially shorter than eukaryotic ones.
  • Linker lengths in prokaryotes show a clear proportional evolution with genome CDS, indicating reductive evolution.
  • Eukaryotic linker lengths are larger than expected and do not correlate with CDS, while domain lengths remain relatively constant across all groups.

Conclusions:

  • Protein length differences are primarily driven by variations in non-domain linker sequences.
  • Prokaryotic linker evolution appears reductive and linked to proteome diversity (CDS).
  • Eukaryotic linker evolution does not follow the same reductive pattern observed in prokaryotes.