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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...
Protein Organization01:13

Protein Organization

Overview
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.
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.
Protein Organization01:13

Protein Organization

Overview
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...

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Related Experiment Video

Updated: Jun 26, 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

Protein domain organisation: adding order.

Sarah K Kummerfeld1, Sarah A Teichmann

  • 1Department of Developmental Biology, 279 Campus Dr, Stanford, 94305, CA, USA. sarahkk@gene.com

BMC Bioinformatics
|January 31, 2009
PubMed
Summary
This summary is machine-generated.

Protein domain order is not always linear; some domain groups are shuffled during evolution, revealing new insights into protein evolution and function. This study identifies non-linear domain organization patterns across 192 genomes.

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Last Updated: Jun 26, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Published on: January 26, 2024

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Proteins are built from domains, which can combine to create new structures and functions.
  • Previous research used graph theory to study domain co-occurrence, but not their order.
  • This study introduces directed graphs to analyze domain order and identify novel organizational patterns.

Purpose of the Study:

  • To identify and analyze non-linear domain organization patterns in proteins.
  • To understand the evolutionary significance of shuffled domain orders.
  • To explore the functional implications of these patterns across different species.

Main Methods:

  • Utilized directed graph theory to represent the linear order of domains in proteins.
  • Analyzed 192 genomes from all three kingdoms of life.
  • Applied graph theoretical methods to identify statistically significant non-linear domain organization patterns.

Main Results:

  • Identified two higher-order domain organization patterns: clusters and bi-directionally associated domain pairs.
  • Found that some domain groups are shuffled, occurring in multiple orders across different proteins.
  • Observed statistically over-represented clustering and domain pairing in both forward and reverse orientations across all analyzed genomes.

Conclusions:

  • Protein domain organization is more complex than linear arrangements, with non-linear patterns playing a significant role.
  • These non-linear patterns, though rare, are functionally important, particularly in protein-protein interactions and signaling pathways like Jak-STAT.
  • Understanding these complex domain organizations provides novel insights into protein evolution and functional diversification.