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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Related Experiment Video

Updated: Jul 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Evolutionary networks in the formatted protein sequence space.

Zakharia M Frenkel1, Edward N Trifonov

  • 1Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. zakharf@research.haifa.ac.il

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|November 8, 2007
PubMed
Summary
This summary is machine-generated.

Researchers developed a novel protein sequence analysis method using sequence space networks. This approach reveals fine details in protein evolutionary history and aids in sequence annotation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Establishing sequence relatedness is crucial for understanding protein function and evolution.
  • Existing methods may not fully capture complex evolutionary relationships within large genomic datasets.

Purpose of the Study:

  • To introduce and analyze a novel method for determining sequence relatedness by exploring protein sequence space.
  • To investigate the topology and evolution of networks formed by protein sequence fragments.

Main Methods:

  • Constructing a sequence space using 20-amino acid fragments from prokaryotic genomes.
  • Connecting fragments based on high sequence identity to form kinship networks.
  • Analyzing network topology at varying sequence identity thresholds.

Main Results:

  • A large, complex network encompassing up to 10% of the sequence space is formed at lower identity thresholds.
  • Increasing the identity threshold causes the main network to fragment into diverse smaller clusters.
  • Observed network structures exhibit varied sizes and topologies.

Conclusions:

  • The analyzed "evolutionary networks" provide a powerful tool for protein sequence annotation.
  • This method offers insights into the fine details of protein evolutionary history.
  • The network-based approach enhances our understanding of sequence relationships and evolutionary pathways.