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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...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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...
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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

Asymmetric relationships between proteins shape genome evolution.

Richard A Notebaart1, Philip R Kensche, Martijn A Huynen

  • 1Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.

Genome Biology
|February 17, 2009
PubMed
Summary
This summary is machine-generated.

Most protein relationships in metabolic networks are asymmetric, meaning one protein depends on another. This dependency impacts gene expression, gene knockouts, and genome evolution predictably.

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Area of Science:

  • Systems biology
  • Metabolic networks
  • Genomics

Background:

  • Protein interactions often exhibit asymmetry, where one protein's function depends on another, but not vice-versa.
  • Metabolic networks feature converging pathways where enzymes in initial steps depend on central pathway enzymes.

Purpose of the Study:

  • To investigate the prevalence and implications of asymmetric relationships between enzymes in metabolic networks.
  • To determine if these asymmetric relationships influence gene expression, gene knockout effects, and genome evolution.

Main Methods:

  • Analysis of metabolic flux models for Escherichia coli and Saccharomyces cerevisiae.
  • Examination of gene expression data, gene knockout essentiality, and genomic evolutionary patterns.

Main Results:

  • The majority of enzyme relationships in metabolic networks are asymmetric.
  • Asymmetric relationships correlate with gene expression patterns, gene essentiality after knockouts, and genome evolution (gene gain/loss).
  • Independent genes in asymmetric pairs are more likely to be present alone, especially when the relationship is evolutionarily conserved.

Conclusions:

  • Asymmetric relations in metabolic networks predictably influence gene expression, gene knockout outcomes, and genome evolution.
  • These findings highlight the systemic nature of metabolic organization and its evolutionary consequences.