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Directional terms are essential for describing the relative locations of different body structures. For instance, an anatomist might describe one band of tissue as "inferior to" another, or a physician might describe a tumor as "superficial to" a deeper body structure. These terms often use comparative terms in pairs to trace out the relative locations of one body part to another or descriptions of body tissues like the deeper ones from superficially present with reference to...
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A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.

Scott G Foy1, Benjamin A Wilson1, Jason Bertram1

  • 1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721.

Genetics
|January 30, 2019
PubMed
Summary
This summary is machine-generated.

Young protein-coding genes avoid hydrophobic amino acids to prevent aggregation, clustering them for folding. Older genes manage aggregation risk through interspersed hydrophobic residues, a trend evolving over billions of years.

Keywords:
aggregation propensitygene agephylostratigraphyprotein foldingprotein misfolding

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Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Protein biophysics

Background:

  • Determining evolutionary direction requires comparing entities at different evolutionary stages.
  • All extant species share a common ancestor, making direct chronological comparison difficult.
  • Gene families originate at different times, offering a proxy for evolutionary age.

Purpose of the Study:

  • To investigate the evolutionary trajectory of protein sequences.
  • To understand how proteins balance function with the avoidance of toxic aggregation.
  • To analyze the role of hydrophobic amino acids in protein evolution.

Main Methods:

  • Comparative analysis of young versus old protein-coding genes.
  • Examination of amino acid composition and sequence patterns.
  • Quantification of hydrophobic residue clustering using the index of dispersion.

Main Results:

  • Young genes exhibit fewer hydrophobic amino acids, clustered together to aid folding.
  • Older genes have higher hydrophobicity but counteract aggregation risk through specific amino acid ordering.
  • Hydrophobic residues become more interspersed in older genes, a pattern evolving over billions of years.

Conclusions:

  • The distribution of hydrophobic amino acids in proteins reflects evolutionary age and adaptation.
  • Interspersion of hydrophobic residues is a hallmark of ancient genes, mitigating aggregation risk.
  • Evolutionary trends in protein sequences can be traced by analyzing amino acid properties over geological time.