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Sequence sizes of eukaryotic enzymes

E Kolker1, E N Trifonov

  • 1Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|January 1, 1996
PubMed
Summary

Protein size periodicity is common in eukaryotes and prokaryotes. This study confirms a preference for typical protein sizes in eukaryotic enzymes, even after data cleaning, suggesting biological significance.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Previous research indicated that a significant portion of proteins exhibit sequence size periodicity.
  • Eukaryotic proteins show periodicity around 123 amino acids (aa), while prokaryotic proteins show periodicity around 152 aa.
  • Potential bias from overrepresented protein families requires careful consideration.

Purpose of the Study:

  • To investigate the size distributions of eukaryotic enzyme sequences.
  • To address potential biases in protein family representation.
  • To confirm or refute the observed preference for typical protein sizes.

Main Methods:

  • Analysis of eukaryotic enzyme sequence ensembles.
  • Application of successive relatedness thresholds for data bank cleaning.
  • Examination of sequence size distributions across different cleaning levels.

Main Results:

  • The preference for typical protein sequence sizes was confirmed in eukaryotic enzymes.
  • Data cleaning, using relatedness thresholds, did not alter the observed size distribution.
  • The findings hold across various levels of data bank curation.

Conclusions:

  • The observed excess of typical size sequences in eukaryotic enzymes is likely not an artifact of data bias.
  • The preference for specific protein sizes suggests underlying biological or evolutionary constraints.
  • Further research is needed to elucidate the reasons behind this size preference.

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