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The structure of the protein universe and genome evolution

Author

Listed:
  • Eugene V. Koonin

    (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health)

  • Yuri I. Wolf

    (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health)

  • Georgy P. Karev

    (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health)

Abstract

Despite the practically unlimited number of possible protein sequences, the number of basic shapes in which proteins fold seems not only to be finite, but also to be relatively small, with probably no more than 10,000 folds in existence. Moreover, the distribution of proteins among these folds is highly non-homogeneous — some folds and superfamilies are extremely abundant, but most are rare. Protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties, which also extend to the number of connections between domains in multidomain proteins. All these distributions follow asymptotic power laws, such as have been identified in a wide variety of biological and physical systems, and which are typically associated with scale-free networks. These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle.

Suggested Citation

  • Eugene V. Koonin & Yuri I. Wolf & Georgy P. Karev, 2002. "The structure of the protein universe and genome evolution," Nature, Nature, vol. 420(6912), pages 218-223, November.
    • Handle: RePEc:nat:nature:v:420:y:2002:i:6912:d:10.1038_nature01256
    DOI: 10.1038/nature01256
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    Cited by:

    1. Esmeralda Vicedo & Avner Schlessinger & Burkhard Rost, 2015. "Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-21, August.
    2. Qing-Ju Jiao & Yan-Kai Zhang & Lu-Ning Li & Hong-Bin Shen, 2011. "BinTree Seeking: A Novel Approach to Mine Both Bi-Sparse and Cohesive Modules in Protein Interaction Networks," PLOS ONE, Public Library of Science, vol. 6(11), pages 1-12, November.
    3. Daniela Barbara Keller & Jörg Schultz, 2014. "Word Formation Is Aware of Morpheme Family Size," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-6, April.
    4. Colizza, Vittoria & Flammini, Alessandro & Maritan, Amos & Vespignani, Alessandro, 2005. "Characterization and modeling of protein–protein interaction networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 352(1), pages 1-27.
    5. Patrick C F Buchholz & Catharina Zeil & Jürgen Pleiss, 2018. "The scale-free nature of protein sequence space," PLOS ONE, Public Library of Science, vol. 13(8), pages 1-14, August.

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