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A Model Of Large-Scale Proteome Evolution

Author

Listed:
  • RICARD V. SOLÉ

    (ICREA-Complex Systems Research Group, FEN, Universitat Politècnica de Catalunya, Campus Nord B4, 08034 Barcelona, Spain;
    Santa Fe Institute, 1399 Hyde Park Road, New Mexico 87501, USA;
    NASA-associated Astrobiology Institute, INTA/CSIC, Carr. del Ajalvir Km4, Madrid, Spain)

  • ROMUALDO PASTOR-SATORRAS

    (ICREA-Complex Systems Research Group, FEN, Universitat Politècnica de Catalunya, Campus Nord B4, 08034 Barcelona, Spain)

  • ERIC SMITH

    (Santa Fe Institute, 1399 Hyde Park Road, New Mexico 87501, USA)

  • THOMAS B. KEPLER

    (Santa Fe Institute, 1399 Hyde Park Road, New Mexico 87501, USA)

Abstract

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have shown that its topology displays a number of surprising features shared by other complex networks, both natural and artificial. In order to understand the origins of this topology and its evolutionary implications, we present a simple model of proteome evolution that is able to reproduce many of the observed statistical regularities reported from the analysis of the yeast proteome. Our results suggest that the observed patterns can be explained by a process of gene duplication and diversification that would evolve proteome networks under a selection pressure, favoring robustness against failure of its individual components.

Suggested Citation

  • Ricard V. Solé & Romualdo Pastor-Satorras & Eric Smith & Thomas B. Kepler, 2002. "A Model Of Large-Scale Proteome Evolution," Advances in Complex Systems (ACS), World Scientific Publishing Co. Pte. Ltd., vol. 5(01), pages 43-54.
    • Handle: RePEc:wsi:acsxxx:v:05:y:2002:i:01:n:s021952590200047x
    DOI: 10.1142/S021952590200047X
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    Citations

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    Cited by:

    1. Hyun-Myung Woo & Hyundoo Jeong & Byung-Jun Yoon, 2020. "NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families," PLOS ONE, Public Library of Science, vol. 15(1), pages 1-20, January.
    2. Tingting Song & Qian Tang & Jinghua Huang, 2019. "Triadic Closure, Homophily, and Reciprocation: An Empirical Investigation of Social Ties Between Content Providers," Information Systems Research, INFORMS, vol. 30(3), pages 912-926, September.
    3. Romualdo Pastor-Satorras & Eric Smith & Ricard V. Solé, 2002. "Evolving Protein Interaction Networks through Gene Duplication," Working Papers 02-02-008, Santa Fe Institute.
    4. Oh, S.M. & Son, S.-W. & Kahng, B., 2021. "Percolation transitions in growing networks under achlioptas processes: Analytic solutions," Chaos, Solitons & Fractals, Elsevier, vol. 146(C).
    5. Bienvenu, François & Débarre, Florence & Lambert, Amaury, 2019. "The split-and-drift random graph, a null model for speciation," Stochastic Processes and their Applications, Elsevier, vol. 129(6), pages 2010-2048.

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