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Embedding Alternative Conformations of Proteins in Protein–Protein Interaction Networks

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

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Abstract

While many proteins act alone, the majority of them interact with others and form molecular complexes to undertake biological functions at both cellular and systems levels. Two proteins should have complementary shapes to physically connect to each other. As proteins are dynamic and changing their conformations, it is vital to track in which conformation a specific interaction can happen. Here, we present a step-by-step guide to embedding the protein alternative conformations in each protein–protein interaction in a systems level. All external tools/websites used in each step are explained, and some notes and suggestions are provided to clear any ambiguous point.

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Author information

Authors and Affiliations

  1. Computer Science and Engineering Department, Koc University, Istanbul, Turkey

    Farideh Halakou & Attila Gursoy

  2. Chemical and Biological Engineering Department, Koc University, Istanbul, Turkey

    Ozlem Keskin

Authors
  1. Farideh Halakou
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  2. Attila Gursoy
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  3. Ozlem Keskin
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Corresponding author

Correspondence to Attila Gursoy .

Editor information

Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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Halakou, F., Gursoy, A., Keskin, O. (2020). Embedding Alternative Conformations of Proteins in Protein–Protein Interaction Networks. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_9

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

  • eBook Packages: Springer Protocols

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