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An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins

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Intrinsically Disordered Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2141))

Abstract

We present an easy protocol for evolutionary analysis of proteins, with an emphasis on studying the evolutionary dynamics of disordered regions. Using the p53 protein family as an example, we provide a guide for finding homologous sequences in a database and refining a dataset before constructing the evolutionary context by building a phylogenetic tree. We show how a multiple sequence alignment and phylogeny for a protein family can be further partitioned into smaller datasets in order to investigate the changes in disorder content across the phylogeny. Based on the evolutionary context, we also investigate site-specific conservation of disorder. Last, we address how to evaluate the evolutionary dynamics of disorder-to-order transitions.

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Author information

Authors and Affiliations

  1. Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA

    Janelle Nunez-Castilla & Jessica Siltberg-Liberles

Authors
  1. Janelle Nunez-Castilla
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  2. Jessica Siltberg-Liberles
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Corresponding author

Correspondence to Jessica Siltberg-Liberles .

Editor information

Editors and Affiliations

  1. Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, København N, Denmark

    Birthe B. Kragelund

  2. Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Karen Skriver

1 Electronic Supplementary Material

P.1.1

Supplementary_materials.zip (1477 KB)

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Nunez-Castilla, J., Siltberg-Liberles, J. (2020). An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins. In: Kragelund, B.B., Skriver, K. (eds) Intrinsically Disordered Proteins. Methods in Molecular Biology, vol 2141. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0524-0_7

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  • DOI: https://doi.org/10.1007/978-1-0716-0524-0_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0523-3

  • Online ISBN: 978-1-0716-0524-0

  • eBook Packages: Springer Protocols

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