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Plant Argonaute Proteins pp 241–256Cite as

Identification and Analysis of WG/GW ARGONAUTE-Binding Domains

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1640))

Abstract

WG/GW domains recruit ARGONAUTE (AGO) proteins to distinct silencing effector complexes using combinations of just two amino acids: tryptophan (W) and glycine (G), forming a wide arsenal of highly simplified interaction surfaces. These unstructured domains exhibit very low sequence identity and excessive length polymorphism, which makes identification of new AGO-binding proteins a challenging task as they escape detection with standard sequence comparison-based methods (e.g., BLAST, HMMER).

In this chapter, we explain the use of tools for prediction of AGO-binding WG/GW domains in protein sequences. We also show how to computationally explore an up-to-date information about AGO-interacting proteins and discover new properties of WG/GW domains. Finally, we encourage readers to explore the game-like web application for in silico designing/modifying AGO-binding sequences as well as modeling mutagenesis experiments and predicting their potential effect on AGO-binding activity.

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Authors and Affiliations

  1. Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland

    Andrzej Zielezinski & Wojciech M. Karlowski

Authors
  1. Andrzej Zielezinski
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  2. Wojciech M. Karlowski
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Corresponding author

Correspondence to Wojciech M. Karlowski .

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Editors and Affiliations

  1. Instituto de Biología Molecular y Celular de Plantas, (Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia), Valencia, Spain

    Alberto Carbonell

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Zielezinski, A., Karlowski, W.M. (2017). Identification and Analysis of WG/GW ARGONAUTE-Binding Domains. In: Carbonell, A. (eds) Plant Argonaute Proteins. Methods in Molecular Biology, vol 1640. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7165-7_18

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  • DOI: https://doi.org/10.1007/978-1-4939-7165-7_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7164-0

  • Online ISBN: 978-1-4939-7165-7

  • eBook Packages: Springer Protocols

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