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Methods Mol Biol. 2017;1640:241-256. doi: 10.1007/978-1-4939-7165-7_18.

Identification and Analysis of WG/GW ARGONAUTE-Binding Domains.

Author information

1
Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
2
Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. wmk@amu.edu.pl.

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.

KEYWORDS:

AGO-binding domain; ARGONAUTE; Protein domain; Sequence analysis; WG/GW domain; Web application

PMID:
28608348
DOI:
10.1007/978-1-4939-7165-7_18
[Indexed for MEDLINE]

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