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Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies

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Multiple Sequence Alignment

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2231))

Abstract

Bioinformatic analysis of functionally diverse superfamilies can help to study the structure-function relationship in proteins, but represents a methodological challenge. The Mustguseal web-server can build large structure-guided sequence alignments of thousands of homologs that cover all currently available sequence variants within a common structural fold. The input to the method is a PDB code of the query protein, which represents the protein superfamily of interest. The collection and subsequent alignment of protein sequences and structures is fully automated and driven by the particular choice of parameters. Four integrated sister web-methods—the Zebra, pocketZebra, visualCMAT, and Yosshi—are available to further analyze the resulting superimposition and identify conserved, subfamily-specific, and co-evolving residues, as well as to classify and study disulfide bonds in protein superfamilies. The integration of these web-based bioinformatic tools provides an out-of-the-box easy-to-use solution, first of its kind, to study protein function and regulation and design improved enzyme variants for practical applications and selective ligands to modulate their functional properties. In this chapter, we provide a step-by-step protocol for a comprehensive bioinformatic analysis of a protein superfamily using a web-browser as the main tool and notes on selecting the appropriate values for the key algorithm parameters depending on your research objective. The web-servers are freely available to all users at https://biokinet.belozersky.msu.ru/m-platform with no login requirement.

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Acknowledgments

This work was supported by the Russian Foundation for Basic Research grant #18-29-13060 and carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University supported by the project RFMEFI62117X0011 [29].

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Authors and Affiliations

  1. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia

    Dmitry Suplatov, Yana Sharapova & Vytas Švedas

  2. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia

    Yana Sharapova & Vytas Švedas

Authors
  1. Dmitry Suplatov
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  2. Yana Sharapova
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  3. Vytas Švedas
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Corresponding author

Correspondence to Dmitry Suplatov .

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Editors and Affiliations

  1. Research Institute for Microbial Disease, Osaka University, Osaka, Japan

    Kazutaka Katoh

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Suplatov, D., Sharapova, Y., Švedas, V. (2021). Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies. In: Katoh, K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1036-7_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1036-7_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1035-0

  • Online ISBN: 978-1-0716-1036-7

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