Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families

Disulfide bonds play a significant role in protein stability, function or regulation but are poorly conserved among evolutionarily related proteins. The Yosshi can help to understand the role of S-S bonds by comparing sequences and structures of homologs with diverse properties and different disulfi...

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Bibliographic Details
Published in:Nucleic acids research 2019-07, Vol.47 (W1), p.W308-W314
Main Authors: Suplatov, Dmitry, Timonina, Daria, Sharapova, Yana, Švedas, Vytas
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Computational Biology - methods
Disulfides - chemistry
Internet
Models, Molecular
Protein Engineering
Proteins - chemistry
Sequence Alignment
Software
Web Server Issue
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Summary:Disulfide bonds play a significant role in protein stability, function or regulation but are poorly conserved among evolutionarily related proteins. The Yosshi can help to understand the role of S-S bonds by comparing sequences and structures of homologs with diverse properties and different disulfide connectivity patterns within a common structural fold of a superfamily, and assist to select the most promising hot-spots to improve stability of proteins/enzymes or modulate their functions by introducing naturally occurring crosslinks. The bioinformatic analysis is supported by the integrated Mustguseal web-server to construct large structure-guided sequence alignments of functionally diverse protein families that can include thousands of proteins based on all available information in public databases. The Yosshi+Mustguseal is a new integrated web-tool for a systematic homology-driven analysis and engineering of S-S bonds that facilitates a broader interpretation of disulfides not just as a factor of structural stability, but rather as a mechanism to implement functional diversity within a superfamily. The results can be downloaded as a content-rich PyMol session file or further studied online using the HTML5-based interactive analysis tools. Both web-servers are free and open to all users at https://biokinet.belozersky.msu.ru/yosshi and there is no login requirement.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkz385