Yosshi

A web-server for disulfide engineering
by bioinformatic analysis of diverse protein families






... to systematically classify and study disulfide bonds in diverse protein families,
and select hot-spots for disulfide engineering in the structure of your query protein



Version 1.0; December 3rd, 2018




Yosshi is "Your web-server for S-S bonds harvesting" to systematically classify and study disulfide bonds in diverse protein families and select hot-spots to introduce naturally occurring crosslinks to improve stability and evolvability of useful proteins/enzymes. Yosshi provides an intuitive and easy-to-use interface to the on-line analysis of disulfide connectivity in proteins with different properties (i.e., stability, function, regulation), and thus facilitates a broader interpretation of disulfides not just as a factor of structural integrity, but rather as a mechanism to implement diversity within a superfamily. The Yosshi's input and output can be created, processed and studied entirely on-line via the web-interface. The only software required on the user side is an HTML5-compatible web-browser. We hope that this bioinformatic tool will be useful at a daily laboratory routine and will provide an opportunity to further explore the value of S-S bonds, establish the structure-function relationship, and further develop more efficient protein engineering strategies.




Publication: Suplatov D.A., Timonina D.S., Sharapova Y.A., Švedas V.K. (2019) Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families. submitted




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Highlights:
  • Disulfide bonds are well-known factors of protein stability, but can also play a key role in function and regulation according to recent studies, and thus have a potential of becoming a particularly effective tool to study protein dynamics, design robust enzymes, and modulate protein stability to facilitate the engineering of new functions, but their practical use at a daily routine has yet been limited by an ambiguous predictive capacity of computer algorithms for stability-oriented disulfide engineering, absence of easy-to-use solutions for a systematic analysis of disulfide connectivity in homologs, and incomplete understanding of the molecular mechanisms that affect protein function as a result of a disulfide bond formation;

  • Disulfide bonds are poorly conserved in structures of homologs with different properties. The Yosshi can help to understand the role of S-S bonds in proteins by systematically comparing sequences and structures of homologs with diverse properties and different disulfide connectivity patterns within a common structural fold of a superfamily, and select hot-spots to introduce naturally occurring crosslinks to improve stability and evolvability of useful proteins/enzymes. Therefore, Yosshi facilitates a broader interpretation of disulfides not just as a factor of structural stability, but rather as a mechanism to implement diversity;

  • The Yosshi's input and output can be created, processed and studied entirely on-line via the web-interface. The only software required on the user side is an HTML5-compatible web-browser. In addition, you may wish to download the output data to your computer and study them off-line. For this you may need the PyMol molecular graphics engine;

  • The Yosshi web-server is integrated with the Mustguseal web-server capable of automatically constructing large structure-guided sequence alignments of functionally diverse protein families that can include thousands of proteins basing on all available information about their structures and sequences in public databases. Press the button to automatically construct a large multiple alignment by Mustguseal based on the PDB structure of your query protein to be further processed by Yosshi.

  • The integration of Yosshi and Mustguseal web-based bioinformatic methods provides an out-of-the-box easy-to-use solution, first of its kind, to predict the hot-spots for disulfide engineering of your query protein based on a systematic analysis of the S-S bonds naturally occurring in other members of a corresponding superfamily.

  • Press the button and then press the Demo mode button to request a demonstration of the Yosshi web-server.





Contacts and support

Dmitry Suplatov






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