Yosshi

Yosshi facilitates disulfide engineering by analyzing disulfide (S–S) bond patterns across homologous protein sequences and structures to identify sites for introducing or studying naturally occurring crosslinks that affect stability and function.

Key Features:

• Comparative Analysis: Performs comparative analysis of sequences and structures across homologous proteins within a common structural fold to reveal varying disulfide connectivity patterns.
• Hot-spot Identification: Identifies promising hot-spots for enhancing protein or enzyme stability and for modulating function by introducing naturally occurring disulfide crosslinks.
• Integration with Mustguseal: Integrates with the Mustguseal web-server to construct large structure-guided sequence alignments of functionally diverse protein families.
• Large-scale Analysis: Enables analysis of thousands of proteins using information aggregated from public databases.
• Systematic Homology-Driven Analysis: Provides systematic homology-driven analysis of disulfide bonds to interpret their roles in structural stability and functional diversity within superfamilies.
• Output Formats: Exports analysis results as content-rich PyMol session files.

Scientific Applications:

• Protein Engineering: Supports protein engineering efforts aimed at designing or stabilizing proteins via introduction or manipulation of disulfide bonds.
• Enzyme Stabilization and Modulation: Aids development of enzymes with enhanced stability or altered function through targeted disulfide engineering.
• Functional Diversity Studies: Enables investigation of how disulfide bonds contribute to functional diversity across protein superfamilies.
• Evolutionary Analysis: Facilitates analysis of conservation and variation of disulfide bonds among evolutionarily related proteins.

Methodology:

Constructs large structure-guided sequence alignments with Mustguseal and applies homology-driven comparative sequence–structure analysis to examine disulfide connectivity patterns and identify candidate S–S bond sites.