Described herein are engineered fusion proteins comprising a variant protease (e.g., an HCV NS3 protease) fused to a polypeptide of interest and a cognate protease cleavage site. The cleavability of the cognate protease cleavage site enables the controllability of one or more functions of the polypeptide of interest. Additionally disclosed are methods for generating engineered fusion proteins as well as their therapeutic use.
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