Ubiquibodies mark proteins for destruction

A newly engineered type of antibody fragment which mark specific proteins inside a cell with a molecular kiss of death could pave the way for new drug therapies and research tools. These ‘ubiquibodies’ can be inserted into the ubiquitin-proteasome pathway (UPP) say chemical engineers from Cornell University. They consist of a modified enzyme bound to an engineered antibody fragment designed to seek out and bind to specific targets. The UPP is a natural cellular pathway which allows cells to get rid of unwanted proteins by tagging them with a chain of ubiquitin and sending them to the proteasome, to be deconstructed into its component amino acids. Professor Matthew DeLisa and colleagues took advantage of the modular nature of the UPP which involves three enzymes, E1, E2 and E3. They modified a particular E3 enzyme called CHIP to alter part of the pathway, removing CHIP’s natural binding domain and replacing it with an engineered binding protein – an antibody fragment. This enabled CHIP to put an ubiquitin chain on any target, guided by the antibody fragment which seeks out and binds to its specific target. To prove this, they modified CHIP with a binding protein that targets the enzyme beta-galactosidase. They introduced DNA encoding for the beta-galactosidase target into a human cell line, along with DNA encoding for their ubiquibodies with a binding protein for the beta-galactosidase enzyme. The levels of beta-galactosidase reduced in the presence of the corresponding ubiquibodies. “Our ability to redirect whatever protein you want to the proteasome is now made possible simply by swapping out different binding proteins with specificity for targets of interest to the researcher,” DeLisa said. Ubiquibodies could provide a powerful means to delete a protein from a cell to study that protein’s effect, but also to discover what happens if a portion of the protein is deleted. Current gene knockouts are all or nothing DeLisa said, ubiquibodies could fine-tune research around protein deletion or reduction. The work – published in Journal of Biological Chemistry – could also prove useful for drug therapies, and DeLisa’s lab are currently exploring the therapeutic potential for ubiquibodies in Alzheimer’s, cancer and Parkinson’s. Ubiquibodies: Synthetic E3 Ubiquitin Ligases Endowed with Unnatural Substrate Specificity for Targeted Protein Silencing