A recent study by Mercer et al. presents a novel approach to overcome the limitations of existing conditional protein degradation tags (degrons). Conditional degrons are typically over 100 amino acids long or triggered by small molecules with substantial off-target effects, hindering their use as specific modulators of endogenous protein levels.

The researchers developed MG-PACE, a phage-assisted continuous evolution platform for molecular glue complexes, and evolved a 36-amino acid zinc finger (ZF) degron, termed SD40. This compact degron binds to the ubiquitin ligase substrate receptor cereblon in complex with PT-179, an orthogonal thalidomide derivative. The otherwise inert PT-179 degrades endogenous proteins tagged in-frame with SD40 using prime editing.

Cryo-electron microscopy structures of SD40 in complex with ligand-bound cereblon provided mechanistic insights into SD40’s activity and specificity and its molecular basis. The study establishes a system to continuously evolve molecular glue complexes and provides ZF tags that overcome the shortcomings of existing degrons.

By using an Aurora Ultimate CSI 25×75 C18 UHPLC column, the researchers were able to achieve efficient separation and highly sensitive detection of peptides, which was critical for their quantitative proteomics analysis.

Publication
Science

Authors

Jaron A. M. Mercer, Stephan J. Decarlo, Shourya S. Roy Burman, Vedagopuram Sreekanth, Andrew T. Nelson, Moritz Hunkeler, Peter J. Chen, Katherine A. Donovan, Praveen Kokkonda, Praveen K. Tiwari, Veronika M. Shoba, Arghya Deb, Amit Choudhary, Eric S. Fischer, & David R. Liu

Title

Continuous evolution of compact protein degradation tags regulated by selective molecular glues