Pup-Click—A New Chemoenzymatic Method for the Generation of Singly Pupylated Targets

Abstract

Conjugation of the prokaryotic ubiquitin-like protein (Pup) to cellular proteins tags these proteins for degradation by a proteasome in actinobacteria. To study the Pup-proteasome system in in vitro biochemical assays, Pup-tagged (i.e., pupylated) proteins are often used. However, the purification of a homogeneous preparation of pupylated proteins often suffers from poor yields and limitations in terms of selecting the target protein and its site of pupylation. Here, we report on the development of a biochemical methodology we term Pup-Click for the generation of pupylated protein mimics in vitro. Pup-Click relies on a natural pupylation reaction combined with the use of a synthetic peptide and genetic code expansion via the use of unnatural amino acids and Click chemistry. In principle, this approach allows for conjugation of Pup to any selected target at potentially any desired position. Importantly, pupylated protein mimics generated by Pup-Click are recognized and processed by enzymes of the Pup-proteasome system. As such, Pup-Click can serve as a powerful tool for studying this protein degradation pathway.

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

“…Accordingly, reconstituted 26S proteasomes were covalently linked at these distinct AzF positions to dibenzocyclooctyne-linked fluorophores, allowing for the performance of FRET- and anisotropy-based assays for substrate interactions and concomitant conformational changes of the proteasome [ 370 ]. In addition, the proteasome-Pup (a ubiquitin equivalent) system of Actinobacteria was studied with pupylated proteins conjugated to synthetic peptides and uAAs employing the classical Cu(I)-catalyzed 1,3-dipolar cycloaddition of an alkyne group in Pup and an azide group in the peptide, resulting in the so-called Pup-click [ 371 ].…”