Scalable insect cell expression and purification screening applied to CRL4-DCAF substrate receptors

Abstract The ubiquitin-proteasome system is one of the primary mechanisms responsible for degradation of intracellular proteins. Cullin-RING E3 ligases (CRL) are modular, multi-subunit complexes that catalyse ubiquitination of a wide variety of proteins, marking them for degradation by the proteasome. Substrate specificity is conferred by the substrate receptor subunit of the CRL, of which there are hundreds. Targeted protein degradation (TPD) is a drug modality that involves hijacking the activity of CRLs to ubiquitinate non-native neosubstrates via compound-induced ternary complex formation between a substrate receptor and the target. Of the many CRL substrate receptors, the DDB1 and Cul4-associated factor (DCAF) family are of high interest and potential for TPD. To enable characterisation of DCAF proteins and ligand screening campaigns, we have undertaken high-throughput recombinant protein expression screening in insect cells and small-scale plate-based purification of 24 DCAF proteins to identify soluble recombinant protein. Co-expression with the stabilising substrate adaptor DDB1 is required for, or enhances, expression of many DCAFs and provides a folding quality control measure through co-purification with tagged DCAF protein. Of 13 DCAF proteins that had not previously been expressed in the literature, we identify 8 that express well as promising candidates for scale-up. We provide sequence and construct information as a resource for the community. This screening method could be expanded to more DCAF proteins and applied to other CRL substrate receptor families.