Publications
bioRxiv : the preprint server for biologySep 2024 DOI:
10.1101/2024.09.02.610852

Design of linked-domain protein inhibitors of UBE2D as tools to study cellular ubiquitination

Bukhari, Zara; Gu, Li; Nederstigt, Anneroos E; Cope, Logan J; Bolhuis, Derek L; Harvey, Kim; Allen, Tristan; Hill, Spencer; Yang, Yujie; Lawson, Guy; Lu, Cai; Tran, Tommy; Pineda, Leah; Low, Leanne; Chiang, Andrew; Song, Jason; Fong, Michelle V; Rangel, Vanessa M; Chan, William K; Kleiger, Gary; Goldfarb, Dennis; Vierra, Craig A; Brown, Nicholas G; Harrison, Joseph S
Product Used
Genes
Abstract
Ubiquitin (Ub) is a post-translational modification that largely controls proteostasis through mechanisms spanning transcription, translation, and notably, protein degradation. Ub conjugation occurs through a hierarchical cascade of three enzyme classes (E1, E2, and E3s) involving >1000 proteins that regulate the ubiquitination of proteins. The E2 Ub-conjugating enzymes are the midpoint, yet their cellular roles remain under-characterized, partly due to a lack of inhibitors. For example, the cellular roles of the promiscuous E2 UBE2D/UBCH5 are not well described. Here, we develop a highly selective, multivalent, engineered protein inhibitor for the UBE2D family that simultaneously targets the RING- and backside-binding sites. In HeLa cells, these inhibitors phenocopy knockdown of UBE2D by reducing the IC50 to cisplatin and whole-cell proteomics reveal an increased abundance of ~20% of the identified proteins, consistent with reduced Ub degradation and proteotoxic stress. These precision tools will enable new studies probing UBE2D's central role in proteome management.
Product Used
Genes

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