PXD047665

PXD047665 is an original dataset announced via ProteomeXchange.

Title	Continuous evolution of compact protein degradation tags regulated by selective cereblon molecular glues
Description	Small molecule-triggered protein degradation tags (degrons) are powerful tools for biology, biotechnology, and therapeutics development. Commonly used degrons, however, are large protein domains (typically >100 amino acids) that cannot be easily or cleanly installed in endogenous protein-coding genes in most cell types. Although some zinc-finger (ZF) degrons are theoretically small enough for facile endogenous tagging, all are triggered by small molecules with substantial off-target effects, precluding their use as highly specific modulators of endogenous protein levels. We developed a phage-assisted continuous evolution platform for molecular glues (MG-PACE) and applied it to evolve ZF degrons that engage cereblon (CRBN) only in the presence of orthogonal thalidomide derivatives. MG-PACE evolved a 36-amino acid ZF degron (SD40) that binds CRBN with high affinity in the presence of PT-179, a thalidomide derivative with no detected neosubstrate activity. The evolved degron is small enough to be efficiently inserted into targeted genomic sites in human cells using prime editing. Human proteins tagged with the evolved degron are rapidly and potently degraded by the otherwise-inert PT-179. To overcome the inactivity of IMiD-based degrons in rodents, we separately used MG-PACE to evolve ZF degrons that engage mouse CRBN, enabling induced target protein degradation in mouse cells. High-resolution cryo-electron microscopy structures of SD40 in complex with CRBN/DDB1 bound to PT-179 or pomalidomide reveal mechanistic insights into the evolution and molecular basis of SD40’s activity and specificity. Collectively, our efforts establish a system for the rapid evolution of molecular glue complexes with novel specificities and compact ZF tags that overcome shortcomings associated with existing degrons.
HostingRepository	PRIDE
AnnounceDate	2024-08-09
AnnouncementXML	Submission_2024-08-09_06:09:05.397.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eric Fischer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-08 18:51:01	ID requested
⏵ 1	2024-08-09 06:09:06	announced

10.1126/science.adk4422;

Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR, Continuous evolution of compact protein degradation tags regulated by selective molecular glues. Science, 383(6688):eadk4422(2024) [pubmed]

submitter keyword: cereblon,Phase assisted evolution, molecular glue, IMiD, protein degradation

Eric Fischer
contact affiliation	Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
contact email	eric_fischer@dfci.harvard.edu
lab head
Eric Fischer
contact affiliation	Dana-Farber Cancer Institute
contact email	eric_fischer@dfci.harvard.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD047665

PRIDE project URI

• PRIDE
  1. PXD047665
     1. Label: PRIDE project
     2. Name: Continuous evolution of compact protein degradation tags regulated by selective cereblon molecular glues