Peking University team publishes breakthrough paper in Nature, deciphering a key mechanism of protein degradation

Today, the journal Nature published online a new paper by a research team from Peking University. Led by Professor Youdong Mao, the team employed cutting-edge innovative technologies to significantly enhance the temporal resolution and analytical precision of cryo-electron microscopy (cryo-EM), thereby revealing the dynamic regulatory mechanism of the human proteasome. The research team noted that the proteasome—a molecular machine governing intracellular protein degradation—is a therapeutic drug target for numerous major diseases; thus, achieving precise observation of its dynamic regulation and conformational changes holds great promise for driving groundbreaking innovation in next-generation drug development. In eukaryotic cells—including human cells—the ubiquitin-proteasome system constitutes a primary pathway for targeted protein degradation. In 2004, the Nobel Prize in Chemistry was awarded to three scientists for their historic discovery of this ubiquitin-mediated protein degradation mechanism. During this process, substrate proteins destined for degradation are tagged with ubiquitin chains and subsequently recognized by the proteasome; the proteasome then functions like a ‘protein shredder’, cleaving substrates into fragments to achieve precise degradation. Dysregulation of proteasome function is associated with a wide range of human diseases, including cancer, neurodegenerative disorders, and immune-related diseases. Building upon prior work on the proteasome, Professor Mao’s laboratory has progressively elucidated, using cryo-EM, its atomic architecture, assembly principles, and fundamental kinetic rules governing the degradation of ubiquitinated substrates. The intact proteasome holoenzyme—termed the 26S proteasome—consists of a central cylindrical 20S core particle capped at one or both ends by a 19S regulatory particle. The 19S particle contains a ring-shaped heterohexameric motor—AAA-ATPase—that regulates degradation of ubiquitinated substrates through multiple coordinated ATP hydrolysis modes. In normal cells, proteasome activity is tightly regulated at multiple levels. One major regulatory molecule is the deubiquitinating enzyme USP14, which reversibly binds to the proteasome and removes ubiquitin chains from substrates. However, this process occurs extremely rapidly—the timescale of proteasomal substrate degradation ranges from milliseconds to seconds—making it a longstanding global challenge to visualize how USP14 is activated by the proteasome and how it modulates proteasome function. This is precisely where the current study achieves its breakthrough: it presents, at atomic resolution, the continuous conformational spectrum of USP14 and the proteasome during protein degradation. To capture intermediate structural states of this process via cryo-EM, the research team first slowed down the reaction. Through extensive optimization of experimental conditions and reconstruction of the reaction kinetics system, researchers acquired over 45,000 time-resolved cryo-EM transmission micrographs of USP14 actively degrading ubiquitinated substrates, and selected more than three million particle images of USP14–26S–ubiquitinated substrate complexes. Next, the critical step was to classify this massive dataset to reconstruct the dynamic progression of the protein reaction. To accomplish this, the team leveraged artificial intelligence, applying a novel deep-learning-based high-precision 3D classification and 4D reconstruction method—developed autonomously over several years—to resolve 13 distinct functional intermediate states of the USP14–26S complex during degradation of polyubiquitinated substrates, all at high resolution (3.0–3.6 Å). This enabled full reconstruction of the controlled proteasome’s complete dynamic working cycle.

David Baker’s Chinese student develops novel protein technology, freeing targeted protein degradation from dependence on natural ligands

Secondly, EndoTag not only enables protein degradation but also promotes intracellular signal transduction. For example, in certain endocytosis-dependent signaling pathways, EndoTag can significantly amplify signal strength. Thirdly, the EndoTag system demonstrates exceptional potential for modular design, making it applicable to the treatment of cancers and neurodegenerative diseases. According to reviewers, this work features five major highlights: Highlight One: A novel protein design strategy. Reviewers noted that the study employs an advanced protein design strategy enabling EndoTag to trigger endocytosis and achieve targeted degradation by binding both cell-surface and soluble targets. This approach allows simultaneous targeting of multiple receptors without interfering with native receptor signaling, and exhibits exceptionally high degradation efficiency. Highlight Two: Logic-gated control enhances specificity. The study introduces a logic-gating strategy that substantially improves the specificity of protein degradation. Especially when integrated with synthetic Notch signaling systems, target degradation can activate cellular signaling cascades, thereby providing a more efficient method for precisely controlling cellular behavior. Highlight Three: High-quality design and broad applicability. EndoTag proteins can target multiple receptors—including ASGPR, IGF-2R/CI-M6PR, transferrin receptor, and Sortilin—demonstrating remarkable efficacy in degrading membrane proteins such as programmed cell death ligand 1 (PD-L1) and epidermal growth factor receptor (EGFR), as well as soluble proteins. Highlight Four: Key distinctions from prior work. Reviewers emphasized that this work extends and surpasses previous studies of the same category published in Nature. Earlier papers focused primarily on antibody-based LYTAC approaches, whereas this study integrates Rosetta-designed protein degradation technology to propose the novel EndoTag platform, showcasing its tremendous potential in the field of targeted protein degradation. Highlight Five: Strong tissue specificity and broad applicability. EndoTag technology is engineered for tissue-specificity—not only enabling targeted degradation in specific tissues but also permitting more precise intracellular signal regulation via logic-gating functionality. Such broad applicability renders it highly promising across multiple biomedical domains. Overall, reviewers commended the experimental rigor and wide-ranging impact of this study, describing it as a compelling proof-of-concept for targeted protein degradation and highlighting the immense practical potential of computational protein design—particularly in leveraging endocytosis for protein degradation. Buwei Huang stated that EndoTag technology holds exceptionally broad application prospects, with potential implementation in the following areas: First, cancer therapy. EndoTag can bind specifically to tumor-associated receptors to precisely deliver anticancer drugs into cancer cells—or directly degrade specific proteins on the cancer cell surface—thereby inhibiting tumor growth.

New Approach Switches On Protein Degradation Machinery

2 days ago

Researchers at UC Berkeley led by Michael Rapé developed a new strategy for stimulated protein degradation that activates enzymes to accelerate cellular protein cleanup. This advance offers a novel method compared to existing targeted protein degradation techniques.

cen

2026-11-03

New Approach Switches On Protein Degradation Machinery

New Approach Switches On Protein Degradation Machinery

FAQ