In the past, scientists believed that protein degradation primarily depended on the ubiquitin-proteasome system (UPS), where the degradation tag of a protein is usually attached through specific post-translational modifications (such as ubiquitination). However, this study shows that the C-terminal amide modification of proteins can itself serve as a degradation signal. This means that some proteins, once synthesized or damaged, will be rapidly cleared by the cell as long as their C-terminus carries an amide.

Researchers constructed a semi-synthetic fluorescent protein reporter system to systematically analyze the effects of different modifications on protein degradation. They found that proteins with C-terminal amides degrade significantly faster in cells than their unmodified counterparts.

To identify the key factor recognizing C-terminal amide modifications, the research team used CRISPR screening technology and ultimately pinpointed the protein FBXO31. FBXO31 is a substrate receptor for the SCF complex (SKP1-CUL1-F-box protein) and can specifically recognize C-terminal amides and mediate their ubiquitination. Further structural biology analysis revealed that FBXO31 contains a pocket specifically binding to C-terminal amides. This binding pocket interacts with C-terminal amides via hydrogen bonding and hydrophobic interactions, whereas unmodified C-terminal carboxylic acids cannot bind due to the lack of necessary hydrogen bonds. This mechanism ensures that FBXO31 targets only amide-modified proteins and avoids misidentifying normal proteins.

The study also found that C-terminal amides are primarily formed after oxidative damage to proteins. For example, under oxidative stress conditions such as hydrogen peroxide (H₂O₂) exposure, certain proteins undergo cleavage, and their newly formed C-terminus often carries an amide modification. These amide-modified proteins are then recognized by FBXO31 and degraded via the ubiquitin-proteasome system. This discovery suggests that FBXO31 may be one of the cell's critical defense mechanisms against oxidative stress. By clearing damaged proteins, FBXO31 helps maintain protein homeostasis and prevents harmful protein aggregation.

Interestingly, the study also revealed an FBXO31 mutant associated with neurological diseases — the D334N mutation. This variant of FBXO31 loses its specificity for C-terminal amides and instead erroneously targets other proteins. Such misrecognition can cause abnormal degradation of key cellular proteins, impacting cell survival. The D334N mutation has been linked to neurodevelopmental disorders and cerebral palsy. This indicates that FBXO31 and its regulation of C-terminal amide degradation pathways may play a crucial role in the nervous system.

This study is the first to reveal the role of C-terminal amides as degradation signals for proteins and identifies FBXO31 as the key recognition factor for this signal. This discovery not only deepens our understanding of protein degradation mechanisms but may also play a vital role in future research on neurological diseases, cancer, and protein homeostasis. As research on FBXO31 and its related pathways progresses, it is possible that new targeted degradation drugs will be developed, offering revolutionary breakthroughs for disease treatment. In the future, precise regulation of FBXO31 may become an important research direction in the field of protein homeostasis regulation.