Purification tags markedly affect self-aggregation of CPEB3

Since protein aggregation—including liquid–liquid phase separation (LLPS) and amyloid fibril formation—plays a critical role in both diseases and biological functions, understanding the mechanisms underlying protein aggregation is essential. Recombinant proteins are commonly used in vitro to investigate protein aggregation processes. However, if the purification tags remain uncleaved, they may affect the results and hinder accurate interpretation. Our findings demonstrate that the His₆₋GFP and His₁₂ tags significantly affect liquid droplet and amyloid fibril formation in the intrinsically disordered region (IDR) of mouse cytoplasmic polyadenylation element-binding protein 3 (CPEB3) and its fragments. This study shows that the purification tags significantly affect aggregation assays, making it essential to account for their influence to accurately interpret protein aggregation.