Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher

Human apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1) is a multifunctional protein central to DNA repair and redox regulation, yet its dynamic post-translational modifications (PTMs) remain poorly understood. Here, we report a biotin-regulated avidin-based nano-catcher (bMIPAPE1) capable of capturing active APE1 in living cells. By leveraging biotin-saturated avidin assembled onto magnetic nanoparticles and surface-imprinted with polydopamine, we engineered highly specific binding cavities for APE1 that enable retention of labile PTMs. This platform revealed 25 previously unreported PTMs across 18 residues of APE1, encompassing acetylation, phosphorylation, ubiquitination, methylation, S-nitrosylation, palmitoylation, and succinylation, and highlighting several PTM hotspots. Representative modifications include phosphorylation at Y264 and Y269, and acetylation at K63, with several PTMs associated with APE1 nuclear export. In addition to high specificity and intracellular compatibility, bMIPAPE1 attenuated both the DNA repair and redox-related functions of APE1. Our findings demonstrate the utility of artificial nanocomposites as tools for live-cell PTM profiling and functional modulation of target proteins, offering a powerful approach to decode protein regulation in living systems and identify potential therapeutic targets in cancer.