Cell-Penetrating Peptides and Supercharged Proteins: A Comprehensive Protocol from Isolation to Cellular Uptake

Cell-penetrating peptides (CPPs) and supercharged proteins (SPs) enable efficient intracellular delivery of macromolecules, with expanding applications in basic research and in therapeutic development. Despite their potential, reproducible workflows for isolation, biochemical characterization, and quantitative uptake analysis remain limited. Here, we present a comprehensive and replicable protocol for the isolation, characterization, and cellular uptake analysis of CPP-fusion proteins (CPP-FPs) and SPs using methyl-CpG-binding protein 2 (MeCP2) constructs as a proof-of-principle model. This workflow combines native protein purification with dynamic light scattering (DLS)-based buffer optimization. Cellular uptake is then assessed and quantified under live-cell conditions using high-content imaging and imaging flow cytometry, with additional assays to probe endocytic trafficking routes, identify CPP-like motifs in SPs, and validate transducing CPP-FP/SP functionality. The protein isolation and DLS-guided buffer screen yield samples with long-term stability. Live-cell fluorescence microscopy and imaging flow cytometry enable discrimination between membrane-bound and internalized signal, providing higher accuracy compared to plate-based readouts. MeCP2 sequence probing has revealed the presence of a CPP-like motif that is critical to its internalization. Finally, validation assays clearly demonstrated CPP-FP/SP activity. This protocol integrates advances in protein biochemistry, structural analysis, and live-cell imaging into a reproducible pipeline adaptable to a wide range of CPP- and SP-based protein constructs and provides a practical framework for downstream mechanistic and therapeutic interventions.