Peroxidase-catalyzed proximity labeling to survey the proteome of nanomaterial-cell interface during macropinocytosis-mediated internalization

Abstract

Abstract Nanomaterials often need to interact with proteins on the plasma membrane to get cross and access their intracellular targets. Therefore, to fully understand the cell entry mechanism, it is of vital importance to gain a comprehensive insight into the proteome at the interface when nanomaterials encounter the cells. However, only very few studies have focused on this aspect. Here, we reported a peroxidase-based proximity labeling method to survey the proteome at the nanoparticle (NP)-cell interface. Horseradish peroxidase (HRP) was conjugated to a variety of NPs and other ligand types while still being able to biotinylate the proteins surrounding NP (or ligand)-receptor complexes. Using two NP-based tracers for macropinocytosis (MP), which is highly relevant to NP internalization, we performed a proteomic survey and revealed the interface proteome difference between traditional and receptor-dependent MP. Moreover, our survey found that E-cadherin (CDH1), while not serving as the primary receptor, is present at the NP-cell interface and is functionally important for the cellular uptake of a wide variety of NPs. Overall, by integrating nanotechnology with proximity labeling, our study provides an approach to map the proteome of NP-cell interface for investigating the molecular mechanism of NP and macromolecule internalization into cells.