Mimicking of a Transient Protein Binding in Mammalian Cells Using a Functionalized Magnetic Nanoparticle

Identification of binding proteins is essential for uncovering biological mechanisms of functional small molecules and proteins, but if the binding is transient it may be quite difficult to find the binding proteins using cell extracts that is commonly used for target identification methods. Usually sticky proteins bind to bait molecule first as long as cell extracts are used. In such cases, it would be very difficult to find transient binding proteins. The best way to circumvent the non-specific bindings might be putting bait molecules into living cells and collects the baits after a certain period of incubation time. In here, we evaluated a new target identification method in living cells with magnetic nanoparticles. For the proof-of-concept, we reproduced a transient interaction between peroxisomal proteins and Pex5p, the peroxisome guiding protein. To that end, carboxyl group-functionalized magnetic nanoparticles were labeled with peroxisomal targeting signal 1 (PTS1) peptide to mimic peroxisomal proteins. The PTS1-labeled magnetic nanoparticles translocated into peroxisomes in the mammalian cells, during which they transiently interacted with Pex5p. These results were confirmed using a fluorescence microscope and "in cell pull-down" experiments. Conclusively, the transient interaction between peroxisomal proteins and Pex5p in cells was reproduced with the PTS1-labeled magnetic nanoparticles in living cells by showing its sequential translocation into peroxisomes and transient interaction with Pex5p in parallel. This result indicates that a magnetic nanoparticle can be a useful tool for analyzing dynamic change of interacting proteins to a functional molecule in living cells depending on circumstances the cells encounter.