Research

a. Super-Resolution Proximity Labeling (SR-PL)

Proximity labeling (PL) is a powerful tool for local proteome mapping in live cells. PL's enzymatic reactions are done in spatially-restricted manner, however, most current works using PL utilize conventional mass analysis which detects the "nonbiotinylated peptides" of streptavidin bead-enriched proteins, which usually provide ambiguous and low resolution result.  Therefore, we developed a direct mass analysis workflow (Spot-ID) for the mass detection of "biotinylated" PTM sites for APEX (e.g. Y+331 Da) and BioID/TurboID (e.g. K+226 Da) which reflect true biotinylation event at the single amino acid residue level.  Our "super-resolution" proximity labeling (SR-PL) have been applied to reveal the local proteome of interest such as Inner mitochondrial membrane (Lee SY et al. JACS, 2017), Mitochondria-ER contact site (Kwak et al. PNAS, 2020), Liver-specific secretome (Kim KE et al. Nat. Commun. 2021) and muscle-specific mitochondrial matrix (Park et al. 2022). We also applied this technique for the finding of new rapamycin interacting partner (i.e. Lee SY et al. ACS Cent. Sci. , 2016), NSUN2 in the mitochondrial matrix (Van Haute et al. NAR, 2019) and EXD2 at the outer mitochondrial membrane (Park et al. NAR, 2019), respectively.  We recently presented that our SR-PL method can be employed in the identification of drug-binding protein in live cells (PROCID, Kwak and Park et al. Cell Chem Biol, 2022). Our super-resolution PL approach is recently highlighted in Kang MG et al. ACR, 2022.  

b.  Mitoatlas project (www.mitoatlas.org)

So far ~1,200 different proteins are known to be targeted to the mitochondria in human cells. These proteins are not uniformly distributed throughout the mitochondria, but they are located in highly specific targeted spaces and form diverse protein complexes that conduct a variety of biochemical reactions for cellular metabolism. To map localized protein information in a sub-mitochondrial complex of interest, we employed our own SR-PL (super-resolution proximity labeling) technique to have a sub-mitochondrial proteomic architecture at single-residue level . Using SR-PL, we are now constructing a super-resolution mitochondrial proteome map (Mitoatlas, www.mitoatlas.org) with Prof. Jong-Seo Kim's lab at SNU Biology. 

c. Fluorescent Reporter development

Genetically encodable fluorescent reporters for calcium ion, pH, ROS level are now essential tools for biological research. However, there are still many biomolecules and biological events that need to be real-time monitored with the new fluorescent reporter system. We are currently developing a new fluorescent reporter system for monitoring biochemical reactions in mitochondria. We have developed endogenous bilirubin mapping system using UnaG (Park et al. ACS Chem Biol. 2016) and endogenous ROS recording system using APEX2 (Mishra and Park et al. Anal. Chem. 2022).  We believe that our new reporter system can lead to a deeper understanding of mitochondrial biology and a new drug discovery.