Table 2.
Sample of proximity labeling studies for mapping PPIs.
| PPI Category | Note(s) | Enzyme | Bait(s) | Reference |
|---|---|---|---|---|
| Protein aggregates | Insoluble complexes by definition | BioID | TDP43 aggregates | 74 |
| Nuclear membrane and nuclear structures | Low solubility complexes due to membrane function and/or complex size | BioID | Lamin A | 21 |
| BioID | Lamin B1 | 72 | ||
| BioID | Various nuclear transport receptors | 73 | ||
| BioID2 | Lamin A, Sun2 | 71 | ||
| Enzyme-substrate interactions | Low-affinity/transient interactions due to enzyme turnover | BioID | Hippo pathway (including Mst1/Mst2 kinases) | 50 |
| BioID | p190/p210 BCR-ABL kinases | 55 | ||
| APEX2 | p38 MAPK | 48 | ||
| BioID2 | p38 MAPK | 49 | ||
| BioID | SCF E3 ligases | 53 | ||
| APEX2 | KREP, Kelch E3 ligase adaptors | 54 | ||
| BioID | ClpP protease | 142 | ||
| Other signaling pathways | Low-affinity/transient interactions | BioID2 | TLR9, MYD88 (NFκB pathway) | 76 |
| BioID2 | KRas4B | 77 | ||
| APEX2 | Cav1.2 GPCR (adrenergic pathway) | 51 | ||
| Intracellular sorting | Transient interactions, low-affinity interactors for trafficking machinery | BioID | Dynein machinery | 143 |
| BioID | Golgin-97, Golgin-245 | 144 | ||
| APEX2 | LAMP1 | 58 | ||
| BioID2 | Golgi glycosyltransferases | 145 | ||
| Dynamic processes | Utilized APEX for minute-scale interactome capture | APEX2 | DOR (GPCR) | 41 |
| APEX2 | AT1R, β2AR (GPCRs) | 52 | ||
| APEX2 | MOR (GPCR) | 87 | ||
| APEX2 | Fzd9b (GPCR) | 81 | ||
| APEX2 | Gal8, Gal3, Gal9 | 146 | ||
| APEX2 | TssA (bacteria) | 60 | ||
| In vivo PL in plants | Proximity labeling in plant systems | BioID | OsFD2 | 147 |
| BioID | HopF2 | 65 | ||
| BioID | AvrPto | 95 | ||
| TurboID | N NLR | 96 | ||
| TurboID | FAMA | 33 | ||
| In vivo PL in other organisms | Biotin-ligase based in vivo PL | BioID | Sun1 (Dictyostelium) | 97 |
| BioID | CDK5RAP2 (Dictyostelium) | 98 | ||
| BioID | ISP3 (Toxoplasma gondii) | 100 | ||
| BioID | Cyst wall proteins (Toxoplasma gondii) | 103 | ||
| BioID | TbMORN1 (Trypanosoma brucei) | 99 | ||
| BioID | TbPLK (Trypanosoma brucei) | 101 | ||
| BioID | Parasitophorous vacuole (Plasmodium falciparum) | 102 | ||
| BioID | c-MYC (mouse xenograft) | 68 | ||
| BioID | Gephyrin (mouse) | 67 | ||
| TurboID | Rmt3 (Schizosaccharomyces pombe) | 62 | ||
| TurboID | Dcp-1, Drice, Dronc (Drosophila melanogaster) | 104 |