Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches

Mol Cell Proteomics. 2020 May;19(5):757-773. doi: 10.1074/mcp.R120.001941. Epub 2020 Mar 3.


The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.

Keywords: APEX; BioID; Protein-protein interactions; biotin ligase; cellular organelles; enzymes; mass spectrometry; molecular biology; peroxidase; protein engineering; proximity-dependent biotinylation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Biotinylation
  • Enzymes / metabolism*
  • Humans
  • Proteomics*
  • Staining and Labeling
  • Substrate Specificity


  • Enzymes

Associated data

  • PDB/2EWN
  • PDB/3EFS
  • PDB/1OAG

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