Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform

James V. Oakley, Benito F. Buksh, David F. Fernández, Daniel G. Oblinsky, Ciaran P. Seath, Jacob B. Geri, Gregory D. Scholes, David W.C. MacMillan

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently "tag"proximal biomolecules. The physical distance that the probes diffuse determines the effective labeling radius of the PLP and is a critical parameter that influences the scale and resolution of interactome mapping. As such, by expanding the degrees of labeling resolution offered by PLPs, it is possible to better capture the various size scales of interactomes. At present, however, there is little quantitative understanding of the labeling radii of different PLPs. Here, we report the development of a superresolution microscopy-based assay for the direct quantification of PLP labeling radii. Using this assay, we provide direct extracellular measurements of the labeling radii of state-of-the-art antibody-targeted PLPs, including the peroxidase-based phenoxy radical platform (269 ± 41 nm) and the high-resolution iridium-catalyzed μMap technology (54 ± 12 nm). Last, we apply these insights to the development of a molecular diffusion-based approach to tuning PLP resolution and introduce a new aryl-azide-based μMap platform with an intermediate labeling radius (80 ± 28 nm).

Original languageEnglish (US)
Article numbere2203027119
JournalProceedings of the National Academy of Sciences of the United States of America
Volume119
Issue number32
DOIs
StatePublished - Aug 9 2022

All Science Journal Classification (ASJC) codes

  • General

Keywords

  • STED microscopy
  • photoredox catalysis
  • proximity labeling

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