Biotin proximity tagging favors unfolded proteins and enables the study of intrinsically disordered regions

Intrinsically Disordered Regions (IDRs) are enriched in disease-linked proteins known to have multiple post-translational modifications, but there is limited in vivo information about how locally unfolded protein regions contribute to biological functions. We reasoned that IDRs should be more accessible to targeted in vivo biotinylation than ordered protein regions, if they retain their flexibility in vivo. Indeed, we observed increased biotinylation density in predicted IDRs in several cellular compartments >20 000 biotin sites from four human proximity proteomics studies. We show that in a biotin ‘painting’ time course experiment biotinylation events in Escherichia coli ribosomes progress from unfolded and exposed regions at 10 seconds, to structured and less accessible regions after five minutes. We conclude that biotin proximity tagging favours sites of local disorder in proteins and suggest the possibility of using biotin ‘painting’ as a method to gain unique insights into in vivo condition-dependent subcellular plasticity of proteins.