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

David-Paul Minde,Manasa Ramakrishna,Kathryn S. Lilley

doi:10.1038/s42003-020-0758-y

David-Paul Minde, Manasa Ramakrishna + Show 1 more

Open Access

https://doi.org/10.1038/s42003-020-0758-y

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Abstract

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 human cells. Indeed, we observed increased biotinylation density in predicted IDRs in several cellular compartments >20,000 biotin sites from four 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 s, 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.

Highlights

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
Disordered regions (IDRs) within proteins often overlap with sites of alternative splicing and post-translational modifications (PTMs)
Interfaces of foldable Intrinsically Disordered Regions (IDRs) tend to be larger than contacts between two ordered proteins and the exposed hydrophobic surface area is often larger, which in some cases limits the solubility of intrinsically disordered proteins (IDPs) and requires tighter subcellular regulation of IDPs compared to ordered proteins[18,19,20]

Summary

Introduction

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. Disordered regions (IDRs) within proteins often overlap with sites of alternative splicing and post-translational modifications (PTMs). Both splicing and PTMs together are estimated to expand the number of proteoforms into the millions despite a relatively compact (~20,000 large) proteincoding human genome[5,6,7]. Co-evolutionary inference suggests that many predicted disordered regions have the capacity to fold and are selected in evolution by contact constraints imposed by the folded conformation in the presence of cellular binding partners[17] In other words, such binding-coupled folding IDPs look similar to folded proteins as determined by (co)evolution statistical analysis. Interfaces of foldable IDRs tend to be larger than contacts between two ordered proteins and the exposed hydrophobic surface area is often larger, which in some cases limits the solubility of IDPs and requires tighter subcellular regulation of IDPs compared to ordered proteins[18,19,20]

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