A Photo‐Caged Cross‐Linker for Identifying Protein‐Protein Interactions

Cross-linking mass spectrometry (XL-MS) has seen significant improvements which have enhanced its utility for studying protein-protein interactions (PPIs), primarily due to the emergence of novel crosslinkers and the development of streamlined analysis workflows. Nevertheless, poor membrane permeability and side reactions with water limit the extent of productive intracellular crosslinking events that can be achieved with current crosslinkers. To address these problems, we have synthesized a novel crosslinker with o-nitrobenzyl-based photoresponsive groups. These o-nitrobenzyl ester (o-NBE) groups enhance the stability and hydrophobic properties of the crosslinker and add the potential for temporal resolution, i. e. the ability to control the initiation of the crosslinking reaction. Upon exposure to UV light the resulting aldehyde product reacts with adjacent amino groups and subsequent reductive amination of the formed Schiff-bases yields stable secondary amine linkages. This controlled activation mechanism enables precise UV-triggered protein crosslinking. We demonstrate proof-of principle of our o-NBE cross-linker to reliably detect PPIs by XL-MS using a recombinant model protein. We also demonstrate its ability to enter intact Hela cells, thereby indicating its future potential as a useful tool to study PPIs within the cellular environment.