Biological advances using the protein footprinting method covalent protein painting

Research techniques are emerging that focus on determining the confirmation of proteins within cells and tissues. One of these techniques, protein footprinting, uses covalent labeling to mark surface-accessible amino acids on proteins, which allows investigations into conformational changes of a protein, such as locating drug binding or epitope mapping. Like hydrogen-deuterium exchange (HDX), which replaces exchangeable hydrogens on proteins with deuterium, protein footprinting attaches a covalent tag to surface-accessible amino acids. In contrast to HDX, covalent labeling is permanent, which allows sample processing without the need to worry about D/H back-exchange. A potential drawback of protein footprinting has been that fewer labeling sites are available in a protein. To overcome this limitation, highly reactive reagents for covalent labeling (such as free radicals) have been employed to achieve more comprehensive coverage of protein surfaces. But the extreme reactivity of radicals, like oxygen, necessitates their generation in situ and leads to promiscuous labeling that makes data analysis challenging.