Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source

The method of synchrotron X-ray protein footprinting (XF-MS) is used to determine protein conformational changes, folding, protein-protein and protein-ligand interactions, providing information which is often difficult to obtain using X-ray crystallography and other common structural biology methods 1 G. Xu and M.R. Chance, Chemical Reviews 107, 3514–3543 (2007).Crossref], PubMed], Web of Science ®] , Google Scholar]–3 V.N. Bavro, Biochem Soc Trans 43, 983–994 (2015).Crossref], PubMed], Web of Science ®] , Google Scholar]]. The technique uses comparative in situ labeling of solvent-accessible side chains by highly reactive hydroxyl radicals (?OH) in buffered aqueous solution under different assay conditions. In regions where a protein is folded or binds a partner, these ?OH susceptible sites are inaccessible to solvent, and therefore protected from labeling. The ?OH are generated by the ionization of water using high-flux-density X-rays. High-flux density is a key factor for XF-MS labeling because obtaining an adequate steady-state concentration of hydroxyl radical within a short irradiation time is necessary to minimize radiation-induced secondary damage and also to overcome various scavenging reactions that reduce the yield of labeled side chains.