Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry (qCLMS). Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of ∼10 Å and use MS2 reporter ions for relative quantification of Qlinker-modified peptides. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints the key conformational and structural changes in biosensors and the RNA polymerase II (pol II) complex.