Transient Cross-linking Mass Spectrometry: Taking Conformational Snapshots of Proteins

The dynamic nature of protein conformations is central to their biological functions. Conventional structural biology techniques provide static snapshots, whereas a comprehensive understanding requires an analysis of the dynamic conformations. In this study, we develop a transient cross-linking mass spectrometry method using a photo-cross-linker DCD. This cross-linker can be transiently activated to accomplish cross-linking, and with sample freezing, transient conformations are preserved, allowing temporal control and on-demand cross-linking. Its cross-linking site covers all amino acids, exhibiting diversity and providing rich structural information. Additionally, we develop a data-processing strategy by integrating a DCD-specific reporter ion and a defined ambiguous site annotation criterion, thereby ensuring the confidence in identification and cross-link site annotation. Thus, the developed transient cross-linking mass spectrometry, leveraging the distinctive features of DCD, has enabled us to analyze protein conformations and protein complexes with high resolution, take conformational snapshots, discern the coexistence of conformational intermediates, and decipher conformational fluctuations, shedding light on how proteins conformationally respond to biological signals and engage with interacting partners. Our results highlight DCD’s potential for probing protein conformational changes, facilitating the elucidation of their pivotal roles within biological systems.