Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins.

Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data. [Display omitted] Sarnowski et al. review methods for the analysis of protein-RNA complexes by cross-linking mass spectrometry. Topics covered include protein-protein cross-linking in ribonucleoproteins for structural analysis; the identification of RNA-binding proteins; and the identification of specific RNA-interacting regions on proteins with and without the simultaneous identification of protein-binding sites on RNA. [ABSTRACT FROM AUTHOR]