A two-step probing method to compare lysine accessibility across macromolecular complex conformations

Structural models of multi-megadalton molecular complexes are appearing in increasing numbers, in large part because of technical advances in cryo-electron microscopy realized over the last decade. However, the inherent complexity of large biological assemblies comprising dozens of components often limits the resolution of structural models. Furthermore, multiple functional configurations of a complex can leave a puzzle as to how one intermediate moves to the next stage. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially powerful for detecting changes in protein-RNA interactions. Probing the E. coli 30S ribosome subunit showed that the reactivity pattern of lysine residues quantitatively reflects structure models from X-ray crystallography. We assessed differences in two conformations of purified human spliceosomes. Our results demonstrate that this method supplies powerful biochemical information that aids in functional interpretation of atomic models of macromolecular complexes at the intermediate resolution often provided by cryo-electron microscopy.