Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells

The function of a protein is determined by its structure, which may change dynamically in response to post-translational modifications, interaction with other molecules, or environmental factors like temperature. Limited proteolysis-coupled mass spectrometry (LiP-MS) captures such structural alterations on a proteome-wide scale via the detection of altered protease susceptibility patterns of proteins. However, this technique has so far required cell lysis, which exposes proteins to non-native conditions and can disrupt labile interactions such as those occurring within biomolecular condensates. To study protein structures directly within cells, we developed in-cell LiP-MS. We optimized conditions for introduction of proteinase K into human cells using electroporation and validated that intracellular cleavage occurs. In-cell LiP-MS captured the known binding of rapamycin to FKBP1A within the cell. Moreover, it detected global protein structural alterations upon sodium arsenite treatment and captured the structural dynamics of hundreds of proteins from biomolecular condensates with peptide level resolution and within live human cells. The data allowed monitoring of structural alterations of individual sites on the involved proteins, such as known RNA-binding and intrinsically-disordered regions, and dissected the timing of the different events. We detected known (G3BP1) and novel structural alterations of proteins from stress granules as well as from nuclear speckles and validated alteration of nuclear speckles by fluorescence microscopy and of the protein SERBP1 by polysome profiling. Our dataset further provides a resource describing the structural changes of human proteins in response to a cellular stress leading to biomolecular condensation and pinpoints structurally altered regions. Comparison of LiP-based structural fingerprints before and after cell lysis revealed which human proteins are susceptible to structural change upon cell lysis, therefore guiding the design of future experiments requiring native protein structures.