Conformational ensembles of intrinsically disordered proteins by native-MS

Mass spectrometry (MS) has developed into a central tool of biochemistry and structural biology. The so-called “native” MS, based on nano-electrospray-ionization (nano-ESI), has paved the way to protein folding and binding studies by MS techniques. Here, native MS and charge-state-distribution (CSD) analysis is applied to the investigation of protein conformational transitions and intermolecular interactions, with a special focus on intrinsically disordered proteins (IDPs). IDPs lack ordered tridimensional structure under physiological conditions, while performing crucial regulatory functions. Their structural characterization implies description of the dynamic conformational ensembles populated by these polymers in solution, posing major challenges to biophysical methods. It is shown that the conformational ensemble of natural and synthetic IDPs can be depicted in terms of compactness and solvent-accessible surface area (SASA), describing rearrangements induced by solvent conditions, ligand binding and post-translational modifications. Finally, an MS-based compaction index (CI) is introduced, evaluating SASA with reference to globular and fully disorder proteins. Such a parameter can be calculated for single conformers or the whole conformational ensemble, offering a continuous index for IDP comparison and classification.