Exploring the Structural Stability of Stable Protein 1 Using Native Mass Spectrometry

Abstract

Self-assembly of the proteins into the unique structures with a high-order complexity occurs throughout all living organisms and in nearly all living tissues. The abnormal association of the biological complexes is involved in a variety of pathologies with different level of severity including paediatric neurodegenerative disorders, traumatic brain injuries, Parkinson disease, heart abnormalities, diabetes, atherosclerosis and many types of cancers. The extensive implication of the complex protein structures requires a functional method to analyse topology, inter-subunit interactions, lower order architecture and overall stability. Native mass spectrometry (MS) allows the study protein complexes in their native state and in some cases even straight out of their physiologic environment. Coupling mass determination of the entire complex with the well-established fragmentation techniques such as collision induced dissociation (CID) and electron capture dissociation (ECD) allows assessment of the oligomeric state of the protein, strength of the interactive interfaces and the level of compactness. The current drawback of the existing native MS techniques is disproportional charge distribution during the ionisation and fragmentation processes, which in some cases may result in non-informative spectra in respect to the oligomeric state and interaction stability. Identifying factors involved in the asymmetric (uneven) charge partitioning will allow to rigorously control gas phase disassembly of the protein complexes and maximise extraction of useful information from the experiments. The aim of this work is to investigate the aspects of intrinsic protein characteristics, properties of the solutions and instrument parameters that govern protein complexes to produce certain dissociation pattern and to provide recommendation on how to extract structural information from the CID and ECD spectra. The boiling stable protein Stable Protein 1 is used as a model system to understand the implications for highly stable proteins. The first experimental part includes analysis of the quaternary structure of the dodecameric complex Stable Protein 1 (SP1) and two mutants using CID, the second part involves comparison of individual subunit's tertiary, secondary and primary structure obtained via different fragmentation pathways using combination of CID and ECD techniques. SP1 preserved its structural integrity in gas phase and dissociated into stable compact oligomers under CID conditions, regardless of the fragmentation route it followed.