Mass spectrometry provides a unique view of large intracellular protein machines. The study of weakly-bound, protein noncovalent complexes by electrospray ionization mass spectrometry (ESI-MS) provides a sensitive and accurate means to determine assembly size and binding partner stoichiometry for a number of important complexes. In addition to identifying the components that are involved in protein interaction networks, MS studies can identify and elucidate the geometry and interactions of protein machines, such as the 14 MDa vault, a ribonucleoprotein particle implicated in multidrug resistance. The proteasome is an intracellular protease complex that is part of the ubiquitin-proteasome pathway responsible for degradation of most proteins in the cytosol and in the nucleus. The 20S proteasome is composed of 4 heptameric rings stacked in a barrel fashion, forming an internal cavity. ESI-MS of the full 20S proteasome yields a MW of 690 kDa. Dissociation of the gas phase complex generates product ions from the loss of only the outer alpha-subunits, consistent with the known architecture of the complex. Proteasome function may be important in a number of neurological diseases such as Parkinson’s disease (PD). The improper degradation of alpha-synuclein (AS) by the proteasome may account for its presence in Lewy bodies, a hallmark of PD. The protease activity profile of the proteasome on substrates such as AS can be easily studied by mass spectrometry.
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