Proteomic identification of novel proteins associated with Lewy bodies

The manifestation of Lewy bodies (LB) in the brain is a hallmark of Parkinson's disease. Here, we present a comprehensive analysis of protein elements in Lewy bodies by comparative mass spectrometry. Cortical LB inclusions were enriched by sucrose gradient centrifugation from postmortem brains, and a negative control sample was prepared from specimen without LB pathology. Whereas -550 proteins were identified in the LB-enriched sample by mass spectrometry, quantitative comparison with the control sample revealed that ∼40 proteins were co-enriched with α-synuclein, the major component in Lewy bodies. As expected, the list of proteins included previously reported constituents, such as those involved in protein folding, membrane trafficking and oxidative stress. More interestingly, we discovered in the LB-enriched sample several kinases (MAPKK1/MEK1, protein kinase C, and doublecortin-like kinase), a novel deubiquitinating enzyme (otubain 1), and numerous ubiquitin ligases (KPC and SCF). The proteomic studies provide enzyme candidates to investigate the regulation of α-synuclein and/or other LB proteins, which may contribute to the formation of Lewy bodies and the toxicity of α-synuclein in the related neurodegenerative disorders.