Tag Archives: IPI-504

Parkinson’s disease (PD) is a progressive neurodegenerative disorder affecting approximately 1-2%

Parkinson’s disease (PD) is a progressive neurodegenerative disorder affecting approximately 1-2% of the overall population over age 60. and and genes encoding components of the mitochondrial fission/fusion machinery indicate an involvement of the pathway in the regulation of mitochondrial dynamics [11] [12]. Parkin is at steady state essentially cytosolic and recent work has shown IPI-504 that it selectively and rapidly translocates from your cytosol to depolarized mitochondria with low membrane potential and subsequently induces their autophagic removal in a process called mitophagy [13]-[16]. Increasing our knowledge about the interactions between Parkin and other cytoplasmic and mitochondrial proteins will provide further biological insights into Parkin function and the intricate relationships between the multiple functions of Parkin. The identification of such Parkin-binding proteins may have a general role in the pathogenesis of PD Mouse monoclonal to TAB2 and elucidate novel therapeutic targets. In this study we report a comprehensive set of novel candidate Parkin-binding proteins recognized by Tandem Affinity Purification (TAP)/mass spectrometry (MS) conversation screens. Following the established “guilt by association” strategy where proteins/genes are prioritized if they are found to be related to known disease genes and processes [17]-[19] a set of “seed” proteins known to be related to genetic parkinsonism was used to prioritize the candidate IPI-504 Parkin-binding proteins. In particular this set of proteins provided the basis for the prioritization of candidate proteins based on the known interactions to these proteins. In addition it was used in an analysis of PD-related pathways and processes and in the prioritization of the candidate Parkin-binding IPI-504 proteins based on their functional relationships. The candidate proteins were also compared to complementary experimental data from genetic interaction IPI-504 screens in and genome-wide association studies (GWAS) in humans. Our study identified novel candidate Parkin-binding proteins for involvement in cell death processes protein folding and response to unfolded protein the fission/fusion machinery and the mitophagy pathway and the combined results of the bioinformatics analyses were used to prioritize them into different selection levels. Results Protein-protein conversation data for the candidate Parkin-binding proteins obtained from the TAP experiments and the proteins known to cause heritable forms of parkinsonism were derived from public databases and the respective biological processes and pathways were analyzed and compared. Network models were applied to investigate the functional relationships between the candidate Parkin-binding proteins and the proteins related to monogenic parkinsonism. In addition the candidate dataset was compared to results from genetic interaction screens in and human GWAS. The candidate proteins were prioritized into different selection levels which were compared to the results of an independent gene prioritization approach. Finally two candidates were tested for conversation to Parkin by co-immunoprecipitation. TAP results and protein datasets TAP-tagged Parkin made up of protein complexes were purified in a two-stage purification process of protein extracts prepared from whole cell lysates and cytosolic and mitochondrial fractions from HEK293T and SH-SY5Y cells and analyzed by MS. The TAP experiments resulted in different protein datasets outlined in Table 1 (ParkinTAP datasets). In total 203 unique peptides were identified as candidate Parkin-binding proteins (Table 1; ParkinTAP candidates); approximately 50% of the candidate proteins were recognized in the mitochondrial fractions (Mito dataset) and 50% in the cytosolic fractions (Cyto dataset) with an overlap of 49 proteins between the fractions. Table 1 Protein datasets. In addition the following datasets were used in the analyses: MonogenicPD which includes proteins encoded by genes implicated in monogenic forms of parkinsonism [20] Pink1TAP which provides a list of candidate PINK1-interacting proteins recognized in a previous TAP study [21] and ParkinIP PINK1IP and MonogenicPDIP which include proteins known to interact with Parkin PINK1 and proteins from MonogenicPD respectively. The dataset RelatedPD includes the ParkinIP and MonogenicPD datasets. The previously reported Pink1TAP dataset mostly overlaps with the ParkinTAP candidates of the present study with the exception of PINK1 itself and.