title: A comprehensive computational study on pathogenic mis-sense mutations spanning the RING2 and REP domains of Parkin protein.
abstract: Various mutations in PARK2 gene, which encodes the protein parkin, are significantly associated with the onset of autosomal recessive juvenile Parkinson (ARJP) in neuronal cells. Parkin is a multi domain protein, the N-terminal part contains the Ubl and the C-terminal part consists of four zinc coordinating domains, viz., RING0, RING1, in between ring (IBR) and RING2. Disease mutations are spread over all the domains of Parkin, although mutations in some regions may affect the functionality of Parkin more adversely. The mutations in the RING2 domain are seen to abolish the neuroprotective E3 ligase activity of Parkin. In this current work, we carried out detailed in silico analysis to study the extent of pathogenicity of mutations spanning the Parkin RING2 domain and the adjoining REP region by SIFT, Mutation Accessor, PolyPhen2, SNPs and GO, GV/GD and I-mutant. To study the structural and functional implications of these mutations on RING2-REP domain of Parkin, we studied the solvent accessibility (SASA/RSA), hydrophobicity, intra-molecular hydrogen bonding profile and domain analysis by various computational tools. Finally, we analysed the interaction energy profiles of the mutants and compared them to the wild type protein using Discovery studio 2.5. By comparing the various analyses it could be safely concluded that except P437L and A379V mutations, all other mutations were potentially deleterious affecting various structural aspects of RING2 domain architecture. This study is based purely on computational approach which has the potential to identify disease mutations and the information could further be used in treatment of diseases and prognosis.
authors.affiliation: Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, Nadia, India.
authors.forename: Ria
authors.initials: R
authors.lastname: Biswas
authors.affiliation: Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, Nadia, India. Electronic address: angshu@klyuniv.ac.in.
authors.forename: Angshuman
authors.initials: A
authors.lastname: Bagchi
mesh_terms: D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D020125:Mutation, Missense; D010300:Parkinson Disease / Q000235:genetics* / Q000378:metabolism; D011487:Protein Conformation; D000072417:Protein Domains; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism
chemical_list: D044767:Ubiquitin-Protein Ligases; C111567:parkin protein
keywords: E3 ligase; Interaction energy; Mis-sense mutation; Parkin; Parkinson's disease; Protein docking; RING2 domain; Ubiquitination