PARPs-DB Project

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We herein describe the architecture and major features of a web-based utility called “PARPs database” (PARPs-DB), which is designed to rationally organize the protein and peptide data generated by the LC-MS/MS analysis of tryptic digest of proteins that co-immunoprecipitate with PARPs proteins into reports meaningful to biological researchers. PARPs-DB offers a LIMS work environment to annotate and study protein-protein interactions and its easy-to-use relational data management system can rapidly supply information pertaining to the biological characteristics of a majority of proteins in a proteomic dataset. The major features of our LIMS are flexibility, compactness, and connectivity to public databases.

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The focus of our laboratory is the study of the action of poly(ADP-ribose) polymerases (PARPs) and their role in the cell. Poly(ADP-ribosylation) is a post-translational protein modification consisting of long chains of poly(ADP-ribose) (pADPr) synthesized by PARPs at the expenses of NAD+. Poly(ADP-ribose) chains are short-lived owing to the activity of the poly(ADP-ribose) glycohydrolase enzyme, which catabolizes the pADPr within minutes of its synthesis15. The PARP family may comprise as many as 17 members which share a common catalytic domain responsible for the synthesis of poly(ADP-ribose)16-18. The best characterized and abundant member of this family is PARP-1, a 113-kDa nuclear protein comprising a DNA-binding domain made of two zinc fingers that allow PARP-1 to be rapidly activated in response to DNA damage. Poly(ADP-ribose) crucially contributes to chromatin remodelling, DNA damage repair, regulation of transcription, and cell division19-21; and PARP-1 is an important actor in many key cellular processes, including BER, transcription, and apoptosis.