In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Rekik, Imen; Chaabene, Zayneb; Grubb, C.; Drira, Noureddine; Cheour, Foued; Elleuch, Amine
• Is Part Of: Theoretical biology and medical modelling. Volume 12:Issue 1(2015)
• Page Start: 1
• Page End: 14
• Publication Date: 2015-12
• Subjects: Biology -- Mathematical models -- Periodicals; Biology -- Periodicals; Medical sciences -- Periodicals; 570.15118
• DOI: 10.1186/s12976-015-0013-2
• Languages: English
• ISSNs: 1742-4682

Abstract

Abstract Background DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic.MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities. Methods The present study aimed toin silico characterization and molecular modeling ofMRE11 fromPhoenix dactylifera L cv deglet nour (DnMRE11 ) by various bioinformatic approaches. To identifyDnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program. Results TheDnMRE11 protein length was 726 amino acids. The results of HUMMER show thatDnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure ofDnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction ofDnMRE11 protein with two Mn2+ ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species. Conclusions A model structure ofDnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn2+ and dAMP).