Comparative Analysis and Modeling of Superoxide Dismutases (SODs) in Brachypodium distachyon L.

FİLİZ E., Koc I., ÖZYİĞİT İ. İ.

APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, cilt.173, sa.5, ss.1183-1196, 2014 (SCI-Expanded) identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 173 Sayı: 5
  • Basım Tarihi: 2014
  • Doi Numarası: 10.1007/s12010-014-0922-2
  • Dergi Adı: APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Sayfa Sayıları: ss.1183-1196
  • Anahtar Kelimeler: Superoxide dismutase, Antioxidant proteins, Brachypodium distachyon, 3D modeling, In silico analysis, ESCHERICHIA-COLI, PROTEIN, EVOLUTION, STRESS, GENE, MITOCHONDRIAL, PHYLOGENIES, EXPRESSION, PREDICTION, ENZYME
  • Marmara Üniversitesi Adresli: Evet

Özet

Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme catalyzing the dismutation of superoxide radical to hydrogen peroxide and dioxygen. To date, four types of SODs - Cu/ZnSOD, MnSOD, FeSOD, and NiSOD - have been identified. In this study, SOD proteins of Brachypodium distachyon (L.) Beauv. were screened by utilization of bioinformatics approaches. According to our results, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found to be in basic and acidic character, respectively. Domain analyzes of SOD proteins revealed that iron/manganese SOD and copper/zinc SOD were within studied SOD proteins. Based on the seconder structure analyzes, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found as having similar sheets, turns and coils. Although helical structures were noticed in the types of Mn/FeSODs, no the type of Cu/ZnSODs were identified having helical structures. The predicted binding sites of Fe/MnSODs and Cu/ZnSODs were confirmed for having His-His-Asp-His and His-His-His-Asp-Ser residues with different positions, respectively. The 3D structure analyzes of SODs revealed that some structural divergences were observed in patterns of SODs domains. Based on phylogenetic analysis, Mn/FeSODs were found to have similarities whereas Cu/ZnSODs were clustered independently in phylogenetic tree.