title: Homology modeling and comparative profiling of superoxide dismutase among extremophiles: exiguobacterium as a model organism.
abstract: Superoxide dismutase (SOD), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. Apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. Here, we have discussed the conservation and the prevalence of SODs among 21 representative extremophiles. A systematic investigation of aligned amino acid sequences of SOD from all the selected extremophiles revealed a consensus motif D-[VLE]-[FW]-E-H-[AS]-Y-[YM]. To computationally predict the correlation of SOD with the various stress conditions encountered by these extremophiles, Exiguobacterium was selected as a model organism which is known to survive under various adverse extremophilic conditions. Interestingly, our phylogenetic study based on SOD homology revealed that Exiguobacterium sibiricum was one of the closest neighbors of Deinococcus radiodurans and Thermus thermophilus. Next, we sought to predict 3-D model structure of SOD for E. sibiricum (PMDB ID: 0078260), which showed >95 % similarity with D. radiodurans R1 SOD. The reliability of the predicted SOD model was checked by using various validation metrics, including Ramachandran plot, Z-score and normalized qualitative model energy analysis score. Further, various physicochemical properties of E. sibiricum SOD were calculated using different prominent resources.
authors.affiliation: CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.
authors.forename: Rajiv
authors.initials: R
authors.lastname: Pathak
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, Delhi, 110067 India.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Narang
authors.affiliation: CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.
authors.forename: Muktesh
authors.initials: M
authors.lastname: Chandra
authors.affiliation: Division of Radiation Biotechnology, Institute of Nuclear Medicine and Allied Sciences, Timarpur, Delhi, 110007 India.
authors.forename: Raj
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Department of Microbiology, Ch. Charan Singh University, Meerut, 250004 India.
authors.forename: P K
authors.initials: PK
authors.lastname: Sharma
authors.affiliation: CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.
authors.forename: Hemant K
authors.initials: HK
authors.lastname: Gautam
keywords: Exiguobacterium sp.; Extremophiles; Homology modeling; Superoxide dismutase