TY - JOUR
T1 - Homology Modeling and Comparative Profiling of Superoxide Dismutase Among Extremophiles
T2 - Exiguobacterium as a Model Organism
AU - Pathak, Rajiv
AU - Narang, Pankaj
AU - Chandra, Muktesh
AU - Kumar, Raj
AU - Sharma, P. K.
AU - Gautam, Hemant K.
N1 - Funding Information:
Fig. 6 a Ramachandran plot of predicted model of E. sibiricum superoxide dismutase (SOD) representing 166 residues in the most favoured region (red), 9 in additional allowed regions (yellow) and 2 in generously allowed regions (light yellow), 2 in disallowed regions (white) with 13 glycine (shown in triangle) and 8 proline residues, respectively; b A Z-score of -8.36 for predicted model with 202 residues calculated using PROSA-web is shown as black rectangle Acknowledgments The authors are grateful to Dr. Rajesh Gokhle, Director of CSIR-IGIB for providing infrastructural facilities and financial assistance from CSIR (BSC0302). R Pathak would also like to acknowledge the University Grants Commission (UGC) India, for providing Senior Research Fellowship. P Narang acknowledges the Department of Biotechnology for providing BINC fellowship.
Publisher Copyright:
© 2014, Association of Microbiologists of India.
PY - 2014/10/7
Y1 - 2014/10/7
N2 - 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.
AB - 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.
KW - Exiguobacterium sp
KW - Extremophiles
KW - Homology modeling
KW - Superoxide dismutase
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U2 - 10.1007/s12088-014-0482-8
DO - 10.1007/s12088-014-0482-8
M3 - Article
AN - SCOPUS:84918799703
SN - 0046-8991
VL - 54
SP - 450
EP - 458
JO - Indian Journal of Microbiology
JF - Indian Journal of Microbiology
IS - 4
ER -