In silico comparative analysis and expression profile of antioxidant proteins in plants

Sheoran, Sonia; Pandey, Bharati; Sharma, Pradeep; Narwal, Sneh; Singh, Ratna; Sharma, Indu; Chatrath, Ravish

doi:10.4238/2013.february.27.3

Cited by 16 publications

(5 citation statements)

References 42 publications

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“…And lastly, the ASN_GLYCOSYLATION_SITE (N-linked glycosylation) (Table), which is associated with Glycosylation, a significant post-translational modification, and is known to influence protein folding, localization and trafficking, protein solubility, biological activity and cell-cell interactions [20]. In MnSOD, the families PKC_PHOSPHO_SITE, CK 2_PHOSPHO_SITE, N-myristoylation site, AMP_PHOPHO_SITE, and ASN_GLYCOSYLATION_SITE were 2, 4, 6, 4 amino acid in length, amongst them AMP_PHOSPHO_SITE was only present in 4 out of 16 species ( G.max, T.aestivum, O.sativa , and A.thaliana )[21]. The PKC_PHOSPHO_SITE was absent in 3 species and present in rest with a signature sequence of [ST]-x-[RK], variable at 2 nd position, and more or less conserved at one and 3 rd position.…”

Section: Resultsmentioning

confidence: 99%

Comparative Insilco functional, structural and phylogenetic characterization of plant Mn-Superoxide Dismutase

Gangwar

2022

Preprint

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The environmental stress is jeopardizing the production as well as the survival of plants. This stress leads to the emergence of ROS, a toxic byproduct of several metabolic processes. To combat the ROS plant possess definite defense machinery, superoxide dismutase is one of the antioxidant enzymes responsible for effectively eradicating these ROS. Amongst several SOD, MnSOD is specialized in eliminating the ROS from mitochondria, a site for cellular energy production. In this study, the MnSOD from 16 plants was considered, and its physiochemical and structural properties were predicted using various computational tools. The physiochemical characterization reveals protein properties such as Mw, PI, AI, GRAVY, and II. The secondary structure and the motif analysis revealed these proteins' functional characteristics. The 3D structure of several proteins was not available, so the SWISS model was used for the homology modeling. The quality of the predicted protein structures was verified using the Ramachandran Plot, VERIFY 3D, and PROCHECK under the SAVES server. These data would provide a foundation for structural and functional characterization of potential MnSOD yet to be characterized, which is expected to enhance the knowledge about its metal binding and catalytic efficiency for future applications.

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Section: Resultsmentioning

confidence: 99%

Comparative Insilco functional, structural and phylogenetic characterization of plant Mn-Superoxide Dismutase

Gangwar

2022

Preprint

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“…Thus, indicating the possibility of their orthologous origin [23]. Many scientists are pursuing similar in-silico (bioinformatics) approaches to identify genes related to stress tolerance in plants from available gene pool of plant genomes [24,25]. This saves researchers from unwanted waste of time and potential funds.…”

Section: Deduction Of Secondary and Tertiary Structures Of Proteinsmentioning

confidence: 99%

Computational identification of six salt stress responsive genes in Cynara scolymus L.

Baloch¹,

Johar

Alvi

et al. 2020

PAB

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Cynara scolymus L. is a perennial plant belonging to family Asteracea. It has many traditional and medicinal values and is also used as a source of vegetable in many countries. This plant thrives well in saline areas and is considered to be moderately salt tolerant but very little information is available about its salt stress tolerance mechanism. In this study six (6) salt stress responsive genes (Four up-regulated i.e. CSD1, RCI3, AFB3, HVA22A and two down-regulated i.e. CSD2, MSD1) were identified in Cynara scolymus L. by using homology search approach with the help of various bioinformatics tools/resources (BLASTn, BLASTp, ORF finder, CD search, Clustal Omega, ProtParam and Phyre2). Furthermore, the secondary and tertiary structures of reference and target genes were predicted and compared for confidence and similarities in structure. All selected salt stress responsive genes were predicted in Cynara scolymus through computational analysis of 36,323 ESTs. The EST based identification of these genes is a confirmation of their expression and these findings will help us understand the salt stress tolerance mechanism in this important plant.

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“…The amino acid and atomic compositions are self-explanatory. All the other parameters will be explained below [13].…”

Section: Identification Of Amino Acid Percentage Composition and Phys...mentioning

confidence: 99%

Interleukin 3, Interleukin 5, and Granulocyte–Macrophage Colony‐Stimulating Factor

Llop‐Guevara¹,

Marcinko²,

Fattouh³

et al. 2011

Inflammation and Allergy Drug Design

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Computational analysis has become an indispensable bioinformatics approaches for the characterization of proteins regarding the physicochemical properties, prediction of signal peptides and 3D structure. Additionally, computational studies of protein-ligand interactions provide a rational basis for the speedy identification of novel leads for drug. To date no any computational analysis evaluating such parameters for GM-CSF-Rα, IL-3-Rα and IL-5-Rα. Hence, the present work aimed at identifying the theoretical basis of the physicochemical, structural and functional proprieties for these proteins using online computational tools. In the present study, different bioinformatics tools were used to characterize the properties and structure of the GM-CSF-Rα, IL3Rα, and IL5Rα proteins. Firstly, the Physico-chemical characterization was computed by ExPasy's (ProtParam). Then Fingerprinting analysis was done with ScanProsite. Followed by the functional characterization of the transmembrane regions and phosphorylation sites using SOSUI server and NetPhos server respectively. Afterwards, secondary structure prediction and the protein-ligand binding site residues were predicted by PDBSUM, and the detected ligands and their interactions were visualized by LIGPLOT and Protein ligand interaction profiler (PILP) softwares. The residues in GM-CSF-Rα, IL-3Rα and IL-5Rα proteins that may undergo ubiquitination were detected by using the UbPred and BDM-PUB programs, the predicted peptides for sumoylation in GM-CSF-Rα, IL-3Rα and IL-5Rα proteins were detected by GPS-SUMO online service. Finally, the 3D structure of proteins was built by Chimera 1.8 program. In addition, the models were surveyed using ERRAT server; as a confirmation for the quality of the models. Our results revealed that GM-CSF-Rα is stable whereas the IL3Rα and IL5Rα are classified as unstable proteins. All proteins are membrane proteins, acidic and hydrophilic in nature, with serine being the most phosphorylated amino acid. Interestingly, fibronectin type-III (FN3) domain was detected among these proteins. Also, we detected the sequences belonging to the following families: HEMATOPO_REC_S_F2, ASN_GLYCOSYLATION, CK2_PHOSPHO_SITE, PKC_PHOSPHO_SITE, MYRISTYL, CAMP_PHOSPHO_SITE, and TYR_PHOSPHO. Moreover, we detected 9 kinases in GM-CSF-Rα, while 13 kinases in IL-3-Rα and 15 kinases in IL-5-Rα. In GM-CSF-Rα 3 binding sites were detected with two ligands (GOL and NAG), and 5 binding sites in IL-3-Rα and IL-5-Rα with 3ligands (NAG, FUL and BMA) and one ligand (BGC) respectively. Secondary structure prediction showed that Beta sheet dominated all the other conformations. Modeling the 3 D structure of proteins resulted in a quality of less than 90%. computational analysis of GM-CSF-Rα, IL-3-Rα and IL-5-Rα will give a deep insight and provide opportunities for understanding the function of these proteins, and developing novel therapeutics for treating certain leukemia and inflammatory diseases.

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In silico comparative analysis and expression profile of antioxidant proteins in plants

Cited by 16 publications

References 42 publications

Comparative Insilco functional, structural and phylogenetic characterization of plant Mn-Superoxide Dismutase

Comparative Insilco functional, structural and phylogenetic characterization of plant Mn-Superoxide Dismutase

Computational identification of six salt stress responsive genes in Cynara scolymus L.

Interleukin 3, Interleukin 5, and Granulocyte–Macrophage Colony‐Stimulating Factor

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