In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach

Sahay, Archna; Shakya, Madhvi

doi:10.4172/jpb.1000134

Cited by 34 publications

(20 citation statements)

References 30 publications

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“…The number of residues in allowed and outlier regions was also high, indicating structural aberrations whereas in Arabidopsis no residues are observed in the outlier region and ∼94% of residues were in the favorable region, indicating the quality of the structure. Similar modeling and Ramachandran plot analyses to those described here have been used in the structural and functional analysis of spinach antioxidant proteins and the models were evaluated by computational tools (Sahay and Shakya, 2010). …”

Section: Resultsmentioning

confidence: 99%

Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases

et al. 2013

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Superoxide dismutase (SOD, EC 1.15.1.1) is an important metal-containing antioxidant enzyme that provides the first line of defense against toxic superoxide radicals by catalyzing their dismutation to oxygen and hydrogen peroxide. SOD is classified into four metalloprotein isoforms, namely, Cu/Zn SOD, Mn SOD, Ni SOD and Fe SOD. The structural models of soybean SOD isoforms have not yet been solved. In this study, we describe structural models for soybean Cu/Zn SOD, Mn SOD and Fe SOD and provide insights into the molecular function of this metal-binding enzyme in improving tolerance to oxidative stress in plants.

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Section: Resultsmentioning

confidence: 99%

Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases

et al. 2013

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“…The distribution of main chain bond angles and length were found to be within the limits. Homology modelling and validation of antioxidant proteins were also shown in similar way in Spinach (Sahay and Shakya, 2010). A single ligand binding site was identified in validated 3D structure of ApCPS ( Figure 17).…”

Section: Elucidation Of Tertiary Structure Of Apcps By 3d Homology Momentioning

confidence: 67%

In silico structural and functional analysis of copalyl diphosphate synthase enzyme in Andrographis paniculata (Burm. f.) Wall. ex Nees: A plant of immense pharmaceutical value

Shailaja¹,

Bindu²,

Srinath³

et al. 2018

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Andrographis paniculata (Burm. f.) Wa ll. ex Nees (Acanthaceae) with immense medicinal importance lacks information on its biosynthetic pathway genes and their regulatory role in the production of pharmaceutically important andrographolide. Copalyl diphosphate synthase (CPS) is involved in the production of copalyl diphosphate, a precursor for many bioactive compounds with particular reference to diterpene lactone. In this study, we elucidated the structural and functional aspects of A. paniculata CPS (ApCPS). Composition of amino acids and hydrophobic nature of ApCPS were analysed and identified as non trans-membrane protein. A chloroplast transit peptide and mitochondrial targeting peptide in ApCPS were identified. Protein secondary structure prediction has given insight on the distribution of helix (52.52%), loop (45.91%) and strands (1.56%) in ApCPS. The homology modelling of ApCPS was carried out with SWISS MODEL. The validation of 3D model using PROCHECK revealed that 91.74% of the residues have averaged 3D-1D score >= 0.2 which is structurally reliable. In Ramachandran plot, 90.9% amino acid residues were found in most favoured region. Phylogenetic tree was constructed using MEGA 7.0 by taking eudicots, monocots, gymnosperms and fungal species. Among them, ApCPS was clustered within eudicots and closely related to Sesumum indicum in Laminales. Protein-protein interaction study using STRING10 revealed that CPS interacts with gibberilic acid and terpene synthase related proteins. In Arabidopsis thaliana, CPS coexpression was seen with gibberelic acid related proteins. The present in silico analysis will be useful in understanding the structural, functional and evolutionary diversification of ApCPS.

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“…At particular P H, the net charge of the protein will be Zero. In that P H the protein will be very stable and compact [18]. The P I of HA 33 is 8.77 which is slight alkaline.…”

Section: Model Validationmentioning

confidence: 96%

“…The Ramachandran plot shows the phi-psi torsion angles for all residues in the structure (except those at the chain termini). All the residues are represented as squares except Glycine residues which are separately identified by triangles as these are not restricted to the regions of the plot appropriate to the other side chain types [18]. The graph for Ramachandran plot was obtained and results were discussed.…”

Section: Model Validationmentioning

confidence: 99%

“…The P I of HA 33 is 8.77 which is slight alkaline. The computed extinction coefficient helps in the quantitative study of protein-protein and protein ligand interaction in solution [18]. The extinction coefficient is 82975 M -1 cm -1 which consider all the cys as cysteine residue and 8285 M -1 cm -1 which consider all the cys as reduced residues.…”

Section: Model Validationmentioning

confidence: 99%

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Insilico Studies on HA 33 Subunit of Haemagglutinin of Clostridium botulinum Construction of Three Dimensional Model and Validation

R¹,

Auxilia²

2014

IJCA

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Botulinum neurotoxin (BoNT) complexes consist of neurotoxin and neurotoxin-associated proteins. The Clostridia releases these as protein aggregate, termed as the progenitor toxins. Heamagglutin -33 (HA-33) plays an essential role in the agglutination activity of the botulinum progenitor toxin; it assists in binding and translocating the progenitor toxins through the alimentary epithelial barriers. A three-dimensional homology model of HA-33 is demonstrated in this paper based upon the crystal structure of HA1 subcomponent of botulinum type C progenitor toxin complexed with galactose. The three dimensional model was designed using MODELLER (9v11) a comparative modelling tool that built a model based on an alignment of a sequence of HA-33 based on the known structure of botulinum type C progenitor toxin complexed with N-acetylgalactosamine. The modelled structure was then evaluated using SAVES. The structural dynamics of the modelled protein was performed by elNemo and based on the scores obtained, it was found to be a reliable and accurate three dimensional structure of the Hemeagglutin component. It gives an idea about the three dimensional structure of a protein which will would serve as a guide to a detailed understanding of its participation in the process of agglutination. This could also aid in molecular drug designing against botulism.

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In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach

Abstract: doi:10.4172/jpb.100013

Cited by 34 publications

References 30 publications

Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases

Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases

In silico structural and functional analysis of copalyl diphosphate synthase enzyme in Andrographis paniculata (Burm. f.) Wall. ex Nees: A plant of immense pharmaceutical value

Insilico Studies on HA 33 Subunit of Haemagglutinin of Clostridium botulinum Construction of Three Dimensional Model and Validation

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