Understanding properties of the master effector of phage shock operon in<i>Mycobacterium tuberculosis</i>via bioinformatics approach

Basharat, Zarrin; Yasmin, Azra

doi:10.1101/050047

Cited by 9 publications

(4 citation statements)

References 22 publications

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“…Conserved domains were studied using Conserved domain database (Marchler-Bauer et al, 2012). Position of phosphorylation sites in arsenate reductase of both species was studied using neural network based tool NetPhos 2.0 (Blom et al, 1999;Basharat and Yasmin, 2016b;Basharat and Yasmin, 2016c). It makes predictions for possible phosphorylation potential at serine, threonine and tyrosine sites in the eukaryotic proteins.…”

Section: Methodsmentioning

confidence: 99%

Digital dissection of arsenate reductase enzyme from an arsenic hyperccumulating fernPteris vittata

Basharat

Baig

Yasmin

2016

Preprint

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Action of arsenate reductase is crucial for the survival of an organism in arsenic polluted area. Pteris vittata, also known as Chinese ladder brake, was the first identified arsenic hyperaccumulating fern with the capability to convert [As(V)] to arsenite [As(III)]. This study aims at sequence analysis of the most important protein of the arsenic reduction mechanism in this specie. Phosphorylation potential of the protein along with possible interplay of phosphorylation with O-β-GlcNAcylation was predicted using neural network based webservers. Secondary and tertiary structure of arsenate reductase was then analysed.Active site region of the protein comprised a rhodanese-like domain. Cursory dynamics simulation revealed that folds remained conserved in the rhodanese main but variations were observed in the structure in other regions. This information sheds light on the various characteristics of the protein and may be useful to enzymologists working on the improvement of its traits for arsenic reduction.

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Section: Methodsmentioning

confidence: 99%

Digital dissection of arsenate reductase enzyme from an arsenic hyperccumulating fernPteris vittata

Basharat

Baig

Yasmin

2016

Preprint

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“…The structure was determined [26] by homology modeling using iterative threading assembly simulations in the I-TASSER [27][28]. The structure was then simulated for 10 ns [29] using CABS-Flex server [30]. This was done to visualize the flexibility and stability of the protein chain.…”

Section: 5structure Modeling and Dynamics Simulationmentioning

confidence: 99%

Degradation of sulphonated mono and di-azo dye as the sole carbon source inSerratia marcescens: Insights from combined wet and dry lab analysis

Basharat¹,

Yasmin

2023

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The high production volume of azo dyes for manufacturing and treating various consumer products leads to deleterious environmental consequences. Bacterial agents present in the environment can degrade these dyes. We, hereby, report the isolation, decolorization and degradation of a mono (Methyl orange) and di-azoic (Congo red) compound of this class of dyes by a versatile bacterium Serratia marcescens. Our isolate showed the capability of sulphonated azo dye utilization/degradation i.e. Methyl orange and Congo red usage, with no inhibitory effects on its growth in the minimal medium. The calorimetric analysis showed 80.83% decolourization of Methyl orange and 92.7% decolourization of Congo red after 7 days of incubation in a shaking incubator at pH: 7 and temperature: 37 degrees Celsius. An azoreductase enzyme of ~25 KDa was detected after SDS-PAGE analysis. Quantitative and qualitative testing of the degradation phenomenon was followed by in silico analysis. Structural modeling followed by molecular docking in Molecular Operating Environment revealed numerous residues involved in binding and assisting degradation. Changes in the apo, holo, and dye-bound enzyme energy profiles were also observed. This is the first study reporting the capability of Serratia marcescens to use azo dyes/sulphonated azo dyes as the sole carbon source and the detailed computational analysis of the degradation phenomenon. We hope that these findings will be of use to environmental scientists, aid in better dye-degrading mutant creation to help craft future remediation strategies for sulphonated azo dyes.

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“…They were converted to PDB format using OpenBabel software (OLBoyle et al 2011). Structure modeling of barbiturase was attempted using I-TASSER as previously described (Zhang, 2008;Roy et al 2010;Basharat and Yasmin, 2015;Basharat and Yasmin, 2016). Model with best confidence score of 2, estimated TM-score of 0.99±0.04 and estimated RMSD of 2.5±1.9Å was selected for further analysis (Fig.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

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Supplemental Information 1: Supplementary Files 1-4

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Barbiturases have scarce structural information available and do not fit in the conventional group of proteins. It is contemplated that they play a role in catabolism of s-triazine herbicide compounds. Structure as well as interaction data information of barbiturase with s-triazine compounds is missing. Sequence data is a goldmine of biological information and acts as raw material for structure and docking analysis. De novo structure prediction of the Sulfobacillus acidophilus DSM 10332 barbiturase has been attempted in this data article. Molecular docking analysis was carried out with atrazine, simazine and hexazinone belonging to s-triazine class of herbicides. The analysis revealed key residues necessary for these interactions. The generated data could be used by environmental scientists working on the enzyme assisted herbicide degradation.

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Understanding properties of the master effector of phage shock operon inMycobacterium tuberculosisvia bioinformatics approach

Cited by 9 publications

References 22 publications

Digital dissection of arsenate reductase enzyme from an arsenic hyperccumulating fernPteris vittata

Digital dissection of arsenate reductase enzyme from an arsenic hyperccumulating fernPteris vittata

Degradation of sulphonated mono and di-azo dye as the sole carbon source inSerratia marcescens: Insights from combined wet and dry lab analysis

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