Homology Modeling, Molecular Docking and DNA Binding Studies of Nucleotide Excision Repair UvrC Protein from M. tuberculosis

Parulekar, Rishikesh S.; Barage, Sagar H.; Jalkute, Chidambar B.; Dhanavade, Maruti J.; Fandilolu, Prayagraj M.; Sonawane, Kailas D.

doi:10.1007/s10930-013-9506-1

Cited by 27 publications

(21 citation statements)

References 51 publications

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“…Assessment of secondary structure prediction of different isoforms gives an idea about structural pattern from the protein sequences in terms of helix, sheets and coils. For this Psipred program was used to observe the variation among different isoforms. ARNTP1 variant was found to attain mostly alpha helical conformation while ARNTP3 shows both strand and helix form (Fig.…”

Section: Resultsmentioning

confidence: 99%

Identification of differentially expressed three novel transcript variants of mouse ARNT gene

et al. 2015

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The aryl hydrocarbon receptor nuclear translocator (ARNT/ HIF1-b) is an obligatory transcriptional partner of the aryl hydrocarbon receptor (AHR) and hypoxia-inducible factor-1a (HIF-1a). It has a basic helix-loop-helix domain that belongs to period-ARNT-single-minded (PAS) protein family. PAS proteins act as heterodimeric transcription factors with ARNT being master dimerization partner. The ARNT-HIF-1a complex is an important transcriptional regulator of the hypoxic response of the tumor cells. Previous studies have reported two transcript variants of the gene produced by alternative splicing in mouse. One transcript variant contains all 22 exons while the other variant lacks exon-E5. In our study, using combinatorial approach comprising bioinformatics tools and molecular biology techniques involving RT-PCR, semi-nested PCR, sequencing and qPCR, we have identified three novel transcript variants of Arnt gene in mouse. All three new transcripts arise as a result of alternative splicing of newly identified exons with exon-E2, replacing reported exon-E1. These transcripts encode for three protein isofoms having different N-termini. The expression of these transcripts was found to be different in different tissues of adult mice. In silico analysis of the upstream region of the new exons revealed three distinct promoter regions designated as PA, PB and PC present upstream of newly identified exons. These promoters possess potential signature sequences for common as well as different transcription factors suggesting complex regulation of Arnt gene. In silico post translational studies of the conceptually translated amino acid sequences of these transcripts show similarity in some of the properties while differ in others. The diversity at N-termini of protein isoforms suggests the possibility of forming different complexes in different tissues and may also be important for unique interactions with partner molecules. V C 2015 IUBMB Life, 68(2): [122][123][124][125][126][127][128][129][130][131][132][133][134][135] 2016

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Section: Resultsmentioning

confidence: 99%

Identification of differentially expressed three novel transcript variants of mouse ARNT gene

et al. 2015

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“…Molecular docking studies have been found useful to understand interactions between enzymes and ligands [34][35][36][37]. Thus, molecular docking studies were carried out between carotenoid dehydrosqualene synthase (PDB ID: 3ACX) and pyrano[2,3-d]pyrimidinediones using Patch dock server [38,39].…”

Section: Molecular Dockingmentioning

confidence: 99%

Cp2ZrCl2: AN EFFICIENT CATALYST FOR MULTICOMPONENT SYNTHESIS OF CAROTENOID DEHYDROSQUALENE SYNTHASE INHIBITING PYRANO[2,3-d]PYRIMIDINEDIONES

Sonawane¹,

Sonawane

et al. 2019

Asian J Pharm Clin Res

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Objectives: The present protocol deals with zirconocene dichloride (Cp2ZrCl2) catalyzed synthesis of pyrano[2,3-d]pyrimidinediones through one-pot multicomponent reactions of aromatic aldehydes with malononitrile and barbituric acid at ambient temperature. All the synthesized compounds were characterized and evaluated for antibacterial, antifungal, and antioxidant activities. Furthermore, a molecular docking was carried out to reveal the atomic insights between synthesized compounds and carotenoid dehydrosqualene synthase (PDB ID: 3ACX). Methods: All the synthesized compounds were evaluated for their in vitro antimicrobial activity by diffusion method. Antioxidant activities such as 1,1-diphenyl-2-picrylhydrazyl and radical scavenging activity. A mixture of barbituric acid 1 (1 mmol), malononitrile 2 (1 mmol), benzaldehyde 3a (1 mmol), ethanol (5 mL), and Cp2ZrCl2 (5 mol %) was stirred at ambient temperature for specified time. After completion of reaction as indicated by thin-layer chromatography, the obtained crude product was filtered and purified by column chromatography on silica gel (Merck, 60–120 mesh) using ethyl acetate:pet. ether to afford pure product which was then characterized by spectroscopic methods such by FTIR, nuclear magnetic resonance (1H NMR), 13C NMR, and mass spectroscopy. Results: All the synthesized pyrano[2,3-d]pyrimidinediones were characterized by spectroscopic analysis. The results revealed that pyrano[2,3-d] pyrimidinediones (4 a-k) displayed the zone of inhibition in the range of 3–13 mm. The most active compound 4b displayed largest zone of inhibition of 13 mm for Escherichia coli (NCIM-2832) and 9 mm for Bacillus subtilis (NCIM-2635). The antifungal and antioxidant activity of all synthesized pyrano[2,3-d]pyrimidinediones (4a-k) showed moderate to good activity. Molecular docking studies suggest that pyrano[2,3-d]pyrimidinediones might inhibit the carotenoid dehydrosqualene synthase activity. Conclusion: All the synthesized pyrano[2,3-d]pyrimidinediones display moderate to good antibacterial, antifungal, and antioxidant activity. This molecular docking studies supported that pyrano[2,3-d]pyrimidinediones might inhibit the carotenoid dehydrosqualene synthase (PDB ID: 3ACX).

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“…For predicting the function of recombinant protein, the interaction of various ligands with the recombinant and natural protein is investigated using MVD (Molegro Virtual Docker) software [11]. As a result of this ligand-protein connection by providing the MolDock score, interaction is estimated.…”

Section: Function Prediction Of Normal and Mutant Lipase Proteinsmentioning

confidence: 99%

The Role of Protein Engineering in the Design and Production of Recombinant Proteins

Nejad

Niri

Fazilati

et al. 2016

IJVV

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Proteins possess many structural and functional characteristics that these features are not seen in any other biomolecules. So many biologists have been persuaded that using protein engineering design and build their desired proteins. These engineered proteins can act as new molecular tools for scientific, medical, industrial, etc. applications, so they can satisfy many human needs that are not met by natural proteins. Protein engineering based on calculations Strategy produces and screens the protein sequences with "in silico" (i.e. before its synthesis in the laboratory). Structure-based protein engineering calculations similarly use the calculations to discover the protein sequences. However, calculation-based protein engineering also emphasizes the new and useful protein engineering and investigating the relationship between structure and function of them. This study investigates the protein engineering tools in producing the recombinant and engineered proteins. For this purpose, bioinformatics studies, how to predict the second and third buildings based on homology and adaptive modeling, predicting protein performance for the production of recombinant proteins are investigated.

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Homology Modeling, Molecular Docking and DNA Binding Studies of Nucleotide Excision Repair UvrC Protein from M. tuberculosis

Cited by 27 publications

References 51 publications

Identification of differentially expressed three novel transcript variants of mouse ARNT gene

Identification of differentially expressed three novel transcript variants of mouse ARNT gene

Cp2ZrCl2: AN EFFICIENT CATALYST FOR MULTICOMPONENT SYNTHESIS OF CAROTENOID DEHYDROSQUALENE SYNTHASE INHIBITING PYRANO[2,3-d]PYRIMIDINEDIONES

The Role of Protein Engineering in the Design and Production of Recombinant Proteins

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