Browsing by Author "Singh, Vinay K."

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    Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach
    (Springer Science and Business Media Deutschland GmbH, 2022) Yadav, Kanchan; Dwivedi, Shruti; Gupta, Supriya; Dubey, Amit K.; Singh, Vinay K.; Tanveer, Aiman; Yadav, Sangeeta; Yadav, Dinesh
    Pectin lyase (PNL) is an important enzyme of the pectinases group which degrades pectin polymer to 4,5-unsaturated oligogalacturonides by a unique ?-elimination mechanism and is used in several industries. The existence of multigene families of pectin lyases has been investigated by mining microbial genomes. In the present study, 52 pectin lyase genes were predicted from sequenced six species of Fusarium, namely F. fujikuroi, F. graminearum, F. proliferatum, F. oxysporum, F. verticillioides and F. virguliforme. These sequences were in silico characterized for several physico-chemical, structural and functional attributes. The translated PNL proteins showed variability with 344�1142 amino acid residues, 35.44�127.41�kDa molecular weight, and pI ranging from 4.63 to 9.28. The aliphatic index ranged from 75.33 to 84.75. Multiple sequence alignment analysis showed several conserved amino acid residues and five distinct groups marked as I, II, III, IV, and V were observed in the phylogenetic tree. The Three-dimensional Structure of five of these PNLs, each representing a distinct group of phylogenetic trees was predicted using I-TASSER Server and validated. The pectin lyase proteins of Fusarium species revealed close similarity with pectin lyase of Aspergillus niger PelA(1IDJ) and PelB(1QCX). Diversity in the structural motifs was observed among Fusarium species with 2 ?-sheets, 1 ?-hairpin, 7�12 ? bulges, 18�25 strands, 6 -11 helices, 1 helix-helix interaction, 32�49 ? turns, 2�6 ? turns and 2- 3 disulfide bonds. The unique Pec_lyase domain was uniformly observed among all PNL proteins confirming its identity. The genome-wide mining of Fusarium species was attempted to provide the diversity of PNL genes, which could be explored for diverse applications after performing cloning and expression studies. � 2022, King Abdulaziz City for Science and Technology.
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    Molecular cloning and structural insights into pectin lyase proteins from different strains of fusarium
    (Bentham Science Publishers, 2021) Yadav, Sangeeta; Anand, Gautam; Singh, Vinay K.; Yadav, Dinesh
    Aim: Molecular cloning and analysis of Pectin Iyase (PNL) genes from different strains of Fusarium for structural predictions and docking studies. Background: PNLs cleave pectin by ?-elimination resulting in the formation of 4,5-unsaturated oli-gogalacturonates, without affecting the ester content of the polymer chain and hence maintaining the specific aroma of fruits. Several PNL lyase genes from Aspergillus and Penicillium have been cloned, but the molecular biology of that from Fusarium has not been explored. Objective: To obtain an insight into the three-dimensional structure of PNL of Fusarium. Methods: PCR amplification-based molecular cloning of PNL genes from Fusarium strains, se-quencing, and sequence analysis using bioinformatics tools for homology search, multiple sequence alignment, motif search, physiochemical characterization, phylogenetic tree construction, 3D structure prediction, and molecular docking were conducted. Results: Five PNL genes were cloned from F. oxysporum MTCC1755, F. monoliforme var. subg-lutinans MTCC2015, F. avenaceum MTCC10572, and F. solani MTCC3004 using the PCR ap-proach. Many conserved amino acids were found at several positions in all the PNL proteins. Phylogenetic analysis of these proteins with other pectinases revealed two major clusters representing members of lyases and hydrolases. In-silico characterization revealed stable PNL proteins. PNL proteins from different Fusarium strains were similar in structural features and biochemical properties owing to their similar primary sequence. Docking studies revealed that electrostatic forces and van der Waal and hydrogen bonds effectuate the interaction between the ligand and the enzyme. As-partate, tyrosine, and tryptophan residues in the active site of the enzyme are responsible for ligand binding. Conclusion: PNL from different Fusarium species show similarity at structural as well as biochemical level. PNL protein from F. moniliforme and F. solani was similar in properties except for the variation of single amino acid. Docking studies on the enzyme and different ligands provided an insight into the interacting residues and forces as well as the suitability of the substrate for catalysis. � 2021 Bentham Science Publishers.
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    Recent Developments and Future Perspectives of Vaccines and Therapeutic Agents against SARS-CoV2 Using the BCOV_S1_CTD of the S Protein
    (MDPI, 2023) Gupta, Amit; Singh, Ashish P.; Singh, Vinay K.; Sinha, Rajeshwar P.
    Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the virus kept developing and mutating into different variants over time, which also gained increased transmissibility and spread in populations at a higher pace, culminating in successive waves of COVID-19 cases. The scientific community has developed vaccines and antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease. Realizing that growing SARS-CoV-2 variations significantly impact the efficacy of antiviral therapies and vaccines, we summarize the appearance and attributes of SARS-CoV-2 variants for future perspectives in drug design, providing up-to-date insights for developing therapeutic agents targeting the variants. The Omicron variant is among the most mutated form; its strong transmissibility and immune resistance capacity have prompted international worry. Most mutation sites currently being studied are in the BCOV_S1_CTD of the S protein. Despite this, several hurdles remain, such as developing vaccination and pharmacological treatment efficacies for emerging mutants of SARS-CoV-2 strains. In this review, we present an updated viewpoint on the current issues faced by the emergence of various SARS-CoV-2 variants. Furthermore, we discuss the clinical studies conducted to assist the development and dissemination of vaccines, small molecule therapeutics, and therapeutic antibodies having broad-spectrum action against SARS-CoV-2 strains. � 2023 by the authors.