@article {45736,
	title = {Functional stability and structural transitions of kallikrein: spectroscopic and molecular dynamics studies},
	journal = {Journal of Biomolecular Structure \& Dynamics},
	volume = {35},
	year = {2017},
	month = {MAR},
	pages = {330-342},
	type = {Article},
	abstract = {<p>Kallikrein, a physiologically vital serine protease, was investigated for its functional and conformational transitions during chemical (organic solvents, Gdn-HCl), thermal, and pH induced denaturation using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach. The enzyme was exceptionally stable in isopropanol and ethanol showing 110\% and 75\% activity, respectively, after 96h, showed moderate tolerance in acetonitrile (45\% activity after 72h) and much lower stability in methanol (40\% activity after 24h) (all the solvents [90\% v/v]). Far UV CD and fluorescence spectra indicated apparent reduction in compactness of KLKp structure in isopropanol system. MD simulation studies of the enzyme in isopropanol revealed (1) minimal deviation of the structure from native state (2) marginal increase in radius of gyration and solvent accessible surface area (SASA) of the protein and the active site, and (3) loss of density barrier at the active site possibly leading to increased accessibility of substrate to catalytic triad as compared to methanol and acetonitrile. Although kallikrein was structurally stable up to 90 degrees C as indicated by secondary structure monitoring, it was functionally stable only up to 45 degrees C, implicating thermolabile active site geometry. In GdnHCl [1.0M], 75\% of the activity of KLKp was retained after incubation for 4h, indicating its denaturant tolerance. A molten globule-like structure of KLKp formed at pH 1.0 was more thermostable and exhibited interesting structural transitions in organic solvents. The above results provide deeper understanding of functional and structural stability of the serine proteases at molecular level.</p>},
	keywords = {isopropanol tolerance, Kallikrein, MD Simulation, Molten globule, Serine protease, Thermostability},
	issn = {0739-1102},
	doi = {10.1080/07391102.2016.1138884},
	author = {Dalal, Sayli and Mhashal, Anil and Kadoo, Narendra and Gaikwad, Sushama M.}
}
@article {49030,
	title = {Transcriptome analysis and Structure-Based drug discovery identifies potential biofungicides for controlling Fusarium wilt in chickpea},
	journal = {Journal of Molecular Liquids},
	volume = {399},
	year = {2024},
	month = {APR },
	type = {Article},
	abstract = {<p>
	Fusarium wilt caused by the fungal pathogen Fusarium oxysporum f.sp. ciceri (Foc) is a devastating chickpea disease. Foc is a soil-borne pathogen that invades plants through roots and can kill them in three to four weeks. Although Fusarium wilt can be controlled by soil solarization or fumigation with chemical fungicides, these are not always effective. Soil fumigation is also hazardous to the beneficial soil microflora, deteriorates soil health, and causes pollution. Hence, there is an urgent need to identify potent and environment-friendly biofungicides to control fungal pathogens. We employed transcriptome analysis and structure-based drug discovery approaches to identify potential biofungicides from four widely used medicinal plants: Lantana camara, Piper betel, Ricinus communis, and Azadirachta indica. Fusarium wilt-resistant and susceptible chickpea varieties were pathogeninoculated and grown under controlled conditions in a greenhouse. Transcriptome analysis was performed to identify pathogenicity-related differentially expressed genes (DEGs). Over 600 phytochemicals from the four medicinal plants and four chemical fungicides were considered for molecular docking against the predicted protein structures of the four most expressed pathogen DEGs. The phytochemicals with the best docking scores and the lowest predicted toxicity risk were considered for molecular dynamics (MD) simulation at 100 ns timescale, and 15 potential biofungicides were identified. This study paves the way for developing biofungicides with enhanced efficacy and safety to manage Fusarium wilt in chickpea.</p>
},
	keywords = {Antifungal molecules, Cicer arietinum, fusarium oxysporum, MD Simulation, medicinal plants, Molecular docking},
	issn = {0167-7322},
	doi = {10.1016/j.molliq.2024.124364},
	author = {Sahoo, Rosaleen and Kadoo, Narendra}
}
