In silico molecular modelling, structural dynamics simulation and characterization of antifungal nature of β-glucosidase enzyme from Sechium edule

References

• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. https://doi.org/10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Baba, S. A., Vishwakarma, R. A., & Ashraf, N. (2017). Functional characterization of CsBGlu12, a β-glucosidase from crocus sativus, provides insights into its role in abiotic stress through accumulation of antioxidant flavonols. The Journal of Biological Chemistry, 292(11), 4700–4713. https://doi.org/10.1074/jbc.M116.762161
   PubMed Web of Science ®Google Scholar
• Bhattacharyya, P., & Van Staden, J. (2016). Ansellia africana (Leopard orchid): A medicinal orchid species with untapped reserves of important biomolecules—A mini review. South African Journal of Botany, 106, 181–185. https://doi.org/10.1016/j.sajb.2016.06.010
   Web of Science ®Google Scholar
• Cai, Y. J., Buswell, J. A., & Chang, S. T. (1998). β-glucosidases component of the cellulolytic system of the edible straw mushroom, Volvariella volvacea. Enzyme and Microbial Technology, 22(2), 122–129. https://doi.org/10.1016/S0141-0229(97)00151-8
   Web of Science ®Google Scholar
• De Lucca, A. J., Cleveland, T. E., & Wedge, D. E. (2005). Plant-derived antifungal proteins and peptides. Canadian Journal of Microbiology, 51(12), 1001–1014. https://doi.org/10.1139/w05-063
   PubMed Web of Science ®Google Scholar
• Gandhu, S., Hussaini, S. F., Kumar, G. S., & Rao, B. S. S. (2012). Anti-ulcer activity of Sechium edule ethanolic fruit extract. The Pharmacy Journal, 1(5), 77–81.
   Google Scholar
• Gómez-Anduro, G., Ceniceros-Ojeda, E. A., Casados-VáZquez, L. E., Bencivenni, C., Sierra-BeltráN. A., Murillo-Amador, B., & Tiessen, A. (2011). Genome-wide analysis of the beta-glucosidase gene family in maize (Zea mays L. var B73). Plant Molecular Biology, 77(1–2), 159–183. https://doi.org/10.1007/s11103-011-9800-2
   PubMed Web of Science ®Google Scholar
• Gordon, E. A., Guppy, L. J., & Nelson, M. (2000). The antihypertensive effects of the Jamaican Cho-Cho (Sechium edule). The West Indian Medical Journal, 49(1), 27–31.
   PubMed Web of Science ®Google Scholar
• Gupta, P., Ravi, I., & Sharma, V. (2013). Induction of β-1,3-glucanase and chitinase activity in the defense response of Eruca sativa plants against the fungal pathogen Alternaria brassicicola. Journal of Plant Interactions, 8(2), 155–161. https://doi.org/10.1080/17429145.2012.679705
   Web of Science ®Google Scholar
• Gurung, A. B., Aguan, K., Mitra, S., & Bhattacharjee, A. (2017). Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential acetylcholinesterase inhibitors against alzheimer’s disease. Journal of Biomolecular Structure and Dynamics, 35(8), 1729–1742. https://doi.org/10.1080/07391102.2016.1192485
   PubMed Web of Science ®Google Scholar
• Haq, I. U., Hussain, Z., Khan, M. A., Muneer, B., Afzal, S., Majeed, S., & Akram, F. (2012). Kinetic and thermodynamic study of cloned thermostable endo-1,4-β-xylanase from Thermotoga petrophila in mesophilic host. Molecular Biology Reports, 39(7), 7251–7726. https://doi.org/10.1007/s11033-012-1555-6
   PubMed Web of Science ®Google Scholar
• He, S., & Withers, S. G. (1997). Assignment of sweet almond β-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. The Journal of Biological Chemistry, 272(40), 24864–24867. https://doi.org/10.1074/jbc.272.40.24864
   PubMed Web of Science ®Google Scholar
• Jiang, F. Y., Shui, B. B., Tang, F. X., & Shan, C. H. (2017). Cloning and expression of class I chitinases in hami melon after Penicillium infection. Genetics and Molecular Research, 16(1), 16019085. https://doi.org/10.4238/gmr16019085
   Web of Science ®Google Scholar
• Jones, G., Willett, P., & Glen, R. C. (1995). Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. Journal of Molecular Biology, 245(1), 43–53. https://doi.org/10.1016/S0022-2836(95)80037-9
   PubMed Web of Science ®Google Scholar
• Karnchanatat, A., Petsom, A., Sangvanich, P., Piaphukiew, J., Whalley, A. J. S., Reynolds, C. D., & Sihanonth, P. (2007). Purification and biochemical characterization of an extracellular β-glucosidase from the wood-decaying fungus Daldinia eschscholzii (Ehrenb.:Fr.) Rehm. FEMS Microbiology Letters, 270(1), 162–170. https://doi.org/10.1111/j.1574-6968.2007.00662.x
   PubMed Web of Science ®Google Scholar
• Leah, R., Kigel, J., Svendsen, I., & Mundy, J. (1995). Biochemical and molecular characterization of a Barley seed β-Glucosidase. The Journal of Biological Chemistry, 270(26), 15789–15797. https://doi.org/10.1074/jbc.270.26.15789
   PubMed Web of Science ®Google Scholar
• Nagasundaram, N., Doss, G. P. C., Chakraborty, C., Karthick, V., Thirumal Kumar, D., Balaji, V., Siva, R., Lu, A., Ge, Z., & Zhu, H. (2016). Mechanism of artemisinin resistance for malaria PfATP6 L263 mutations and discovering potential antimalarials: An integrated computational approach. Scientific Reports, 6, 30106. https://doi.org/10.1038/srep30106
   PubMed Web of Science ®Google Scholar
• Oard, S. V., & Enright, F. M. (2006). Expression of the antimicrobial peptides in plants to control phytopathogenic bacteria and fungi. Plant Cell Reports, 25(6), 561–572. https://doi.org/10.1007/s00299-005-0102-5
   PubMed Web of Science ®Google Scholar
• Ordonez, A., Gomez, J., Vattuone, M., & Lsla, M. (2006). Antioxidant activities of Sechium edule (Jacq.) Swartz extracts. Food Chemistry, 97(3), 452–458. https://doi.org/10.1016/j.foodchem.2005.05.024
   Web of Science ®Google Scholar
• Park, S. C., Kim, J. Y., Lee, J. K., Hwang, I., Cheong, H., Nah, J. W., Hahm, K. S., & Park, Y., Y. (2009). Antifungal mechanism of a novel antifungal protein from Pumpkin rinds against various fungal pathogens. Journal of Agricultural and Food Chemistry, 57(19), 9299–9304. https://doi.org/10.1021/jf902005g
   PubMed Web of Science ®Google Scholar
• Salas, C. E., Badillo-Corona, J. A., Ramírez-Sotelo, G., & Oliver-Salvador, C. (2015). Biologically active and antimicrobial peptides from plants. BioMed Research International, 2015, 102129. https://doi.org/10.1155/2015/102129
   PubMed Web of Science ®Google Scholar
• Sandhu, J. S., Sidhu, M. K., & Yadav, I. S. (2017). Control of fungal diseases in agricultural crops by chitinase a glucanase transgenes. Sustainable Agriculture Reviews, 22, 163–212. https://doi.org/10.1007/978-3-319-48006-0_62017.
   Google Scholar
• Savary, S., Ficke, A., Aubertot, J. N., & Hollier, C. (2012). Crop losses due to diseases and their implications for global food production losses and food security. Food Security, 4(4), 519–537. https://doi.org/10.1007/s12571-012-0200-5
   Web of Science ®Google Scholar
• Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., & Van Gunsteren, W. F. (1999). The GROMOS Biomolecular Simulation Program Package. The Journal of Physical Chemistry A, 103(19), 3596–3607. 10.1021/jp984217f
   Web of Science ®Google Scholar
• Siciliano, T., De Tommasi, N., Morelli, I., & Braca, A. (2004). Study of Flavonoids of Sechium edule (Jacq) Swartz (Cucurbitaceae) Different Edible Organs by Liquid Chromatography Photodiode Array Mass Spectrometry. Journal of Agricultural and Food Chemistry, 52(21), 6510–6515. 10.1021/jf040214q
   PubMed Web of Science ®Google Scholar
• Trimbur, D., Warren, R. A. J., & Withers, S. G. (1992). Region-directed mutagenesis of residues surrounding the active site nucleophile in β-glucosidase from Agrobacterium faecalis. Journal of Molecular Biology, 267, 10248–10251.
   Google Scholar
• Wang, H., & Ng, T. B. (2002). Isolation of Cicadin, a novel and potent antifungal peptide from dried juvenile cicadas. Peptides, 23(1), 7–11. https://doi.org/10.1016/S0196-9781(01)00573-3
   PubMed Web of Science ®Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54, 5.6.1–5.6.37. https://doi.org/10.1002/cpbi.3
   PubMedGoogle Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Yadav, S., Tomar, A. K., Yadav, R. N., & Yadav, S. (2013). Screening of antifungal proteins from plants of cucurbitaceae family against Fusarium oxysporum: Potential as biofungicides. International Research Journal of Environmental Sciences, 2(6), 91–96.
   Google Scholar
• Zhang, L., Fu, Q., Li, W., Wang, B., Yin, X., Liu, S., Xu, Z., & Niu, Q. (2017). Identification and characterization of a novel β-glucosidase via metagenomic analysis of Bursaphelenchus xylophilus and its microbial flora. Scientific Reports, 7(1), 14850. https://doi.org/10.1038/s41598-017-14073-w
   PubMed Web of Science ®Google Scholar