Comparative modelling, molecular docking and immobilization studies on Rhizopus oryzae lipase: evaluation of potentials for fatty acid methyl esters synthesis

References

• Amini, Z., Ong, H. C., Harrison, M. D., Kusumo, F., Mazaheri, H., & Ilham, Z. (2017). Biodiesel production by lipase catalyzed transesterification of Ocimum basilicum L. (sweet basil) seed oil. Energy Conversion and Management, 132, 82–90. https://doi.org/10.1016/j.enconman.2016.11.017
   Web of Science ®Google Scholar
• Aransiola, E. F. (2013). Lipase catalyzed ethanolysis of Jatropha oil for biodiesel production. Energy and Environment Research, 3(1), 85–92. https://doi.org/10.5539/eer.v3n1p180
   Google Scholar
• Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. (2006). The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics (Oxford, England), 22(2), 195–201. https://doi.org/10.1093/bioinformatics/bti770
   PubMed Web of Science ®Google Scholar
• Ayinla, Z. A., Ademakinwa, A. N., Agboola, F. K. (2017). Studies on the Optimization of Lipase Production by Rhizopus sp. ZAC3 Isolated from the Contaminated Soil of a Palm Oil Processing Shed. J App Biol Biotech., 5(02), 030–037. https://doi.org/10.7324/JABB.2017.50205
   Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350.
   PubMed Web of Science ®Google Scholar
• Benkert, P., Künzli, M., & Schwede, T. (2009a). QMEAN server for protein model quality estimation. Nucleic Acids Research, 37(suppl_2), W510–W514. https://doi.org/10.1093/nar/gkp322
   PubMed Web of Science ®Google Scholar
• Benkert, P., Schwede, T., & Tosatto, S. C. E. (2009b). QMEANclust: Estimation of protein model quality by combining a composite scoring function with structural density information. BMC Structural Biology, 9, 35. https://doi.org/10.1186/1472-6807-9-35
   PubMed Web of Science ®Google Scholar
• Bienert, S., Waterhouse, A., De Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL repository - new features and functionality. Nucleic Acids Research, 45(D1), D313–D319.
   PubMed Web of Science ®Google Scholar
• Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., & Schwede, T. (2009). Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols, 4(1), 1–13. https://doi.org/10.1038/nprot.2008.197
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Science, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Dodds, E. D., McCoy, M. R., Rea, L. D., & Kennish, J. M. (2005). Gas chromatographic quantification of fatty acid methyl esters: Flame ionization detection vs. Electron impact mass spectrometry. Lipids, 40(4), 419–428. https://doi.org/10.1007/s11745-006-1399-8
   PubMed Web of Science ®Google Scholar
• Kumar, V., Kumar, C. S., Hari, G., Venugopal, N. K., Vijendra, P. D., & Basappa, G. B. (2013). Homology modeling and docking studies on oxidosqualene cyclases associated with primary and secondary metabolism of Centella asiatica. SpringerPlus, 2(1), 189. https://doi.org/10.1186/2193-1801-2-189
   PubMedGoogle Scholar
• Lanka, S., Rao Tallur, V., Ganesh, V., & Lavanya La, J. N. (2015). Homology modeling, Molecular dynamic simulations and docking stufies of a new cold active extracellular lipase EnLA from Emericella nidulans NFCCI 3643. Trends in Bioinformatics, 8(2), 37–51. https://doi.org/10.3923/tb.2015.37.51
   Google Scholar
• Li, C., Li, Q., Zhang, Y., Gong, Z., Ren, S., Li, P., & Xie, J. (2017). Characterization and function of Mycobacterium tuberculosis H37Rv Lipase Rv1076 (LipU). Microbiological Research, 196, 7–16.
   PubMed Web of Science ®Google Scholar
• Li, M., Zheng, H., Lin, M., Zhu, W., & Zhang, J. (2020). Characterization of the protein and peptide of excipient zein by the multienzyme digestion coupled with nano-LC-MS/MS. Food Chemistry, 321, 126712. https://doi.org/10.1016/j.foodchem.2020.126712
   PubMed Web of Science ®Google Scholar
• Mehta, A., Bodh, U., & Gupta, R. (2017). Fungal lipases: A review. Journal of Biotech Research, 8, 58–77.
   Google Scholar
• Mei, Y., Miller, L., Gao, W., & Gross, R. A. (2003). Imaging the distribution and secondary structure of immobilized enzymes using infrared microspectroscopy. Biomacromolecules, 4(1), 70–74. https://doi.org/10.1021/bm025611t
   PubMed Web of Science ®Google Scholar
• Moya-Salazar, J., Vértiz-Osores, J., Jibaja, S., Acevedo-Espinola, R., Rupa, R., Alarcon-Diaz, M., Vega-Guevara, M., & Cucho-Flores, R. (2019). Fungi lipases homology modeling and molecular docking with fatty acids and tripalmitin of palm oil effluent. Archives of Organic and Inorganic Chemical Sciences, 4(2), 493–500.
   Google Scholar
• Okoro, O. V., Sun, Z., & Birch, J. (2018). Lipases for biofuel production. In Reference module in food science. https://doi.org/10.1016/b978-0-08-100596-5.21650-
   Google Scholar
• Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., & Schrag, J. (1992). The alpha/beta hydrolase fold. Protein Engineering, 5(3), 197–211.
   PubMedGoogle Scholar
• Park, E. Y., Sato, M., & Kojima, S. (2006). Fatty acid methyl ester production using lipase-immobilizing silica particles with different particle sizes and different specific surface areas. Enzyme and Microbial Technology, 39(4), 889–896. https://doi.org/10.1016/j.enzmictec.2006.01.022
   Web of Science ®Google Scholar
• Qin, X., Zhong, J., & Wang, Y. (2021). A mutant T1 lipase homology modeling, and its molecular docking and molecular dynamics simulation with fatty acids. Journal of Biotechnology, 337, 24–34. https://doi.org/10.1016/j.jbiotec.2021.06.024
   PubMed Web of Science ®Google Scholar
• Rodrigues, J., Canet, A., Rivera, I., Osorio, N. M., Sandoval, G., Valero, F., & Ferreira-Dias, S. (2016). Biodiesel production from crude Jatropha oil catalysed by non-commercial immobilized heterologous Rhizopus oryzae and Carica papaya lipases. Bioresource Technology, 213, 88–95. https://doi.org/10.1016/j.biortech.2016.03.011
   PubMed Web of Science ®Google Scholar
• Rost, B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85–94.
   PubMedGoogle Scholar
• Schrodinger, L. L. C. (2015). The PyMOL molecular graphics system, open source project and code. http://sourceforge.net/projects/pymol/.
   Google Scholar
• Sharma, A., Meena, K. R., & Kanwar, S. S. (2018). Molecular characterization and bioinformatics studies of a lipase from Bacillus thermoamylovorans BHK67. International Journal of Biological Macromolecules, 107(Pt B), 2131–2140.
   PubMedGoogle Scholar
• Sivozhelezov, V., Bruzzese, D., Pastorino, L., Pechkova, E., & Nicolini, C. (2009). Increase of catalytic activity of lipase towards olive oil by Langmuir-film immobilization of lipase. Enzyme and Microbial Technology, 44(2), 72–76. https://doi.org/10.1016/j.enzmictec.2008.10.017
   Web of Science ®Google Scholar
• Souza, L. T. A., Oliveira, J. S., Rodrigues, M. Q. R. B., Santos, V. L. D., Pessela, B. C., & Resende, R. R. (2015). Macaúba (Acrocomia aculeata) cake from biodiesel processing: A low-cost substrate to produce lipases from Moniliella spathulataR25L270 with potential application in the oleochemical industry. Microbial Cell Factories, 14(1), 87. https://doi.org/10.1186/s12934-015-0266-9
   PubMedGoogle Scholar
• Su, A., Shirk, A., Baik, J., Zou, Y., & Gross, R. (2018). Immobilized cutinases: Preparation, solvent tolerance and thermal stability. Enzyme and Microbial Technology, 11, 33–40.
   Google Scholar
• Tariq, M., Ali, S., Ahmad, F., Ahmad, M., Zafar, M., Khalid, N., & Khan, M. A. (2011). Identification, FT-IR, NMR (1H and 13C) and GC/MS studies of fatty acid methyl esters in biodiesel from rocket seed oil. Fuel Processing Technology, 92(3), 336–341. https://doi.org/10.1016/j.fuproc.2010.09.025
   Web of Science ®Google Scholar
• Venkatesagowda, B., Ponugupaty, E., Barbosa-Dekker, A. M., & Dekker, R. F. H. (2018). The purification and characterization of lipases from Laiodiplodia theobromae, and their immobilization and use for biodiesel production from coconut oil. Applied Biochemistry and Biotechnology, 185(3), 619–640. https://doi.org/10.1007/s12010-017-2670-6
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., De Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303.
   PubMed Web of Science ®Google Scholar
• Wilmot, C. M., & Thornton, J. M. (1988). Analysis and prediction of the different types of β-turn in proteins. Journal of Molecular Biology, 203(1), 221–232.
   PubMed Web of Science ®Google Scholar
• Yang, A. S., & Honig, B. (2000). An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. Journal of Molecular Biology, 301(3), 691–711. https://doi.org/10.1006/jmbi.2000.3975
   PubMed Web of Science ®Google Scholar
• Yang, Z., Zhang, K. P., Huang, Y., & Wang, Z. (2010). Both hydrolytic and transesterification activities of Penicillium expansum lipase are significantly enhanced in ionic liquid [BMIm][PF6]. Journal of Molecular Catalysis B: Enzymatic, 63(1–2), 23–30. https://doi.org/10.1016/j.molcatb.2009.11.014
   Google Scholar