300
Views
2
CrossRef citations to date
0
Altmetric
Research Article

Molecular modeling, docking and dynamics studies of fenugreek (Trigonella foenum-graecum) α-amylase

, & ORCID Icon
Pages 9297-9312 | Received 01 Sep 2022, Accepted 01 Nov 2022, Published online: 11 Nov 2022

References

  • Altschul, S. F., Madden, T. L., Schäffer, 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.
  • Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E., Grosdidier, A., Hernandez, C., Ioannidis, V., Kuznetsov, D., Liechti, R., Moretti, S., Mostaguir, K., Redaschi, N., Rossier, G., Xenarios, I., & Stockinger, H. (2012). ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40(Web Server issue), W597–W603.
  • Baum, D. (2008). Reading a phylogenetic tree: The meaning of monophyletic groups. Nature Education, 1(1), 190.
  • Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: Modeling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), W252–W258. https://doi.org/10.1093/nar/gku340
  • Cava, C., Bertoli, G., & Castiglioni, I. (2021). Potential drugs against COVID-19 revealed by gene expression profile, molecular docking and molecular dynamic simulation. Future virology. https://doi.org/10.2217/fvl-2020-0392
  • Christ, B.,Xu, C.,Xu, M.,Li, F.-S.,Wada, N.,Mitchell, A. J.,Han, X.-L.,Wen, M.-L.,Fujita, M., &Weng, J.-K. (2019). Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants. Nature Communications, 10(1), 3206 10.1038/s41467-019-11286-7PMC: 31324795
  • Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M., & Ashburner, M. (2008). ChEBI: A database and ontology for chemical entities of biological interest. Nucleic Acids Research, 36(Database issue), D344–D350.
  • Gasteiger, E. G. A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). PROSITE: A documented database using patterns and profiles as motif descriptors. Nucleic Acids Research, 31(13), 3784–3788. https://doi.org/10.1093/nar/gkg563
  • Geourjon, C., & Deleage, G. (1995). SOPMA: Significant improvement in protein secondary structure prediction by c prediction from alignments and joint prediction. Canadian Associates of BIOS, 11, 681–684.
  • Henrissat, B. (1991). A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochemical Journal, 280(2), 309–316. https://doi.org/10.1042/bj2800309
  • Janec˘ek, S. (1997). α-Amylase family: Molecular biology and evolution. Progress in Biophysics and Molecular Biology, 67(1), 67–97. https://doi.org/10.1016/S0079-6107(97)00015-1
  • Kumari, A., Singh, V. K., Fitter, J., Polen, T., & Kayastha, A. M. (2010). α-Amylase from germinating soybean (Glycine max) seeds-purification, characterization, and sequential similarity of conserved and catalytic amino acid residues. Phytochemistry, 71(14–15), 1657–1666. https://doi.org/10.1016/j.phytochem.2010.06.012
  • Kumari, A., Singh, K., & Kayastha, A. M. (2012). α-Amylase: General properties, mechanism, and biotechnological applications-A review. Current Biotechnology e, 1(1), 98–107. https://doi.org/10.2174/2211550111201010098
  • Kumar, S., Nei, M., Dudley, J., & Tamura, K. (2008). MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics, 9(4), 299–306. https://doi.org/10.1093/bib/bbn017
  • Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular biology and evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
  • Kuriki, T., & Imanaka, T. (1999). The concept of the α-amylase family: Structural similarity and common catalytic mechanism. Journal of Bioscience and Bioengineering, 87(5), 557–565.
  • Land, H., & Humble, M. S. (2018). YASARA: A tool to obtain structural guidance in biocatalytic investigations. In Protein engineering (pp. 43–67). Humana Press.
  • Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. Journal ofBiomolecule NMR, 8(4), 477–486.
  • Metin, K., Koc, O., Ateşlier, B. B., & Biyik, H. H. (2010). Purification and characterization of α-amylase produced by Penicillium citrinumHBF62. African Journal of Biotechnology, 9(45), 7692–7701.
  • Mitaku, S., Hirokawa, T., & Tsuji, T. (2002). Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. Bioinformatics (Oxford, England), 18(4), 608–616. https://doi.org/10.1093/bioinformatics/18.4.608
  • Navabshan, I., Sakthivel, B., Pandiyan, R., Antoniraj, M. G., Dharmaraj, S., Ashokkumar, V., Khoo, K. S., Chew, K. W., Sugumaran, A., & Show, P. L. (2021). Computational lock and key and dynamic trajectory analysis of natural biophors against COVID-19 spike protein to identify effective lead molecules. Molecular Biotechnology, 63(10), 898–908. Octhttps://doi.org/10.1007/s12033-021-00358-z
  • Ngounou Wetie, A. G., Sokolowska, I., Woods, A. G., Roy, U., Deinhardt, K., & Darie, C. C. (2014). Protein-protein interactions: Switch from classical methods to proteomics and bioinformatics-based approaches. Cellular and Molecular Life Sciences : CMLS, 71(2), 205–228.
  • Nielsen, A. D., Fuglsang, C. C., & Westh, P. (2003). Effect of calcium ions on the irreversible denaturation of a recombinant Bacillus halmapalus alpha-amylase: A calorimetric investigation. The Biochemical Journal, 373(Pt 2), 337–343.
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612.
  • Pujadas, G., & Palau, J. (2001). Evolution of α-amylases: Architectural features and key residues in the stabilization of the (β/α)8 scaffold. Molecular Biology and Evolution, 18(1), 38–54.
  • Raveendran, S., Parameswaran, B., Ummalyma, S. B., Abraham, A., Mathew, A. K., Madhavan, A., Rebello, S., & Pandey, A. (2018). Applications of microbial enzymes in food industry. Food Technology and Biotechnology, 56(1), 16–30.
  • Robert, X., Haser, R., Gottschalk, T. E., Ratajczak, F., Driguez, H., Svensson, B., & Aghajari, N. (2003). The structure of barley α-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: A pair of sugar tongs. Structure, 11(8), 973–984. https://doi.org/10.1016/S0969-2126(03)00151-5
  • Svensson, B. (1994). Protein engineering in the α-amylase family: Catalytic mechanism, substrate specificity, and stability. Plant Molecular Biology, 25(2), 141–157. https://doi.org/10.1007/BF00023233
  • Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J., & von Mering, C. (2015). STRING V10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43(D1), D447–D452. https://doi.org/10.1093/nar/gku1003
  • Tripathi, P., Leggio, L. L., Mansfeld, J., Ulbrich-Hofmann, R., & Kayastha, A. M. (2007). α-Amylase from mung beans (Vigna radiata)–Correlation of biochemical properties and tertiary structure by homology modeling. Phytochemistry, 68(12), 1623–1631. https://doi.org/10.1016/j.phytochem.2007.04.006
  • Vallee, B. L., Stein, E. A., Sumerwell, W. N., & Fischer, E. H. (1959). Metal content of α-amylases of various origins. The Journal of Biological Chemistry, 234(11), 2901–2905.
  • Vallée, F., Kadziola, A., Bourne, Y., Juy, M., Rodenburg, K. W., Svensson, B., & Haser, R. (1998). Barley alpha-amylase bound to its endogenous protein inhibitor BASI: Crystal structure of the complex at 1.9 Å resolution. Structure, 6(5), 649–659. https://doi.org/10.1016/S0969-2126(98)00066-5
  • Van Der Maarel, M. J., Van der Veen, B., Uitdehaag, J. C., Leemhuis, H., & Dijkhuizen, L. (2002). Properties and applications of starch-converting enzymes of the α-amylase family. Journal of Biotechnology, 94(2), 137–155. https://doi.org/10.1016/S0168-1656(01)00407-2
  • Yamauchi, D., &Minamikawa, T. (1990). Nucleotide sequence of cDNA for alpha-amylase from cotyledons of germinating Vigna mungo seeds. Nucleic Acids Research, 18(14), 4250 10.1093/nar/18.14.4250PMC: 2377468

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.