In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors

References

• Aier, I., Varadwaj, P. K., & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6, 34984. https://doi.org/10.1038/srep34984
   PubMed Web of Science ®Google Scholar
• Blanch, M., Dorca-Arévalo, J., Not, A., Cases, M., Gomez de Aranda, I., Martínez-Yélamos, A., Martínez-Yélamos, S., Solsona, C., & Blasi, J. (2018). The cytotoxicity of epsilon toxin from Clostridium perfringens on lymphocytes is mediated by MAL protein expression. Molecular and Cellular Biology, 38(19), e00086-18. https://doi.org/10.1128/MCB.00086-18
   PubMed Web of Science ®Google Scholar
• Bokori‐Brown, M., Kokkinidou, M. C., Savva, C. G., Fernandes da Costa, S., Naylor, C. E., Cole, A. R., Moss, D. S., Basak, A. K., & Titball, R. W. (2013). Clostridium perfringens epsilon toxin H149A mutant as a platform for receptor binding studies. Protein Science, 22(5), 650–659. https://doi.org/10.1002/pro.2250
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Dorca-Arévalo, J., Gómez de Aranda, I., & Blasi, J. (2022). New mutants of epsilon toxin from Clostridium perfringens with an altered receptor-binding site and cell-type specificity. Toxins, 14(4), 288. https://doi.org/10.3390/toxins14040288
   PubMed Web of Science ®Google Scholar
• Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9(1), 1–9. https://doi.org/10.1186/1741-7007-9-71
   PubMed Web of Science ®Google Scholar
• Fennessey, C. M., Sheng, J., Rubin, D. H., & McClain, M. S. (2012). Oligomerization of Clostridium perfringens epsilon toxin is dependent upon caveolins 1 and 2. PLoS One, 7(10), e46866. https://doi.org/10.1371/journal.pone.0046866
   PubMed Web of Science ®Google Scholar
• Finnie, J. W., & Uzal, F. A. (2022). Pathology and pathogenesis of brain lesions produced by clostridium perfringens type D epsilon toxin. International Journal of Molecular Sciences, 23(16), 9050. https://doi.org/10.3390/ijms23169050
   PubMed Web of Science ®Google Scholar
• Gangwar, N. K., Pawaiya, R. V. S., Gururaj, K., Andani, D., Kumar, A., Singh, R., & Singh, A. P. (2022). Enterocolitis in goats associated with enterotoxaemia in the perspective of two toxins: Epsilon toxin and beta-2 toxin – An immunohistochemical and molecular study. Comparative Immunology, Microbiology and Infectious Diseases, 87, 101837. https://doi.org/10.1016/j.cimid.2022.101837
   PubMed Web of Science ®Google Scholar
• Hooft, R. W. W., Vriend, G., Sander, C., & Abola, E. E. (1996). Errors in protein structures. Nature, 381(6580), 272–272. https://doi.org/10.1038/381272a0
   PubMed Web of Science ®Google Scholar
• Khalili, S., Jahangiri, A., Hashemi, Z. S., Khalesi, B., Mard-Soltani, M., & Amani, J. (2017). Structural pierce into molecular mechanism underlying Clostridium perfringens Epsilon toxin function. Toxicon, 127, 90–99. https://doi.org/10.1016/j.toxicon.2017.01.010
   PubMed Web of Science ®Google Scholar
• Kumar, R., Gururaj, K., Pawaiya, R. V. S., Mishra, A. K., Chaturvedi, V., Varshney, M., Andani, D., Jena, D., Sharma, A., Gangwar, N. K., & Singh, R. (2019). Pathology of experimental Clostridium perfringens type D entero-toxaemia in goats.
   Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Manni, M. M., Sot, J., & Goñi, F. M. (2015). Interaction of Clostridium perfringens epsilon-toxin with biological and model membranes: A putative protein receptor in cells. Biochimica et Biophysica Acta, 1848(3), 797–804. https://doi.org/10.1016/j.bbamem.2014.11.028
   PubMed Web of Science ®Google Scholar
• Mathur, D. D., Deshmukh, S., Kaushik, H., & Garg, L. C. (2010). Functional and structural characterization of soluble recombinant epsilon toxin of Clostridium perfringens D, causative agent of enterotoxaemia. Applied Microbiology and Biotechnology, 88(4), 877–884. https://doi.org/10.1007/s00253-010-2785-y
   PubMed Web of Science ®Google Scholar
• Mitchell, A., Chang, H.-Y., Daugherty, L., Fraser, M., Hunter, S., Lopez, R., McAnulla, C., McMenamin, C., Nuka, G., Pesseat, S., Sangrador-Vegas, A., Scheremetjew, M., Rato, C., Yong, S.-Y., Bateman, A., Punta, M., Attwood, T. K., Sigrist, C. J. A., Redaschi, N., … Finn, R. D. (2015). The InterPro protein families database: The classification resource after 15 years. Nucleic Acids Research, 43(Database issue), D213–21. https://doi.org/10.1093/nar/gku1243
   PubMedGoogle Scholar
• Nagahama, M., Seike, S., Ochi, S., Kobayashi, K., & Takehara, M. (2020). Clostridium perfringens epsilon-toxin impairs the barrier function in MDCK cell monolayers in a Ca2+-dependent manner. Toxins, 12(5), 286. https://doi.org/10.3390/toxins12050286
   PubMed Web of Science ®Google Scholar
• Pawaiya, R. S., Gururaj, K., Gangwar, N. K., Singh, D. D., Kumar, R., & Kumar, A. (2020). The challenges of diagnosis and control of enterotoxaemia caused by Clostridium perfringens in small ruminants. Advances in Microbiology, 10(05), 238–273. https://doi.org/10.4236/aim.2020.105019
   Google Scholar
• Pontius, J., Richelle, J., & Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology, 264(1), 121–136. https://doi.org/10.1006/jmbi.1996.0628
   PubMed Web of Science ®Google Scholar
• Singh, D. D., Pawaiya, R. V. S., Gururaj, K., Gangwar, N. K., Mishra, A. K., Singh, R., Andani, D., & Kumar, A. (2018). Detection of Clostridium perfringens toxinotypes, enteropathogenic E. coli, Rota and corona viruses in the intestine of neonatal goat kids by molecular techniques. The Indian Journal of Animal Sciences, 88(6), 655–661. https://doi.org/10.56093/ijans.v88i6.80863
   Web of Science ®Google Scholar
• Uzal, F. A., & Kelly, W. R. (1998). Experimental Clostridium perfringens type D enterotoxemia in goats. Veterinary Pathology, 35(2), 132–140. https://doi.org/10.1177/030098589803500207
   PubMed Web of Science ®Google Scholar
• Vaguine, A. A., Richelle, J., & Wodak, S. J. (1999). SFCHECK: A unified set of procedure for evaluating the quality of macromolecular structure-factor data and their agreement with atomic model. Acta Crystallographica, Section D, Biological Crystallography, 55(Pt 1), 191–205. https://doi.org/10.1107/S0907444998006684
   PubMedGoogle Scholar
• Weng, X., Hamel, L., Martin, L. M., & Peckham, J. (2005). A genetic algorithm for energy minimization in bio-molecular systems. Evolutionary Computation, The 2005 IEEE Congress (Vol. 1, pp. 49–56).
   Google Scholar
• Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
   PubMed Web of Science ®Google Scholar
• Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40. https://doi.org/10.1186/1471-2105-9-40
   PubMed Web of Science ®Google Scholar
• Zhang, J., Liang, Y., & Zhang, Y. (2011). Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (London, England: 1993), 19(12), 1784–1795. https://doi.org/10.1016/j.str.2011.09.022
   PubMed Web of Science ®Google Scholar