Molecular phylogeny, structure modeling and in silico screening of putative inhibitors of aerolysin of Aeromonas hydrophila EUS112

References

• Abraham M. J., Murtola T., Schulz R., Páll S., Smith J. C., Hess B., & Erik L (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1/2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Abrami, L., & van der Goot, F. G. (1999). Plasma membrane microdomains act as concentration platforms to facilitate intoxication by aerolysin. The Journal of Cell Biology, 147(1), 175–184. https://doi.org/10.1083/jcb.147.1.175
   PubMed Web of Science ®Google Scholar
• Abrami, L., Fivaz, M., Glauser, P. E., Sugimoto, N., Zurzolo, C., & van der Goot, F. G. (2003). Sensitivity of polarized epithelial cells to the pore-forming toxin aerolysin. Infection and Immunity, 71(2), 739–746. https://doi.org/10.1128/iai.71.2.739-746.2003
   PubMed Web of Science ®Google Scholar
• Bairoch, A., Bucher, P., & Hofmann, K. (1997). The PROSITE database, its status in 1997. Nucleic Acids Research, 25(1), 217–221. https://doi.org/10.1093/nar/25.1.217
   PubMed Web of Science ®Google Scholar
• Bendtsen, J. D., Nielsen, H., von Heijne, G., & Brunak, S. (2004). Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology, 340(4), 783–795. https://doi.org/10.1016/j.jmb.2004.05.028
   PubMed Web of Science ®Google Scholar
• Cao, C., Li, M. Y., Cirauqui, N., Wang, Y. Q., Dal Peraro, M., Tian, H., & Long, Y. T. (2018). Mapping the sensing spots of aerolysin for single oligonucleotides analysis. Nature Communications, 9(1), 2823. https://doi.org/10.1038/s41467-018-05108-5
   PubMedGoogle Scholar
• Cao, C., Liao, D. F., Yu, J., Tian, H., & Long, Y. T. (2017). Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis. Nature Protocols, 12(9), 1901–1911. https://doi.org/10.1038/nprot.2017.077
   PubMed Web of Science ®Google Scholar
• Cirauqui, N., Abriata, L. A., van der Goot, F. G., & Dal Peraro, M. (2017). Structural, physicochemical and dynamic features conserved within the aerolysin pore-forming toxin family. Scientific Reports, 7(1), 13932. https://doi.org/10.1038/s41598-017-13714-4
   PubMedGoogle Scholar
• Cumberbatch, N., Gurwith, M. J., Langston, C., Sack, R. B., & Brunton, J. L. (1993). Cytotoxic enterotoxin produced by Aeromonas hydrophila: Relationship of toxigenic isolates to diarrheal disease. Infection and Immunity, 23(3), 267–277. https://doi.org/10.1128/IAI.23.3.829-837.1979
   Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. In J. E. Hempel, C. H. Williams, & C. C. Hong (Eds.), Chemical biology: Methods and protocols, methods in molecular biology (pp. 243–250). Springer.
   Google Scholar
• Delano, W. L., & Palo Alto, C. A. (2002). The PYMOL molecular graphics system.
   Google Scholar
• Discovery Studio Visualizer Software, Version 4.0. (2012). http://www.accelrys.com
   Google Scholar
• Dong, J., Liu, Y., Xu, N., Yang, Q. & Ai, X. (2018). Morin protects channel catfish from Aeromonas hydrophila infection by blocking aerolysin activity. Frontiers in Microbiology, 9, 2828. https://doi.org/10.3389/fmicb.2018.02828
   PubMed Web of Science ®Google Scholar
• Dong, J., Zhang, L., Liu, Y., Xu, N., Zhou, S., Yang, Q., Yang, Y., & Ai, X. (2020). Thymol protects channel catfish from Aeromonas hydrophila infection by inhibiting aerolysin expression and biofilm formation. Microorganisms, 8(5), 636. https://doi.org/10.3390/microorganisms8050636
   PubMed Web of Science ®Google Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404. https://doi.org/10.1016/s0076-6879(97)77022-8
   PubMed Web of Science ®Google Scholar
• Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution International Journal of Organic Evolution, 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
   PubMed Web of Science ®Google Scholar
• Ferguson, M. R., Xu, X. J., Houston, C. W., Peterson, J. W., & Chopra, A. K. (1995). Amino-acid residues involved in biological functions of the cytolytic enterotoxin from Aeromonas hydrophila. Gene, 156(1), 79–83. https://doi.org/10.1016/0378-1119(95)00043-6
   PubMed Web of Science ®Google Scholar
• Gauthier, J., Vincent, A. T., Charette, S. J., & Derome, N. (2017). Strong genomic and phenotypic heterogeneity in the Aeromonas sobria species complex. Frontiers in Microbiology, 8, 2434. https://doi.org/10.3389/fmicb.2017.02434
   PubMed Web of Science ®Google Scholar
• Gosling, P. J. (1996). Pathogenic mechanisms. In B. Austin, M. Altwegg, P. J. Gosling, & S. W. Joseph (Eds.), The genus Aeromonas (pp. 245–265). John Wiley & Sons Ltd..
   Google Scholar
• Janda, J. M., & Abbott, S. L. (2010). The genus Aeromonas: Taxonomy, pathogenicity, and infection. Clinical Microbiology Reviews, 23(1), 35–73. https://doi.org/10.1128/CMR.00039-09
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereo chemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford University Press.
   Google Scholar
• Ramachandran, G. N., & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Advances in Protein Chemistry, 23, 283–438. https://doi.org/10.1016/s0065-3233(08)60402-7
   PubMedGoogle Scholar
• Rasmussen-Ivey, C. R., Figueras, M. J., McGarey, D., & Liles, M. R. (2016). Virulence factors of Aeromonas hydrophila: In the wake of reclassification. Frontiers in Microbiology, 7, 1337. https://doi.org/10.3389/fmicb.2016.01337
   PubMed Web of Science ®Google Scholar
• Rost, B., Yachdav, G., & Liu, J. (2004). The PredictProtein server. Nucleic Acids Research, 32 (Web Server issue), W321–W326. https://doi.org/10.1093/nar/gkh377
   PubMed Web of Science ®Google Scholar
• Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
   PubMed Web of Science ®Google Scholar
• Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
   PubMed Web of Science ®Google Scholar
• Santos, K. B., Guedes, I. A., Karl, A., & Dardenne, L. E. (2020). Highly flexible ligand docking: benchmarking of the DockThor Program on the LEADS-PEP protein-peptide data set. Journal of Chemical Information and Modeling, 60(2), 667–683. https://doi.org/10.1021/acs.jcim.9b00905
   PubMed Web of Science ®Google Scholar
• Schneider, G. F., & Dekker, C. (2012). DNA sequencing with nanopores. Nature Biotechnology, 30(4), 326–328. https://doi.org/10.1038/nbt.2181
   PubMed Web of Science ®Google Scholar
• Singh, V., & Somvanshi, P. (2009). Inhibition of oligomerization of aerolysin from Aeromonas hydrophila: Homology modeling and docking approach for exploration of hemorrhagic septicemia. Letters in Drug Design & Discovery, 6(3), 215, 223. https://doi.org/10.2174/157018009787847864
   Web of Science ®Google Scholar
• Singh, V., Somvanshi, P., Rathore, G., Kapoor, D., & Mishra, B. N. (2010). Gene cloning, expression, and characterization of recombinant aerolysin from Aeromonas hydrophila. Applied Biochemistry and Biotechnology, 160(7), 1985–1991. https://doi.org/10.1007/s12010-009-8752-3
   PubMed Web of Science ®Google Scholar
• Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins, 17(4), 355–362. https://doi.org/10.1002/prot.340170404
   PubMed Web of Science ®Google Scholar
• Stefureac, R., Long, Y. T., Kraatz, H. B., Howard, P., & Lee, J. S. (2006). Transport of alpha-helical peptides through alpha-hemolysin and aerolysin pores. Biochemistry, 45(30), 9172–9179. https://doi.org/10.1021/bi0604835
   PubMed Web of Science ®Google Scholar
• Studer, G., Rempfer, C., Waterhouse, A. M., Gumienny, R., Haas, J., & Schwede, T. (2020). QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics (Oxford, England), 36(6), 1765–1771. https://doi.org/10.1093/bioinformatics/btz828
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Véron M. (1965). La position taxonomique des Vibrio et de certaines bactéries comparables [The taxonomic position of Vibrio and certain comparable bacteria]. Comptes Rendus Hebdomadaires Des Seances de L'Academie Des Sciences. Serie D: Sciences Naturelles, 261(23), 5243–5246.
   PubMedGoogle Scholar
• Wang, G., Clark, C. G., Liu, C., Pucknell, C., Munro, C. K., Kruk, T. M., Caldeira, R., Woodward, D. L., & Rodgers, F. G. (2003). Detection and characterization of the hemolysin genes in Aeromonas hydrophila and Aeromonas sobria by multiplex PCR. Journal of Clinical Microbiology, 41(3), 1048–1054. https://doi.org/10.1128/JCM.41.3.1048-1054.2003
   PubMed Web of Science ®Google Scholar
• Wang, Y. Q., Cao, C., Ying, Y. L., Li, S., Wang, M. B., Huang, J., & Long, Y. T. (2018). Rationally designed sensing selectivity and sensitivity of an aerolysin nanopore via site-directed mutagenesis. ACS Sensors, 3(4), 779–783. https://doi.org/10.1021/acssensors.8b00021
   PubMed Web of Science ®Google Scholar
• Zhu, D., Li, A., Wang, J., Li, M., & Cai, T. (2007). Cloning, expression and characterization of aerolysin from Aeromonas hydrophila in Escherichia coli. Indian Journal of Biochemistry & Biophysics, 44(4), 204–208. PMID: 17970277
   PubMed Web of Science ®Google Scholar