Bioinformatics Analysis of B. Abortus Strain 2308 Protein and Its Drug Docking
Keywords:
Brucellosis, Brucella abortus, bioinformatics, protein homology modelling, structure prediction, infectious diseases, drug dockingAbstract
Brucellosis is among the fast-spreading disease on Earth causing casualties in livestock as well as in humans. It’s an alarming situation to kick off the study of Brucellosis causing agent. Brucellosis is an infective sickness caused by Brucella abortus. Here, we have carried out the Insilco analysis of Brucella abortus strain 2308. This strain is mainly responsible for the disease. Here, we have tried to study the B. abortus strain 2308 by the means of bioinformatics methodology. We have run several Insilco tools to predict its structure and function. Moreover, we have carried out the methodology of protein homology modelling on this strain. Furthermore, we have also carried out several protein chain analyses, protein-protein interface, structure alignment, structure prediction and active site prediction. To make our study more productive we have also performed drug docking. These results will add on a little info in the emerging bioinformatics data regarding Brucella abortus.
Downloads
References
Khan, M. Y., Mah, M. W., & Memish, Z. A. (2001). Brucellosis in pregnant women. Clinical infectious diseases, 32(8), 1172-1177.
Samartino, L. E., & Enright, F. M. (1993). Pathogenesis of abortion of bovine brucellosis. Comparative immunology, microbiology and infectious diseases, 16(2), 95-101.
Hajibemani, A., & Sheikhalislami, H. Zoonotic pathogens cause of animal abortion and fetal loss.
Priyanka, S. B., & SK, K. (2019). Bovine brucellosis, A review on background information and perspective. Journal of Entomology and Zoology Studies, 7(2), 607-613.
He, Y. (2012). Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Frontiers in cellular and infection microbiology, 2, 2.
Ragan, V. E. (2002). The animal and plant health inspection service (APHIS) brucellosis eradication program in the United States. Veterinary microbiology, 90(1-4), 11-18.
Ragan, V. E. (2002). The animal and plant health inspection service (APHIS) brucellosis eradication program in the United States. Veterinary microbiology, 90(1-4), 11-18.
Corbel, M. J. (2006). Brucellosis in humans and animals. World Health Organization.
YAEGER, M.J. and HOLLER, L.D., 2007. Bacterial causes of bovine infertility and abortion. In Current therapy in large animal theriogenology (pp. 389-399). WB Saunders.
Reichel, M.P., Wahl, L.C. and Hill, F.I., 2018. Review of diagnostic procedures and approaches to infectious causes of reproductive failures of cattle in Australia and New Zealand. Frontiers in veterinary science, 5, p.222
Suárez-Esquivel, M., Ruiz-Villalobos, N., Castillo-Zeledón, A., Jiménez-Rojas, C., Roop Ii, R.M., Comerci, D.J., Barquero-Calvo, E., Chacón-Díaz, C., Caswell, C.C., Baker, K.S. and Chaves-Olarte, E., 2016. Brucella abortus strain 2308 Wisconsin genome: importance of the definition of reference strains. Frontiers in microbiology, 7, p.1557.
Ikpeazu, O. V., Otuokere, I. E., & Igwe, K. K. (2017). In silico structure-activity relationship and virtual screening of monosubstituted doxycycline with Pseudomonas aeruginosa Lipase. J Anal Pharm Res, 5(3), 00139.
Yoshizawa, S., Fourmy, D., & Puglisi, J. D. (1998). Structural origins of gentamicin antibiotic action. The EMBO journal, 17(22), 6437-6448.
The UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47: D506-515 (2019)
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.
Gish, W. & States, D.J. (1993) "Identification of protein coding regions by database similarity search." Nature Genet. 3:266-272.
Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.
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 Res. 25:3389-3402.
Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.
Zhang, J. & Madden, T.L. (1997) "PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation." Genome Res. 7:649-656.
Morgulis A., Coulouris G., Raytselis Y., Madden T.L., Agarwala R., & Schäffer A.A. (2008) "Database indexing for production MegaBLAST searches." Bioinformatics 15:1757-1764.
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., & Madden T.L. (2008) "BLAST+: architecture and applications." BMC Bioinformatics 10:421.
Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, & Madden T.L. (2012) "Domain enhanced lookup time accelerated BLAST." Biol Direct. 2012 Apr 17;7:12.
Boratyn GM, Thierry-Mieg J, Thierry-Mieg D, Busby B, Madden T.L. (2019) "Magic-BLAST, an accurate RNA-seq aligner for long and short reads." BMC Bioinformatics. 2019 Jul 25;20(1):405.
Garnier, J., Osguthorpe, D.J., and Robson, B. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97-120.
Laskowski, R. A. (2009). PDBsum new things. Nucleic acids research, 37(suppl_1), D355-D359.
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. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
Guex, N., Peitsch, M.C., Schwede, T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis 30, S162-S173 (2009).
Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).
Willett, J. W., Herrou, J., Briegel, A., Rotskoff, G., & Crosson, S. (2015). Structural asymmetry in a conserved signaling system that regulates division, replication, and virulence of an intracellular pathogen. Proceedings of the National Academy of Sciences, 112(28), E3709-E3718.
Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992). Stereochemical quality of protein structure coordinates. Proteins, 12, 345-364.
DeLano, W. L. (2002). PyMOL. DeLano Scientific, San Carlos, CA, 700.
DeLano, W. L. (2009). The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, 2002. There is no corresponding record for this reference.
DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool.
-Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
editor@ijrasb.com 