In silico study of cox protein from P2 type enteric bacteriophages based on sequence, structure and dynamics to understand its functional integrity

References

• Abedon, S. T. (2019). Phage-antibiotic combination treatments: Antagonistic impacts of antibiotics on the pharmacodynamics of phage therapy? Antibiotics, 8(4), 182. https://doi.org/10.3390/antibiotics8040182
   Web of Science ®Google Scholar
• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Amadei, A., Ceruso, M. A., & Di Nola, A. (1999). On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins: Structure, Function, and Genetics, 36(4), 419–424. https://doi.org/10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Anderson, W. F., Ohlendorf, D. H., Takeda, Y., & Matthews, B. W. (1981). Structure of the cro repressor from bacteriophage λ and its interaction with DNA. Nature, 290(5809), 754–758. https://doi.org/10.1038/290754a0
   PubMed Web of Science ®Google Scholar
• Antimicrobial Resistance Global Report on Surveillance. (2014). https://apps.who.int/iris/bitstream/handle/10665/112647/WHO_HSE_PED_AIP_2014.2_eng.pdf?sequence=1.
   Google Scholar
• Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016). ConSurf 2016: An improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research, 44(W1), W344–W350. https://doi.org/10.1093/nar/gkw408
   PubMed Web of Science ®Google Scholar
• Banushkina, P. V., & Krivov, S. V. (2015). High-resolution free energy landscape analysis of protein folding. Biochemical Society Transactions, 43(2), 157–161.
   PubMedGoogle Scholar
• Basak, S., Singh, P., & Rajurkar, M. (2016). Multidrug resistant and extensively drug resistant bacteria: A study. Journal of Pathogens, 2016, 4065603. https://doi.org/10.1155/2016/4065603
   PubMedGoogle Scholar
• Basu, R., Hazra, S., Shanks, M., Paterson, D. I., & Oudit, G. Y. (2014). Novel mutation in exon 14 of the sarcomere gene MYH7 in familial left ventricular noncompaction with bicuspid aortic valve. Circulation: Heart Failure, 7(6), 1059–1062.
   PubMed Web of Science ®Google Scholar
• Berntsson, R. P. A., Odegrip, R., Sehlen, W., Skaar, K., Svensson, L. M., Massad, T., Högbom, M., Haggård-Ljungquist, E., & Stenmark, P. (2014). Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2. Nucleic Acids Research, 42(4), 2725–2735.
   PubMed Web of Science ®Google Scholar
• Bharatiy, S. K., Hazra, M., Paul, M., Mohapatra, S., Samantaray, D., Dubey, R. C., Sanyal, S., Datta, S., & Hazra, S. (2016). In silico designing of an industrially sustainable carbonic anhydrase using molecular dynamics simulation. ACS Omega, 1(6), 1081–1103.
   PubMed Web of Science ®Google Scholar
• Bhatia, R. (2018). Antimicrobial resistance: Threat, consequences and options. The National Medical Journal of India, 31(3), 133–135. https://doi.org/10.4103/0970-258X.255752
   PubMed Web of Science ®Google Scholar
• Cores de Vries, G., Wu, X. S., & Haggård-Ljungquist, E. (1991). Genetic analysis of the DNA recognition sequence of the P2 Cox protein. Journal of Virology, 65(9), 4665–4669.
   PubMed Web of Science ®Google Scholar
• Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 16(22), 10881–10890. https://doi.org/10.1093/nar/16.22.10881
   PubMed Web of Science ®Google Scholar
• Darden, T., Perera, L., Li, L., & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure (London, England : 1993), 7(3), R55–R60. https://doi.org/10.1016/S0969-2126(99)80033-1
   PubMed Web of Science ®Google Scholar
• Das, V., Kalyan, G., Hazra, S., & Pal, M. (2018). Understanding the role of structural integrity and differential expression of integrin profiling to identify potential therapeutic targets in breast cancer. Journal of Cellular Physiology, 233(1), 168–185.
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
   Google Scholar
• Echols, H., & Green, L. (1971). Establishment and maintenance of repression by bacteriophage lambda: The role of the cI, cII, and cIII proteins. Proceedings of the National Academy of Sciences, 68(9), 2190–2194. https://doi.org/10.1073/pnas.68.9.2190
   PubMed Web of Science ®Google Scholar
• Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010). Features and development of Coot. Acta Crystallographica Section D Biological Crystallography, 66(4), 486–501. https://doi.org/10.1107/S0907444910007493
   PubMedGoogle Scholar
• Eriksson, J. M., & Haggård-Ljungquist, E. (2000). The multifunctional bacteriophage P2 Cox protein requires oligomerization for biological activity. Journal of Bacteriology, 182(23), 6714–6723.
   PubMed Web of Science ®Google Scholar
• Felline, A., Seeber, M., & Fanelli, F. (2020). webPSN v2. 0: A webserver to infer fingerprints of structural communication in biomacromolecules. Nucleic Acids Research, 48(W1), W94–W103. https://doi.org/10.1093/nar/gkaa397
   PubMed Web of Science ®Google Scholar
• Fogg, P. C., Colloms, S., Rosser, S., Stark, M., & Smith, M. C. (2014). New applications for phage integrases. Journal of Molecular Biology, 426(15), 2703–2716.
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. https://doi.org/10.1002/prot.21123
   PubMed Web of Science ®Google Scholar
• Kakodkar, P., Kaka, N., & Baig, M. N. (2020). A comprehensive literature review on the clinical presentation, and management of the pandemic coronavirus disease 2019 (COVID-19). Cureus, 12(4), e7560.
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A. (2001). PDBsum: Summaries and analyses of PDB structures. Nucleic Acids Research, 29(1), 221–222. https://doi.org/10.1093/nar/29.1.221
   PubMed Web of Science ®Google Scholar
• Lindahl, G., & Sunshine, M. (1972). Excision-deficient mutants of bacteriophage P2. Virology, 49(1), 180–187.
   PubMed Web of Science ®Google Scholar
• Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/10.1002/jcc.540130805
   Web of Science ®Google Scholar
• Nikaido, H. (2009). Multidrug resistance in bacteria. Annual Review of Biochemistry, 78, 119–146. https://doi.org/10.1146/annurev.biochem.78.082907.145923
   PubMed Web of Science ®Google Scholar
• Nikolich, M. P., & Filippov, A. A. (2020). Bacteriophage therapy: Developments and directions. Antibiotics, 9(3), 135. https://doi.org/10.3390/antibiotics9030135
   Google Scholar
• Paul, M., Hazra, M., Barman, A., & Hazra, S. (2014). Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”. Journal of Biomolecular Structure & Dynamics, 32(6), 928–949.
   PubMed Web of Science ®Google Scholar
• Paul, M., Panda, G., Mohapatra, P. K. D., & Thatoi, H. (2020). Study of structural and molecular interaction for the catalytic activity of cellulases: An insight in cellulose hydrolysis for higher bioethanol yield. Journal of Molecular Structure, 1204, 127547. https://doi.org/10.1016/j.molstruc.2019.127547
   Web of Science ®Google Scholar
• Paul, M., Panda, M. K., & Thatoi, H. (2019). Developing Hispolon-based novel anticancer therapeutics against human (NF-κβ) using in silico approach of modelling, docking and protein dynamics. Journal of Biomolecular Structure & Dynamics, 37(15), 3947–3967.
   PubMed Web of Science ®Google Scholar
• Paul, M., Pranjaya, P. P., & Thatoi, H. (2020). In silico studies on structural, functional, and evolutionary analysis of bacterial chromate reductase family responsible for high chromate bioremediation efficiency. SN Applied Sciences, 2(12), 1–21. https://doi.org/10.1007/s42452-020-03830-8
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Piazzolla, D., Cali, S., Spoldi, E., Forti, F., Sala, C., Magnoni, F., Deho, D., & Ghisotti, D. (2006). Expression of phage P4 integrase is regulated negatively by both Int and Vis. Journal of General Virology, 87(8), 2423–2431. https://doi.org/10.1099/vir.0.81875-0
   PubMedGoogle Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(W1), W320–W324.
   PubMed Web of Science ®Google Scholar
• Sabini, E., Hazra, S., Konrad, M., & Lavie, A. (2008). Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase. Journal of Medicinal Chemistry, 51(14), 4219–4225.
   PubMed Web of Science ®Google Scholar
• Saha, S., Haggård-Ljungquist, E., & Nordström, K. (1989). Activation of prophage P4 by the P2 Cox protein and the sites of action of the Cox protein on the two phage genomes. Proceedings of the National Academy of Sciences, 86(11), 3973–3977. https://doi.org/10.1073/pnas.86.11.3973
   PubMed Web of Science ®Google Scholar
• Saha, S., Haggård‐Ljungquist, E., & Nordström, K. (1987). The cox protein of bacteriophage P2 inhibits the formation of the repressor protein and autoregulates the early operon. The EMBO Journal, 6(10), 3191–3199.
   PubMed Web of Science ®Google Scholar
• Six, E. W., & Lindqvist, B. H. (1978). Mutual derepression in the P2-P4 bacteriophage system. Virology, 87(2), 217–230.
   PubMed Web of Science ®Google Scholar
• Swalla, B. M., Cho, E. H., Gumport, R. I., & Gardner, J. F. (2003). The molecular basis of co‐operative DNA binding between lambda integrase and excisionase. Molecular Microbiology, 50(1), 89–99.
   PubMed Web of Science ®Google Scholar
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680.
   PubMed Web of Science ®Google Scholar
• Tiwari, S. P., Fuglebakk, E., Hollup, S. M., Skjaerven, L., Cragnolini, T., Grindhaug, S. H., Tekle, K. M., & Reuter, N. (2014). WEBnm@ v2. 0: Web server and services for comparing protein flexibility. BMC Bioinformatics, 15(1), 1–12. https://doi.org/10.1186/s12859-014-0427-6
   PubMedGoogle Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718.
   PubMed Web of Science ®Google Scholar
• Vandamme, E. J. (2014). Phage therapy and phage control: To be revisited urgently!!. Journal of Chemical Technology & Biotechnology, 89(3), 329–333. https://doi.org/10.1002/jctb.4245
   Web of Science ®Google Scholar
• Vaught, A. (1996). Graphing with Gnuplot and Xmgr: Two graphing packages available under linux. Linux Journal, 1996(28es), 7-es.
   Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54(1), 5–6. https://doi.org/10.1002/cpbi.3
   PubMedGoogle Scholar
• Weber, W., Hünenberger, P. H., & McCammon, J. A. (2000). Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. The Journal of Physical Chemistry B, 104(15), 3668–3675. https://doi.org/10.1021/jp9937757
   Web of Science ®Google Scholar
• Yan, Y., Zhang, D., Zhou, P., Li, B., & Huang, S. Y. (2017). HDOCK: A web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research, 45(W1), W365–W373. https://doi.org/10.1093/nar/gkx407
   PubMed Web of Science ®Google Scholar
• Young, R., & Gill, J. J. (2015). Phage therapy redux—What is to be done? Science (New York, N.Y.), 350(6265), 1163–1164.
   PubMed Web of Science ®Google Scholar