Transferrin binding protein-B from Neisseria meningitidis C as a novel carrier protein in glycoconjugate preparation: an in silico approach

References

• Adamiak, P., Calmettes, C., Moraes, T. F., & Schryvers, A. B. (2015). Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system. MicrobiologyOpen, 4(3), 491–504. https://doi.org/10.1002/mbo3.254
   PubMed Web of Science ®Google Scholar
• Avery, O. T., & Goebel, W. F. (1929). Chemo-Immunological studies on conjugated carbohydrate-proteins: II. Immunological specificity of synthetic sugar-protein antigens. The Journal of Experimental Medicine, 50(4), 533–550. https://doi.org/10.1084/jem.50.4.533
   PubMedGoogle Scholar
• Calmettes, C., Alcantara, J., Yu, R. H., Schryvers, A. B., & Moraes, T. F. (2012). The structural basis of transferrin sequestration by transferrin-binding protein B. Nature Structural & Molecular Biology, 19(3), 358–360. https://doi.org/10.1038/nsmb.2251
   PubMed Web of Science ®Google Scholar
• Dagan, R., Poolman, J., & Siegrist, C. A. (2010). Glycoconjugate vaccines and immune interference: A review. Vaccine, 28(34), 5513–5523. https://doi.org/10.1016/j.vaccine.2010.06.026
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103(19), 8577–8593. 1995); https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Farid, R., Day, T., Friesner, R. A., & Pearlstein, R. A. (2006). New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorganic & Medicinal Chemistry, 14(9), 3160–3173. https://doi.org/10.1016/j.bmc.2005.12.032
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Gorring, A., Robinson, A., Hudson, M. J., & Reddin, K. M. (2001). Major iron-regulated protein of Neisseria gonorrhoeae and its use as vaccine (Patent No. WO2001072337A1). Google Patents.
   Google Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. https://doi.org/10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins, 55(2), 351–367. https://doi.org/10.1002/prot.10613
   PubMed Web of Science ®Google Scholar
• McHugh, J. (2020). The sweet success of conjugate vaccines: Milestones, nature portfolio. http://www.nature.com/collections/vaccines-milestone. https://www.nature.com/articles/d42859-020-00017-4
   Google Scholar
• Jin, Z., Chu, C., Robbins, J. B., & Schneerson, R. (2003). Preparation and characterization of group A meningococcal capsular polysaccharide conjugates and evaluation of their immunogenicity in mice. Infection and Immunity, 71(9), 5115–5120. https://doi.org/10.1128/IAI.71.9.5115-5120.2003
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006, November 11–17). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida.
   Google Scholar
• Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science: A Publication of the Protein Society, 27(1), 129–134. https://doi.org/10.1002/pro.3289
   PubMed Web of Science ®Google Scholar
• Lees, A. (2015). Activation of polysaccharides via the cyanylating agent, 1-cyano-4-pyrrolidinopyridinium tetra fluoroborate (CPPT), in the preparation of polysaccharide/protein conjugate vaccines (Patent No. US9044517B2). Google Patents.
   Google Scholar
• Lees, A., Barr, J. F., & Gebretnsae, S. (2020). Activation of soluble polysaccharides with 1-cyano-4-dimethylaminopyridine tetrafluoroborate (CDAP) for use in protein-polysaccharide conjugate vaccines and immunological reagents. Vaccines, 8(4), 777. https://doi.org/10.3390/vaccines8040777
   Web of Science ®Google Scholar
• Lokhande, K., Nawani, N., K Venkateswara, S., & Pawar, S. (2020). Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: A molecular docking and molecular dynamics approach. Journal of Biomolecular Structure & Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1858165
   Google Scholar
• Al-Refaei, M. A., Makki, R. M., & Ali, H. M. (2020). Structure prediction of transferrin receptor protein 1 (TfR1) by homology modelling, docking, and molecular dynamics simulation studies. Heliyon, 6(1), e03221. https://doi.org/10.1016/j.heliyon.2020.e03221
   PubMed Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant-pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
   Web of Science ®Google Scholar
• Perciani, C. T., Barazzone, G. C., Goulart, C., Carvalho, E., Cabrera-Crespo, J., Gonçalves, V. M., Leite, L. C., & Tanizaki, M. M. (2013). Conjugation of polysaccharide 6B from Streptococcus pneumoniae with pneumococcal surface protein A: PspA conformation and its effect on the immune response. Clinical and Vaccine Immunology, 20(6), 858–866. https://doi.org/10.1128/CVI.00754-12
   PubMed Web of Science ®Google Scholar
• Rokbi, B., Mignon, M., Maitre-Wilmotte, G., Lissolo, L., Danve, B., Caugant, D. A., & Quentin-Millet, M. J. (1997). Evaluation of recombinant transferrin-binding protein B variants from Neisseria meningitidis for their ability to induce cross-reactive and bactericidal antibodies against a genetically diverse collection of serogroup B strains. Infection and Immunity, 65(1), 55–63. https://doi.org/10.1128/iai.65.1.55-63.1997
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Suárez, N., Massaldi, H., Franco Fraguas, L., & Ferreira, F. (2008). Improved conjugation and purification strategies for the preparation of protein-polysaccharide conjugates. Journal of Chromatography. A, 1213(2), 169–175. https://doi.org/10.1016/j.chroma.2008.10.030
   PubMed Web of Science ®Google Scholar
• UniProt Consortium (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar