Construction of immunoglobulin-binding peptides based on analysis of the protein A of Staphylococcus aureus interaction with immunoglobulins Fc fragment
https://doi.org/10.29235/1561-8331-2019-55-4-447-454
Abstract
Over the past decades, molecular docking has become an increasingly popular tool for the development of new drugs. To search and design new compounds, a detailed study of the interaction of existing complexes of ligands with the target protein is necessary. According to the purpose to identify amino acid residues of the B domain of protein A of Staphylococcus aureus involved in interaction with immunoglobulins G, we studied the interaction mechanisms during the formation of a complex of protein A of the Staphylococcus aureus cell wall and immunoglobulins G by molecular docking. By the means of molecular docking we selected four amino acid residues of Phe132, Gln129, Tyr133 and Phe124, which we can use to construct a peptide analog of the active binding site of protein A with the Fc fragment of immunoglobulins G. The obtained results can serve as starting point for an effective strategy for finding new medicines, in particular, they can be used to further develop biospecific sorbent for the selective removal of immunoglobulins G from human blood.
About the Authors
A. V. Lapko
Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus
Belarus
Belarus
Anastasiya V. Lapko – Researcher.
5/2, acad. V. F. Kuprevich Str., 220141, Minsk
E. S. Pustyul’ga
Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus
Belarus
Belarus
Egor S. Pustyul’ga – Junior Researcher.
5/2, acad. V. F. Kuprevich Str., 220141, Minsk
V. P. Golubovich
Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus
Belarus
Belarus
Vladimir P. Golubovich – D. Sc. (Biology), Professor, Head of the Laboratory.
5/2, acad. V. F. Kuprevich Str., 220141, Minsk
References
1. Ray P. K., Das T., Sa G. Ghosh A. K., Chattopadhyay S. Protection of apoptotic cell death by protein A. Apoptosis, 2000, vol. 5, no. 6, pp. 509–514. https://doi.org/10.1023/a:1009633412009
2. Graille M., Stura E. A., Corper A. L., Sutton B. J., Taussig M. J., Charbonnier J. B., Silverman G. J. Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity. Proceedings of the National Academy of Sciences of the United States of America, 2000, vol. 97, no. 10, pp. 5399–5404. https://doi.org/10.1073/pnas.97.10.5399
3. Kim H. K., Emolo C., DeDent A. C., Falugi F., Missiakas D. M., Schneewind O. Protein A-specific monoclonal antibodies and prevention of Staphylococcus aureus disease in mice. Infection and Immunity, 2012, vol. 80, № 10, pp. 3460–3470. https://doi.org/10.1128/iai.00230-12
4. Peterson P. K., Verhoef J., Sabath L. D., Quie P. G. Effect of protein A on staphylococcal opsonization. Infection and Immunity, 1977, vol. 15, no. 3, pp. 760–764.
5. Sjodahl J. Repetitive sequences in protein A from Staphylococcus aureus. Arrangement of five regions within the protein, four being highly homologous and Fc-binding. European Journal Biochemistry, 1977, no. 73, pp. 343–351. https://doi. org/10.1111/j.1432-1033.1977.tb11324.x
6. Sinha P., Ghosh A. K., Das T., Sa G., Ray P. K. Protein A of Staphylococcus aureus evokes Th1 type response in mice. Immunogy letters, 1999, vol. 67, no. 3, pp. 157–165. https://doi.org/10.1016/s0165-2478(98)00187-4
7. Foster T. J. Immune evasion by staphylococci. Nature reviews Microbiology, 2005, vol. 3, pp. 948–958. https://doi.org/10.1038/nrmicro1289
8. Pyrkov T. V., Ozerov I. V., Balitskaya E. D., Efremov R. G. Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides. Russian Journal of Bioorganic Chemistry, 2010, vol. 36, no. 4, pp. 446–455. https://doi.org/10.1134/s1068162010040023
9. Kosinsky Y. A., Pyrkov T. V., Lutsenko C. V., Efremov R. G. Prediction of protein-Iigand complexes structures: from computer-aided model to biological function. Rossiiskii khimicheskii zhurnal [Russian chemical journal], 2006, vol. L, no. 2, pp. 36–44 (in Russian).
10. Deisenhofer J. Crystallographic Refinement and Atomic Models of a Human FC Fragment and its Complex with Fragment B of Protein A from Staphylococcus Aureus at 2.9-and 2.8-Angstroms Resolution. RCSB Protein Data Bank, 1981. https://doi.org/10.2210/pdb1fc2/pdb
11. Deisenhofer J. Crystallographic refinement and atomic models of a human fc fragment and its complex with fragment b of protein a from staphylococcus aureus at 2.9-and 2.8-angstroms resolution. RCSB Protein Data Bank, 1981. https://doi. org/10.2210/pdb1fc1/pdb .
12. Ultsch M. H., Eigenbrot C. IgG Fc bound to 3 helix of the B-domain from Protein A. Protein Data Bank, 2016. https://doi.org/10.2210/pdb5u4y/pdb
13. Pettersen E. F., Goddard T. D., Huang C. C., Couch G. S., Greenblatt D. M., Meng E. C., Ferrin T. E. UCSF Chimera – a visualization system for exploratory research and analysis. Journal of computational chemistry, 2004, vol. 25, no. 13, pp. 1605–1612. https://doi.org/10.1002/jcc.20084
14. Goddard T. D., Huang C. C., Meng E. C., Pettersen E. F., Couch G. S., Morris J. H., Ferrin T. E. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Science, 2018, no. 1, pp. 14–25. https://doi.org/10.1002/pro.3235
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