Study of the binding of copper (II) ions to the heavy chain of silk fibroin using the charmm22 force field

  • Authors

    • Gulinur Polvonova
    • Khushnudbek Eshchanov Urgench state university
    • Risolat Esomurodova
    2024-01-06
    https://doi.org/10.14419/8ngyt551
  • Abstract

    Silk fibroin is of great interest due to its unique mechanical properties and preparation of biomaterials. It is important to study the mechanisms of the interaction of fibroin with metal ions and the composition of the resulting complexes. We studied the possibilities of coordination binding of copper (II) ions to the heavy chain of the silk fibroin molecule of calculations using the CHARMM22 force field and determined the optimal parts for coordination bonds. To practically confirm the results obtained in theoretical calculations, samples of fibroin containing copper (II) ions were analyzed by ATR-FTIR spectroscopy, and it was proved that copper ions are coordinately bound to the groups in fibroin. The agreement of the results obtained in the theoretical calculations with the results of the actual analysis confirms that indeed, copper (II) ions correspond to the conditions studied by modelling.

     

  • References

    1. Sarymsakov, A. A., Yarmatov, S. S., & Yunusov, K. E. (2023). Physicochemical, Sorption, and Morphological Characteristics of Bombyx Mori Silkworm Cocoon Fibroin and a Multifunctional Hemosorbent Obtained on Its Basis. Polymer Science, Series A, Vol. 65, 256–263. https://doi.org/10.1134/S0965545X23700906.
    2. Acharya C., Ghosh S. K., Kundu S. C. (2009). Silk fibroin film from non-mulberry tropical tasar silkworms: A novel substrate for in vitro fibroblast culture. Acta Biomaterialia, Vol. 5. No. 1. 429-437. https://doi.org/10.1016/j.actbio.2008.07.003.
    3. Zhou C. Z. et al. (2000). Fine organization of Bombyx mori fibroin heavy chain gene. Nucleic acids research, Vol. 28. No. 12. 2413-2419. https://doi.org/10.1093/nar/28.12.2413.
    4. Kim H. et al. (2012). Dietary silk protein, sericin, improves epidermal hydration with increased levels of filaggrins and free amino ac-ids in NC/Nga mice. British Journal of Nutrition, Vol. 108. No. 10. 1726-1735. https://doi.org/10.1017/S0007114511007306.
    5. Huang J., Wong Po Foo C., Kaplan D. L. (2007). Biosynthesis and Applications of Silk‐like and Collagen‐like Proteins. Journal of Macromolecular Science, Part C: Polymer Reviews, Vol. 47. No. 1. 29-62. https://doi.org/10.1080/15583720601109560.
    6. Bini E., Knight D. P., Kaplan D. L. (2004). Mapping domain structures in silks from insects and spiders related to protein assembly. Journal of molecular biology, Vol. 335. No. 1. 27-40. https://doi.org/10.1016/j.jmb.2003.10.043.
    7. Inoue S. et al. (2000). Silk fibroin of Bombyx mori is secreted, assembling a high molecular mass elementary unit consisting of H-chain, L-chain, and P25, with a 6:6:1 molar ratio. Journal of Biological Chemistry, Vol. 275. No. 51. 40517-40528. https://doi.org/10.1074/jbc.M006897200.
    8. Tanaka K. et al. (1999). Determination of the site of disulfide linkage between heavy and light chains of silk fibroin produced by Bombyx mori. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, Vol. 1432. No. 1. 92-103. https://doi.org/10.1016/S0167-4838(99)00088-6.
    9. https://www.uniprot.org/uniprot/?query=Silk+fibroin&sort=score
    10. Vepari C., Kaplan D. L. (2007). Silk as a biomaterial. Progress in polymer science, Vol. 32. No.8-9. 991-1007. https://doi.org/10.1016/j.progpolymsci.2007.05.013.
    11. Zhou C. Z. et al. (2001). Silk fibroin: structural implications of a remarkable amino acid sequence. Proteins: Structure, Function, and Bioinformatics, Vol. 44. No. 2. 119-122. https://doi.org/10.1002/prot.1078.
    12. Chen WX, Lu SF, Yao YY, Pan Y, Shen ZQ. (2005). Copper (II)-Silk Fibroin Complex Fibers as Air-Purifying Materials for Removing Ammonia. Textile Research Journal, Vol. 75, No. 4. 326-330. https://doi.org/10.1177/004051750505732.
    13. Zong, X. H., Zhou, P., Shao, Z. Z., Chen, S. M., Chen, X., Hu, B. W., & Yao, W. H. (2004). Effect of pH and copper (II) on the con-formation transitions of silk fibroin based on EPR, NMR, and Raman spectroscopy. Biochemistry, Vol. 43. No. 38. 11932-11941. https://doi.org/10.1021/bi049455h.
    14. Hua, J., You, H., Li, X., You, R., & Ma, L. (2020). Cu (II) ion loading in silk fibroin scaffolds with silk I structure. International jour-nal of biological macromolecules, Vol. 158. 275-281. https://doi.org/10.1016/j.ijbiomac.2020.04.094.
    15. Mackerell Jr, A. D., Feig, M., & Brooks III, C. L. (2004). Extending the treatment of backbone energetics in protein force fields: Limi-tations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Jour-nal of computational chemistry, Vol. 25, No. 11. 1400-1415. https://doi.org/10.1002/jcc.20065.
    16. Chen, J., Im, W., & Brooks, C. L. (2006). Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. Journal of the American Chemical Society, Vol. 128. No. 11. 3728-3736. https://doi.org/10.1021/ja057216r.
    17. Vanommeslaeghe, K.; MacKerell, A. D. (2015). CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1850. No. 5. 861–871. https://doi.org/10.1016/j.bbagen.2014.08.004.
    18. ESHCHANOV, K., & BALTAYEVA, M. (2022). Determination of the molecular mass of hydrolyzed fibroin obtained from natural silk fibroin by spectrophotometry. Journal of the Turkish Chemical Society Section A: Chemistry, Vol. 9. No. 1. 115-120. https://doi.org/10.18596/jotcsa.969482.
    19. Eshchanov, K. O., & Baltaeva, M. (2022). Study of the interaction of sorbed silver, gold and copper ions with functional groups on hydrolyzed fibroin using Charmm22 force field calculations. Chemical Review and Letters, Vol. 5. No. 3. 161-168.
    20. K. Nakamoto, Infrared and Raman Spectra of Inorganic and Coordination Compounds, 5th edition, John Wiley, New York (1997).
    21. Hua J. et al. (2020). Cu(II) ion loading in silk fibroin scaffolds with silk I structure. International journal of biological macromolecules, Vol. 158. 275-281. https://doi.org/10.1016/j.ijbiomac.2020.04.094.
    22. Sarimsakov A.A., Rashidova S. Sh., Baltaeva M.M., Eshchanov Kh.O., Shigabutdinov A.A. (2018). Study of copper-polymer com-plexes and their production. Actual problems of modern science, education and training in the region, Vol. 3. No. 3. 22-25.
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  • How to Cite

    Polvonova , G., Eshchanov, K., & Esomurodova , R. (2024). Study of the binding of copper (II) ions to the heavy chain of silk fibroin using the charmm22 force field. International Journal of Advanced Chemistry, 12(1), 1-6. https://doi.org/10.14419/8ngyt551