A thermodynamic model for the formation of protein aggregates on a matrix

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Abstract

The development of many neurodegenerative diseases is associated with the formation of pathological protein aggregates. In some cases, these aggregates can be formed by multilayer adsorption of ligands on a matrix, for example, the set of membrane protein receptors. The paper proposes a thermodynamic model describing the formation of linear aggregates in which ligands can be stacked. The cases when these stacks consist of complexes of one or two different types are considered. The developed model can be applied to the study of pathological aggregation of proteins of different nature, primarily beta-amyloid and its isoforms. The mean, variance and entropy of the theoretical distributions of aggregate sizes are calculated. A comparison with other theoretical models of the formation of amyloid aggregates is made.

About the authors

E. O Vasilenko

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences;Moscow Institute of Physics and Technology

Email: vasilenko.eo@phystech.edu
Moscow, Russia

S. A Kozin

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Moscow, Russia

V. A Mitkevich

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Moscow, Russia

A. S Buchelnikov

Sevastopol State University

Email: tolybas@rambler.ru
Sevastopol, Russia

Yu. D Nechipurenko

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences;Sevastopol State University

Email: nech99@mail.ru
Moscow, Russia;Sevastopol, Russia

References

  1. A. M. Morris, M. A. Watzky, and R. G. Finke, Biochimica et Biophysica Acta - Proteins and Proteomics, 1794 (3), 375 (2009).
  2. R. J. Loureiro, et al., In Proc. of Int. Conf. on Multidisciplinary Sciences MOL2NET 2018, 4th edition (MD-PI, 2018), p. 1.
  3. R. B. Martin, Chem. Rev., 96 (8), 3043 (1996).
  4. V. P. Evstigneev, et al., J. Chem. Phys., 134 (19) (2011).
  5. A. S. Buchelnikov, V. P. Evstigneev, and M. P. Evstigneev, Chem. Phys., 421, 77 (2013).
  6. T. L. Hill, Thermodynamics of Small Systems (Courier Corp., 1994).
  7. S. Lifson, J. Chem. Phys., 40 (12), 3705 (1964).
  8. M. P. Heyn and R. Bretz, Biophys. Chem., 3 (1), 35 (1975).
  9. J. Spouge, Macromolecules, 16 (1), 121 (1983). doi: 10.1021/ma00235a024
  10. S. Brunauer, P. H. Emmett, and E. Teller, J. Am. Chem. Soc., 60 (2), 309 (1938).
  11. Z. L. Almeida, R. M. M. Brito, Molecules, 25 (5), 1195 (2020).
  12. W. F. Xue, S. W. Homans, and S. E. Radford, Prot. Engineering, Design & Selection, 22 (8), 489 (2009). doi: 10.1093/protein/gzp026
  13. J. Hinz, L. M. Gierasch, and Z. Ignatova, Biochemistry, 47 (14), 4196 (2008).
  14. W. F. Xue, S. W. Homans, and S. E. Radford, Proc. Natl. Acad. Sci. USA, 105 (26), 8926 (2008).
  15. W. F. Xue and S. E. Radford, Biophys J., 105 (12), 2811 (2013).
  16. P. J. Flory, J. Am. Chem. Soc., 58 (10), 1877 (1936).
  17. G. W. Platt, et al., J. Mol. Biol., 378 (1), 251 (2008).
  18. M. I. Ivanova, et al., Biophys. Chem., 269, 106507 (2021).
  19. W. Zheng, M. Y. Tsai, and P. G. Wolynes, J. Am. Chem. Soc., 139 (46), 16666 (2017).
  20. S. A. Kozin, et al., Biochemistry (Moscow), 83, 1057 (2018).
  21. В. В. Аристов и др., Применение понятий энтропии и информации для исследования биосистем: от молекул до организмов (2023).
  22. L. M. Smith and S. M. Strittmatter, Cold Spring Harbor Perspectives in Medicine, 7 (5), a024075 (2017).
  23. V. A. Mitkevich, et al., Aging and Disease, 14 (2), 309 (2023).
  24. V. V. Aristov, A. S. Buchelnikov, and Y. D. Nechipurenko, Entropy, 24 (2), 172 (2022).
  25. S. A. Kozin, Biochemistry (Moscow), 88 (Suppl. 1), S75 (2023). doi: 10.1134/S0006297923140055
  26. Y. Kong, J. Chem. Phys., 135 (15) (2011).
  27. Ю. Д. Нечипуренко, Анализ связывания биологически активных соединений с нуклеиновыми кислотами (Ин-т компл. исслед., Москва - Ижевск, 2015).

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