Quantum entangle in a zinc ion pair of RNA-dependent RNA polymerase of flaviviruses and its role in the polymerization reaction
https://doi.org/10.29235/1561-8323-2024-68-5-365-372
Abstract
The flavivirus polymerase protein undergoes structural changes during the polymerization reaction. The protein contains two zinc atoms, each of which is coordinated by four amino acids of the protein. The possibility of a quantum transition in zinc atoms is considered. It is shown that due to quantum entanglement this transition occurs jointly in both atoms. Using molecular dynamics modeling, it is shown that small perturbations of the structure associated with the joint transition of zinc atoms lead to structural changes in the polymerase. The prevalence of this phenomenon on other zinc-containing proteins is discussed.
About the Authors
U. V. PotapovaBelarus
Ulyana V. Potapova – Assistant, Belarusian State Technological University.
13a, Sverdlov Str., 220006, Minsk
S. I. Feranchuk
Belarus
Sergey I. Feranchuk – Ph. D. (Physics and Mathematics).
A. V. Batyanovskii
Belarus
Alexander V. Batyanovskii – Ph. D. (Physics and Mathematics), Senior Researcher, United Institute of Informatics Problems of the National Academy of Sciences of Belarus.
6, Surganov Str., 220012, Minsk
D. S. Matuskov
Belarus
Dmitry S. Matuskov – Student, Belarusian State Technological University.
13a, Sverdlov Str., 220006, Minsk
I. D. Feranchuk
Belarus
Ilya D.Feranchuk – D. Sc. (Physics and Mathematics), Professor. Belarusian State University.
4, Nezavisimosti Ave., 220030, Minsk
References
1. Lambert N., Chen Y. N., Cheng Y. C., Li C. M., Chen G. Y., Nori F. Quantum biology. Nature Physics, 2013, vol. 9, pp. 10–18. https://doi.org/10.1038/nphys2474
2. Garmaza Yu. M., Slobozhanina E. I. Zinc in the living organism: biological role and mechanisms of action. Minsk, 2021. 189 p. (in Russian).
3. Malet H., Egloff M. P., Selisko B., Butcher R. E., Wright P. J., Roberts M., Gruez A., Sulzenbacher G., Vonrhein C., Bricogne G., Mackenzie J. M., Khromykh A. A., Davidson A. D., Canard B. Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5. Journal of Biological Chemistry, 2007, vol. 282, no. 14, pp. 10678–10689. https://doi.org/10.1074/jbc.m607273200
4. Yap T. L., Xu T., Chen Y. L., Malet H., Egloff M. P., Canard B., Vasudevan S. G., Lescar J. Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. Journal of Virology, 2007, vol. 81, no. 9, pp. 4753–4765. https://doi.org/10.1128/jvi.02283-06
5. Zhao Y., Soh T. S., Zheng J., Chan K. W., Phoo W. W., Lee C. C., Tay M. Y., Swaminathan K., Cornvik T. C., Lim S. P., Shi P. Y., Lescar J., Vasudevan S. G., Luo D. A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication. PLoS Pathogens, 2015, vol. 11, no. 3, art. e1004682. https://doi.org/10.1371/journal.ppat.1004682
6. Lu G., Gong P. Crystal Structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface. PLoS Pathogens, 2013, vol. 9, no. 8, art. e1003549. https://doi.org/10.1371/journal.ppat.1003549
7. Skoromnik O. D., Feranchuk I. D., Leonau A. U., Keitel C. H. Analytic model of a multi-electron atom. Journal of Physics B: Atomic, Molecular and Optical Physics, 2017, vol. 50, art. 245007. https://doi.org/10.1088/1361-6455/aa92e6
8. Tavis M., Cummings F. W. Approximate Solutions for an N-Molecule-Radiation-Field Hamiltonian. Physical Review, 1969, vol. 188, no. 2, pp. 692–695. https://doi.org/10.1103/physrev.188.692
9. Feranchuk I. D., San N. Q., Leonau A. U., Skoromnik O. D. Radiation-induced interaction potential of two qubits strongly coupled with a quantized electromagnetic field. Physical Review A, 2020, vol. 102, no. 4, art. 043702. https://doi.org/10.1103/physreva.102.043702
10. Case D. A., Cheatham T. E., Darden T., Gohlke H., Luo R., Merz K. M. Jr., Onufriev A., Simmerling C., Wang B., Woods R. J. The Amber biomolecular simulation programs. Journal of Computational Chemistry, 2005, vol. 26, no. 16, pp. 1668–1688. https://doi.org/10.1002/jcc.20290
11. Gong P., Peersen O. B. Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proceedings of the National Academy of Sciences USA, 2010, vol. 107, no. 52, pp. 22505–22510. https://doi.org/10.1073/pnas.1007626107
12. Klug A., Rhodes D. Zinc fingers: a novel protein fold for nucleic acid recognition. Cold Spring Harbor Symposia on Quantative Biology, 1987, vol. 52, pp. 473–482. https://doi.org/10.1101/sqb.1987.052.01.054
13. Iwahara J., Levy Y. Speed-stability paradox in DNA-scanning by zinc-finger proteins. Transcription, 2013, vol. 4, no. 2, pp. 58–61. https://doi.org/10.4161/trns.23584