Molecular dynamics and small-angle x-ray scattering: a comparison computational and experimental approaches to studying the structure of biological complexes

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Resumo

The results of studying DNA-protein complexes using two independent structural methods – molecular dynamics (MD) and small-angle X-ray scattering (SAXS) – are compared. MD is a computational method that allows visualization of macromolecule behavior in real environmental conditions based on the laws of physics but suffers from numerous simplifications. SAXS is an X-ray method that allows the reconstruction of the three-dimensional structure of an object in solution based on the one-dimensional profile of small-angle scattering, which presents the problem of ambiguity in solving inverse problems. The use of structural characteristics of complexes obtained by the SAXS method for validating 3D structural models obtained in MD experiments has significantly reduced the ambivalence of theoretical predictions and demonstrated the effectiveness of combining MD and SAXS methods for solving structural biology problems.

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Sobre autores

M. Petoukhov

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”; Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences

Autor responsável pela correspondência
Email: pmxmvl@yandex.ru
Rússia, Moscow; Moscow; Moscow

T. Rakitina

National Research Centre "Kurchatov Institute"; Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: pmxmvl@yandex.ru
Rússia, 123182 Moscow; Moscow

Yu. Agapova

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Rússia, 123182 Moscow

D. Petrenko

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Rússia, 123182 Moscow

D. Podshivalov

National Research Centre "Kurchatov Institute"; M.V. Lomonosov Moscow State University

Email: pmxmvl@yandex.ru
Rússia, 123182 Moscow; Moscow

V. Timofeev

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”

Email: pmxmvl@yandex.ru
Rússia, Moscow

G. Peters

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Rússia, 123182 Moscow

Yu. Gaponov

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Rússia, 123182 Moscow

E. Bocharov

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: pmxmvl@yandex.ru
Rússia, Moscow

E. Shtykova

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”; A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences

Email: pmxmvl@yandex.ru
Rússia, Moscow; Moscow

Bibliografia

  1. Feigin L.A., Svergun D.I. Structure analysis by small-angle x-ray and neutron scattering. New York: Plenum Press, 1987. 335 p.
  2. Svergun D.I., Koch M.H., Timmins P.A. et al. Small Angle X-ray and Neutron Scattering from Solutions of Biological Macromolecules. London: Oxford University Press, 2013. 358 p.
  3. Petrenko D.E., Timofeev V.I., Britikov V.V. et al. // Biology (Basel). 2021. V. 10. № 10. P. 1021. https://doi.org/10.3390/biology10101021
  4. Bengtsen T., Holm V.L., Kjolbye L.R. et al. // Elife. 2020. V. 9. P. e56518. https://doi.org/10.7554/eLife.56518
  5. Gaponov Y.A., Timofeev V.I., Agapova Y.K. et al. // Mendeleev Commun. 2022. V. 32. № 6. P. 742. https://doi.org/10.1016/j.mencom.2022.11.011
  6. Shtykova E.V., Petoukhov M.V., Mozhaev A.A. et al. // J. Biol. Chem. 2019. V. 294. № 47. https://doi.org/10.1074/jbc.RA119.010390
  7. Kamyshinsky R., Chesnokov Y., Dadinova L. et al. // Biomolecules. 2020. V. 10. № 1. https://doi.org/Artn 3910.3390/Biom10010039
  8. Larsen A.H., Wang Y., Bottaro S. et al. // PLoS Comput. Biol. 2020. V. 16. № 4. P. e1007870. https://doi.org/10.1371/journal.pcbi.1007870
  9. Timofeev V.I., Gaponov Y.A., Petrenko D.E. et al. // Crystals. 2023. V. 13. P. 1642. https://doi.org/10.3390/cryst13121642
  10. He W., Henning-Knechtel A., Kirmizialtin S. // Front. Bioinform. 2022. V. 2. P. 781949. https://doi.org/10.3389/fbinf.2022.781949
  11. Bhowmick T., Ghosh S., Dixit K. et al. // Nat. Commun. 2014. V. 5. P. 4124. https://doi.org/10.1038/ncomms5124
  12. Agapova Y.K., Altukhov D.A., Timofeev V.I. et al. // Sci. Rep. 2020. V. 10. № 1. P. 15128. https://doi.org/10.1038/s41598-020-72113-4
  13. Altukhov D.A., Talyzina A.A., Agapova Y.K. et al. // J. Biomol. Struct. Dyn. 2016. V. 36. № 1. P. 45. https://doi.org/10.1080/07391102.2016.1264893
  14. Timofeev V.I., Altukhov D.A., Talyzina A.A. et al. // J. Biomol. Struct. Dyn. 2018. V. 36. № 16. P. 4392. https://doi.org/10.1080/07391102.2017.1417162
  15. Emsley P., Lohkamp B., Scott W.G. et al. // Acta Cryst. D. 2010. V. 66. Pt 4. P. 486. https://doi.org/10.1107/S0907444910007493
  16. Mouw K.W., Rice P.A. // Mol. Microbiol. 2007. V. 63. № 5. P. 1319. https://doi.org/10.1111/j.1365-2958.2007.05586.x
  17. Abraham M.J., Murtola T., Schulz R. et al. // SoftwareX. 2015. V. 1–2. P. 19. https://doi.org/10.1016/j.softx.2015.06.001
  18. Voevodin V., Antonov A., Nikitenko D. et al. // Supercomputing Frontiers and Innovations. 2019. V. 6. № 2. P. 4. https://doi.org/10.14529/jsfi190201
  19. Lindorff-Larsen K., Piana S., Palmo K. et al. // Proteins. 2010. V. 78. № 8. P. 1950. https://doi.org/10.1002/prot.22711
  20. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F. et al. // J. Chem. Phys. 1984. V. 81. № 8. P. 3684. https://doi.org/10.1063/1.448118
  21. Parrinello M., Rahman A. // J. Chem. Phys. 1982. V. 76. № 5. P. 2662. https://doi.org/10.1063/1.443248
  22. Hess B., Bekker H., Berendsen H.J.C. et al. // J. Comput. Chem. 1997. V. 18. № 12. P. 1463. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  23. Roe D.R., Cheatham T.E. // J. Chem. Theory Comput. 2013. V. 9. № 7. P. 3084. https://doi.org/10.1021/ct400341p
  24. Peters G.S., Zakharchenko O.A., Konarev P.V. et al. // Nucl. Instrum. Methods Phys. Res. A. 2019. V. 945. P. 162616.
  25. Peters G.S., Gaponov Y.A., Konarev P.V. et al. // Nucl. Instrum. Methods Phys. Res. A. 2022. V. 1025. P. 166170.
  26. Hammersley A.P. // J. Appl. Cryst. 2016. V. 49. № 2. P. 646.
  27. Konarev P.V., Volkov V.V., Sokolova A.V. et al. // J. Appl. Cryst. 2003. V. 36. P. 1277. https://doi.org/10.1107/S0021889803012779
  28. Guinier A., Fournet G. Small Angle Scattering of X-Rays. New York: Wiley, 1955. 268 p.
  29. Porod G. // Small-angle X-ray scattering / Ed Glatter O., Kratky O. London: Academic Press, 1982. P. 17.
  30. Petoukhov M.V., Franke D., Shkumatov A.V. et al. // J. Appl. Cryst. 2012. V. 45. № 2. P. 342. https://doi.org/10.1107/S0021889812007662
  31. Manalastas-Cantos K., Konarev P.V., Hajizadeh N.R. et al. // J. Appl. Cryst. 2021. V. 54. P. 343. https://doi.org/10.1107/S1600576720013412
  32. Svergun D.I. // J. Appl. Cryst. 1992. V. 25. P. 495. https://doi.org/10.1107/S0021889892001663
  33. Svergun D.I., Nierhaus K.H. // J. Biol. Chem. 2000. V. 275. № 19. P. 14432.
  34. Svergun D.I., Barberato C., Koch M.H.J. // J. Appl. Cryst. 1995. V. 28. P. 768. https://doi.org/10.1107/S0021889895007047

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