Oligomerization of IHF protein in the presence of metal cations

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Тек жазылушылар үшін

Аннотация

The oligomeric state of the nucleoid-associated protein IHF (integration host factor) plays a significant role in organizing and compacting bacterial nucleoids, as well as in the process of bacterial resistance to adverse environmental conditions, including antibiotics. Although IHF was identified more than 25 years ago, the molecular mechanisms of its involvement in such processes remain poorly understood. In this study, using small-angle X-ray scattering, various oligomeric forms of IHF were first identified in aqueous solution depending on the presence of metal cations. It was found that the presence of Mg2+ and K+ ions inhibits the formation of high-order oligomers. The obtained data can be useful in developing strategies to overcome bacterial resistance to drugs.

Толық мәтін

Рұқсат жабық

Авторлар туралы

A. Gordienko

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

Хат алмасуға жауапты Автор.
Email: alex.gor99@mail.ru
Ресей, Moscow

L. Dadinova

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

Email: alex.gor99@mail.ru
Ресей, Moscow

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, Russian Academy of Sciences

Email: alex.gor99@mail.ru
Ресей, Moscow; Moscow; Moscow

A. Mozhaev

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

Email: alex.gor99@mail.ru
Ресей, Moscow; Moscow

V. Manuvera

Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency; Moscow Institute of Physics and Technology

Email: alex.gor99@mail.ru
Ресей, Moscow; Dolgoprudny

V. Lazarev

Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency; Moscow Institute of Physics and Technology

Email: alex.gor99@mail.ru
Ресей, Moscow; Dolgoprudny

E. Shtykova

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

Email: alex.gor99@mail.ru
Ресей, Moscow

Әдебиет тізімі

  1. Dame R.T., Rashid F.-Z.M., Grainger D.C. // Nat. Rev. Genet. 2020. V. 21. P. 227. https://doi.org/10.1038/s41576-019-0185-4
  2. Rohs R., West S., Sosinsky A. et al. // Nature. 2009. V. 461. P. 1248. https://doi.org/10.1038/nature08473
  3. Shahul Hameed U.F., Liao C., Radhakrishnan A.K. et al. // Nucl. Acids Res. 2019. V. 47. P. 2666. https://doi.org/10.1093/nar/gky1299
  4. Bai L., Morozov A.V. // Trends Genet. 2010. V. 26. P. 476. https://doi.org/10.1016/j.tig.2010.08.003
  5. Wang W., Li G.W. Chen C. et al. // Science. 2011. V. 333. P. 1445. https://doi.org/10.1126/science.1204697
  6. Frenkiel-Krispin D., Ben-Avraham I., Englander J. et al. // Mol. Microbiol. 2004. V. 51. P. 395. https://doi.org/10.1046/j.1365-2958.2003.03855.x
  7. Rice P.A., Yang S., Mizuuchi K. et al. // Cell. 1996. V. 87. P. 1295. https://doi.org/10.1016/s0092-8674(00)81824-3
  8. Grant R., Filman D., Finkel S. et al. // Nat. Struct. Mol. Biol. 1998. V. 5. P. 294. https://doi.org/10.1038/nsb0498-294
  9. Luijsterburg M.S., Noom M.C., Wuite G.J. et al. // J. Struct. Biol. 2006. V. 156. P. 262. https://doi.org/10.1016/j.jsb.2006.05.006
  10. Frenkiel-Krispin D., Minsky A. // J. Struct. Biol. 2006. V. 156. P. 311. https://doi.org/10.1016/j.jsb.2006.05.014
  11. Дадинова Л.А., Петухов М.В., Гордиенко А.М. et al. // Биохимия. 2023. Т. 88. № 5. С. 785. https://doi.org/10.31857/S032097252305007X
  12. Lee S.Y., Lim C.J., Droge P. et al. // Sci. Rep. 2016. V. 5. P. 18146. https://doi.org/10.1038/srep18146
  13. Nash H.A., Robertson C.A. // J. Biol. Chem. 1981. V. 256. P. 9246. https://doi.org/10.1016/S0021-9258(19)52537-6
  14. Hales L.M., Gumport R.I., Gardner J.F. // J. Bacteriol. 1994. V. 176. P. 2999. https://doi.org/10.1128/jb.176.10.2999-3006.1994
  15. Lin J., Chen H., Dröge P. et al. // PLoS One. 2012. V. 7. № 11. https://doi.org/10.1371/journal.pone.0049885
  16. Holbrook J.A., Tsodikov O.V., Saecker R.M. et al. // J. Mol. Biol. 2001. V. 310. № 2. P. 379. https://doi.org/10.1006/jmbi.2001.4768
  17. Feigin L.A., Svergun D.I. Structure analysis by small-angle x-ray and neutron scattering. New York: Plenum Press, 1987. 335 p.
  18. Peters G.S., Zakharchenko O.A., Konarev P.V. et al. // Nucl. Instrum. Methods Phys. Res. A. 2019. V. 945. P. 162616. https://doi.org/10.1016/j.nima.2019.162616
  19. Peters G.S., Gaponov Y.A., Konarev P.V. et al. // Nucl. Instrum. Methods Phys. Res. A. 2022. V. 1025. P. 166170. https://doi.org/10.1016/j.nima.2021.166170
  20. Hammersley A.P. // J. Appl. Cryst. 2016. V. 49. P. 646. https://doi.org/10.1107/S1600576716000455
  21. 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
  22. 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
  23. Konarev P.V., Svergun D.I. // IUCr J. 2015. V. 2. P. 352. https://doi.org/10.1107/S2052252515005163
  24. Svergun D.I. // J. Appl. Cryst. 1992. V. 25. P. 495. https://doi.org/ 10.1107/S0021889892001663
  25. Porod G. Small-Angle X-Ray Scattering ed O Glatter and O Kratky. London: Academic, 1982.
  26. 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
  27. Svergun D.I., Barberato C., Koch M.H.J. // J. Appl. Cryst. 1995 V. 28. P. 768. https://doi.org/10.1107/S0021889895007047
  28. 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
  29. Свергун Д.И., Фейгин Л.А. Рентгеновское и нейтронное малоугловое рассеяние. М.: Наука, 1986. 278 c.
  30. Jacques D.A., Guss J.M., Svergun D.I. et al. // Acta Cryst. D. 2012. V. 68. P. 620. https://doi.org/10.1107/S0907444912012073.
  31. Guinier A. // Ann. Phys. 1939. V. 12. P. 161.

Қосымша файлдар

Қосымша файлдар
Әрекет
1. JATS XML
Жүктеу
2. Fig. 1. Analysis of MURR curves from IHF protein: a - experimental small-angle scattering curves from IHF: 1 - concentration of 10 mg/mL in buffer I, 2 - concentration of 4.8 mg/mL in buffer I, 3 - concentration of 10 mg/mL in buffer II, 4 - concentration of 4.8 mg/mL in buffer II; a, b, c, d - corresponding curves calculated from the distance distribution function (color gamma corresponds to pair functions). The curves are separated in pairs vertically for better visualization; b - distance distribution functions p(r): a, b, c, d correspond to concentrations 1, 2, 3, 4, respectively, in panel a; c - plots in Kratky coordinates: 1, 2, 3, 4 correspond to concentrations in panel a

Жүктеу (482KB)
Метадеректер
3. Fig. 2. Approximation of experimental MURR data by equilibrium mixtures from IHF in buffer I: a - at a concentration of 4.8 mg/mL, b - at a concentration of 10 mg/mL, 1 - experimental data, 2 - calculated scattering curve obtained in the OLIGOMER program from a mixture of oligomers obtained in HEMIX; c, d - models of hexamer and dimer of IHF at a concentration of 4. 8 mg/mL; f, g - models of IHF dodecamer and tetramer at a concentration of 10 mg/mL; e, f - histograms of volume and number fractions in the equilibrium oligomer mixture

Жүктеу (371KB)
Метадеректер
4. Fig. 3. Approximation of experimental MPR data by equilibrium mixtures from IHF in buffer II: a – at a concentration of 10 mg/ml, 1 – experimental data, 2 – calculated scattering curve obtained in the OLIGOMER program from a mixture of dimers, tetramers and hexamers obtained in HEMIX (χ2 = 1.7); b – model IHF hexamer, b – IHF tetramer model, d – IHF dimer model; d – histogram of volume and numerical fractions of oligomers in an equilibrium mixture

Жүктеу (433KB)
Метадеректер

© Russian Academy of Sciences, 2024