Comparative Structural Investigation of Histone-Like HU Proteins by Small-Angle X-ray Scattering

M. V. Petoukhov; Петухов М. В.; T. V. Rakitina; Ракитина Т. В.; Yu. K. Agapova; Агапова Ю. К.; D. E. Petrenko; Петренко Д. Е.; P. V. Konarev; Конарев П. В.; V. V. Britikov; Бритиков В. В.; E. V. Britikova; Бритикова Е. В.; E. V. Bocharov; Бочаров Э. В.; E. V. Shtykova; Штыкова Э. В.

doi:10.31857/S0023476123600143

Comparative Structural Investigation of Histone-Like HU Proteins by Small-Angle X-ray Scattering

Authors: Petoukhov M.V.¹^,2^,3, Rakitina T.V.⁴^,5, Agapova Y.K.⁴, Petrenko D.E.⁴, Konarev P.V.¹^,4, Britikov V.V.⁶, Britikova E.V.⁶, Bocharov E.V.², Shtykova E.V.¹
Affiliations:
1. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia
2. Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
3. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071, Moscow, Russia
4. National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia
5. Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
6. Institute of Bioorganic Chemistry, National Academy of Science of Belarus, Minsk, Belarus
Issue: Vol 68, No 6 (2023)
Pages: 914-921
Section: STRUCTURE OF MACROMOLECULAR COMPOUNDS
URL: https://rjmseer.com/0023-4761/article/view/673286
DOI: https://doi.org/10.31857/S0023476123600143
EDN: https://elibrary.ru/FZWVGJ
ID: 673286

Cite item

Full Text

Open Access
Restricted Access

Access granted
Restricted Access

Subscription Access

Abstract
About the authors
References
Supplementary files
Statistics

Abstract

Nucleoid-associated proteins (NAPs) control the structure and functions of bacterial nucleoid. Histone-like HU proteins are most abundant NAPs in dividing bacterial cells. Previously, structural ensembles of conformations of HU proteins from pathogenic mycoplasmas Spiroplasma melliferum and Mycoplasma gallisepticum were obtained using NMR spectroscopy. A structural study of these mycoplasma proteins is performed by small-angle X-ray scattering (SAXS). The occurrence of individual conformations from the ensemble, obtained by NMR, is estimated from the scattering data on HU protein solutions. In particular, an approach based on characterization of equilibrium mixtures in terms of volume fractions of their components was applied. The general shape of the proteins and their oligomeric state are independently confirmed using ab initio bead modelling. The flexibility of DNA-binding protein domains is analyzed by the ensemble optimization method, which is based on comparison of the structural characteristics of conformations fitting the SAXS data to the distribution of these characteristics in a randomly generated set. The results obtained give a new insight on the variability of the structure of HU proteins, which is necessary for their functioning.

About the authors

M. V. Petoukhov

Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071, Moscow, Russia

Email: pmxmvl@yandex.ru
Россия, Москва; Россия, Москва; Россия, Москва

References

Dorman C.J. // J. Mol. Microbiol. Biotechnol. 2014. V. 24. № 5–6. P. 316. https://doi.org/10.1159/000368850
Rouviere-Yaniv J., Gros F. // Proc. Natl. Acad. Sci. USA. 1975. V. 72. № 9. https://doi.org/10.1073/pnas.72.9.3428
Kamashev D., Agapova Y., Rastorguev S. et al. // PLoS One. 2017. V. 12. № 11. P. e0188037. https://doi.org/10.1371/journal.pone.0188037
Verma S.C., Harned A., Narayan K. et al. // Mol. Microbiol. 2023. V. 119. № 4. P. 439. https://doi.org/10.1111/mmi.15033
Stojkova P., Spidlova P., Stulik J. // Front. Cell. Infect. Microbiol. 2019. V. 9. P. 159. https://doi.org/10.3389/fcimb.2019.00159
Holowka J., Zakrzewska-Czerwinska J. // Front. Microbiol. 2020. V. 11. P. 590. https://doi.org/10.3389/fmicb.2020.00590
Glass J.I., Assad-Garcia N., Alperovich N. et al. // Proc. Natl. Acad. Sci. USA. 2006. V. 103. № 2. P. 425. https://doi.org/10.1073/pnas.0510013103
Bhowmick T., Ghosh S., Dixit K. et al. // Nat. Commun. 2014. V. 5. P. 4124. https://doi.org/10.1038/ncomms5124
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
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
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
Дадинова Л.А., Петухов М.В., Гордиенко А.М. и др. // Биохимия. 2023. Т. 88. № 5. С. 785. https://doi.org/10.31857/S032097252305007X
Remesh S.G., Verma S.C., Chen J.H. et al. // Nat. Commun. 2020. V. 11. № 1. P. 2905. https://doi.org/10.1038/s41467-020-16724-5
Nikolaeva A.Y., Timofeev V.I., Boiko K.M. et al. // Crystallography Reports. 2015. V. 60. P. 880. https://doi.org/10.1134/S1063774515060231
Boyko K.M., Rakitina T.V., Korzhenevskiy D.A. et al. // Sci. Rep. 2016. V. 6. P. 36366. https://doi.org/10.1038/srep36366
Feigin L.A., Svergun D.I. Structure analysis by small-angle x-ray and neutron scattering. New York: Plenum Press, 1987. 335 p.
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
Blanchet C.E., Spilotros A., Schwemmer F. et al. // J. Appl. Cryst. 2015. V. 48. № 2. P. 431. https://doi.org/10.1107/S160057671500254X
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
Guinier A., Fournet G. Small Angle Scattering of X-Rays. New York: Wiley, 1955. 268 p.
Svergun D.I. // J. Appl. Cryst. 1992. V. 25. P. 495. https://doi.org/10.1107/S0021889892001663
Svergun D.I., Semenyuk A.V., Feigin L.A. // Acta Cryst. A. 1988. V. 44. P. 244. https://doi.org/10.1107/S0108767387011255
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
Porod G. // General theory, in Small-angle X-ray scattering / Eds. Glatter O., Kratky O. London: Academic Press, 1982. P. 17.
Petoukhov M.V., Franke D., Shkumatov A.V. et al. // J. Appl. Cryst. 2012. V. 45. № 2. P. 342. 10.1107/S0021889812007662' target='_blank'>https://doi.org/doi: 10.1107/S0021889812007662
Svergun D.I. // Biophys. J. 1999. V. 76. № 6. P. 2879. https://doi.org/10.1016/S0006-3495(99)77443-6
Petoukhov M.V., Svergun D.I. // Acta Cryst. D. 2015. V. 71. P. 1051. https://doi.org/10.1107/S1399004715002576
Svergun D.I., Barberato C., Koch M.H.J. // J. Appl. Cryst. 1995. V. 28. P. 768. https://doi.org/10.1107/S0021889895007047
Bernado P., Mylonas E., Petoukhov M.V. et al. // J. Am. Chem. Soc. 2007. V. 129. № 17. P. 5656. https://doi.org/10.1021/ja069124n
Petoukhov M.V., Svergun D.I. // Biophys. J. 2005. V. 89. № 2. P. 1237. https://doi.org/10.1529/biophysj.105.064154