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

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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

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