Oligomerization of IHF protein in the presence of metal cations

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Abstract

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.

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About the authors

A. M. Gordienko

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

Author for correspondence.
Email: alex.gor99@mail.ru
Russian Federation, Moscow

L. A. Dadinova

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

Email: alex.gor99@mail.ru
Russian Federation, Moscow

M. V. 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
Russian Federation, Moscow; Moscow; Moscow

A. 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
Russian Federation, Moscow; Moscow

V. A. 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
Russian Federation, Moscow; Dolgoprudny

V. N. 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
Russian Federation, Moscow; Dolgoprudny

E. V. Shtykova

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

Email: alex.gor99@mail.ru
Russian Federation, Moscow

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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

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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

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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

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