Presentations

Comparative study of the effect of small molecules of antibiotics and anabiosis inducers on DNA and Dps protein of Escherichia coli bacteria

Tereshkina K.B., Tereshkin E.V., Kovalenko V.V., Loiko N.G.¹, Krupyanskii Y.F.

Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia

¹Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, Moscow, Russia

The transition of bacterial cells to a dormant state under stress is accompanied by a significant decrease in their sensitivity to antibiotics [1]. Important bacterial metabolites produced in the cytoplasm during the stationary growth phase include autoinducers of anabiosis [2]. Ferritin-like DNA-binding proteins Dps and their homologues play an important role in preserving bacterial genetic material in such states [3].

As previously shown in cellulo experiments using E. coli K12 and BL21-Gold(DE3)/pET-Dps strains (with and without Dps protein induction), Escherichia coli bacteria are sensitive to the presence of a chemical analogue of the bacterial anabiosis inducer 4-hexylresorcinol (4HR) and the antibiotic ciprofloxacin (CIP). Crystallographic experiments demonstrate similarities in the structural responses of stationary cells to stress exposures of these small molecules, revealing a dose-dependent effect. The aim of this study was to use molecular modeling and bioinformatics to investigate the effects of these compounds on the DNA-binding protein Dps (DNA-binding protein from starved cells), DNA in the absence of Dps, and Dps-DNA complexes. Molecular dynamics simulations were performed using the GROMACS package in the AMBER99-PARMBSC1 all-atom force field using classical approaches and umbrella sampling.

It was shown that CIP and 4HR molecules exhibit similar behavior in solution and at the protein and DNA surfaces. They are capable of modulating the dynamic behavior of the studied bacterial cell components. Clusters of the compounds are capable of organizing DNA and influencing the DNA-binding activity of Dps. Furthermore, a study of the potential of mean force suggests that some ciprofloxacin molecules can penetrate into the protein cavity.

References

1. Windels EM, Van den Bergh B, Michiels J. Bacteria under antibiotic attack: Different strategies for evolutionary adaptation. // PLoS Pathog. 16, 5, 2020. e1008431. https://doi.org/10.1371/journal.ppat.1008431

2. Bukharin O. V., Ginzburg A. L., Romanova Yu. M., El-Registan G. I. Mechanisms of bacterial survival. Moscow: Meditsina, 2005. [In Russian]

3. Orban K, Finkel SE. Dps Is a Universally Conserved Dual-Action DNA-Binding and Ferritin Protein. // J Bacteriol. 204, 2022. e0003622. https://doi.org/10.1128/jb.00036-22.

• abstract in Russian (PDF)