Interaction of deoxyribonucleic acid with deoxyribonucleic acid-binding protein from starved cells: cluster formation and crystal growing as a model of initial stages of nucleoid biocrystallization

Терешкин, Э. В.; Терешкина, К. Б.; Лойко, Н. Г.; Chulichkov, A. L.; Kovalenko, Vladislav; Krupyanskiǐ, Yu. F.

doi:10.1080/07391102.2018.1492458

Cited by 18 publications

(12 citation statements)

References 14 publications

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“…coli) cells [ 13 , 14 ]. Its structure [ 15 ] and interactions with DNA were recently excessively studied in vitro [ 14 , 16 , 17 ], and in silico [ 18 , 19 ]. Increased synthesis of Dps in the E .…”

Section: Introductionmentioning

confidence: 99%

“…Dps carries on a regulatory and protective role within Escherichia coli (E. coli) cells [13,14]. Its structure [15] and interactions with DNA were recently excessively studied in vitro [14,16,17], and in silico [18,19]. Increased synthesis of Dps in the E. coli cells occurs in the stationary phase, under starving conditions, allowing for the protection of DNA from oxidative stress, heat, acid, alkaline shock, toxic effects of heavy metals, antibiotics, UV radiation, etc.…”

Section: Introductionmentioning

confidence: 99%

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Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells

et al. 2020

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One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline , liquid crystalline , and the folded nucleosome-like . We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of the Dps protein is tightly bound to nucleoid DNA. The dps -null cells contained only one type of condensed DNA structure, liquid crystalline , thus, differing from those with Dps. The results obtained here shed some light on the phenomenon of DNA condensation in dormant prokaryotic cells and on the general problem of developing a response to stress. We demonstrated that the population of dormant cells is structurally heterogeneous, allowing them to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells

et al. 2020

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“…During starvation, Dps is very active and can greatly alter the structure of bacterial DNA. Its structure [21] and interaction with DNA have recently been studied in vitro [21,22] and in silico [23,24]. Dps is a dodecamer consisting of 12 identical chains [21].…”

Section: Bacterial Growth Dps Proteinmentioning

confidence: 99%

Architecture of Nucleoid in the Dormant Cells of Escherichia coli

Krupyanskiǐ

2021

Russ. J. Phys. Chem. B

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The review presents the results of the experimental studies of the structure of condensed DNA in the nucleoid of the dormant cells of Escherichia coli bacteria that appear in response to starvation stress. The conformation of DNA was studied by synchrotron radiation diffraction and transmission electron microscopy. The series of diffraction experiments revealed a periodic ordered organization (most likely, nanocrystalline) of DNA with DNA-associated proteins in all objects under study subjected to starvation stress: bacteria E. coli, spores and bacteria Bacillus Cereus, and filamentous fungi Umbelopsis ramanniana. A transmission electron microscopy study gave fine visual information about the type of DNA condensation in the nucleoid of the E. coli bacterium. The TEM study made it possible to find the intracellular nanocrystalline, liquid crystalline, and folded nucleosome-like DNA structures. The proportion of specific structure depends on the strain and cultivation conditions. The folded nucleosome-like structure was observed and described in the authors' original studies for the first time. The electron microscopy studies do not allow direct visualization of DNA; therefore, the DNA conformation is hypothetical. To obtain a clear picture of the DNA structure in intracellular crystals, the crystals were studied in vitro by X-ray macromolecular crystallography and electron microscopy. In contrast to diffraction experiments, the electron microscopy studies made it possible to see DNA traces in thin (2D) DNA-Dps crystals. A hypothetical model of DNA conformation in intracellular nanocrystals was proposed. The results of experiments made it possible to visualize the structures of the lower hierarchical tier of DNA compaction in the nucleoid of dormant cells.

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“…The structure of this protein and probable interactions with DNA was studied in vitro [6,7,9,16,26,34]. In silico studies have shown how the DPS protein can form crystals and co-crystals with DNA under various conditions [36][37][38]. The long N-terminal regions and the surface of the protein are rich in lysine residues.…”

Section: Introductionmentioning

confidence: 99%

Predicting Binding Free Energies for DPS Protein-DNA Complexes and Crystals Using Molecular Dynamics

2022

JSFI

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The interaction between deoxyribonucleic acid (DNA) and deoxyribonucleic acid-binding protein from starved cells (DPS) in bacterial cells leads to intracellular crystallization of the genetic material of bacteria, which contributes to the survival of bacteria under stress factors, including antibacterial agents. Molecular modeling can help explain the molecular mechanisms of DNA binding to this protein. In this paper, we report a supercomputer simulation of the molecular dynamics of several types DNA-DPS complexes and crystals ranging from DPS+DNA dimer to DNA in periodic crystal channels of Escherichia coli DPS protein using a coarse-grained Martini force field. By modeling DNA of 24 base pairs, comparable in size to the diameter of the DPS protein, we use the slow-growth thermodynamic integration method to find binding protein-DNA free energy and discuss the contribution of ions and the length of trajectories sufficient for this type of simulations. The results obtained are important for further research in the field of simulation of biological DNA-protein crystals and the study of the molecular mechanisms of DNA interaction with the DPS protein.

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Interaction of deoxyribonucleic acid with deoxyribonucleic acid-binding protein from starved cells: cluster formation and crystal growing as a model of initial stages of nucleoid biocrystallization

Cited by 18 publications

References 14 publications

Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells

Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells

Architecture of Nucleoid in the Dormant Cells of Escherichia coli

Predicting Binding Free Energies for DPS Protein-DNA Complexes and Crystals Using Molecular Dynamics

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