Modeling of DNA and DNA-Stabilizing Protein DPS Nanocrystals Dynamics

Tereshkin E.V., Chulichkov A.L., Kovalenko V.V., Tereshkina K.B., Krupyanskii Y.F.

Semenov Institute of Chemical Physics RAS, Moscow, Russia

In this work, the molecular modeling methods were used to study the dynamics of the histone-like DNA-stabilizing DPS protein with DNA molecules. The dynamics of small DNA fragments of plasmid pBluescript SK (+) [1] has been studied. The work is part of a project that includes in vivo and in vitro experimental studies of the biocrystallization of starved E. coli cells using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and theoretical molecular dynamics studies [2]. The biocrystallization of a nucleoid is an adaptation mechanism used by stress-treated bacterial cells, which has not been sufficiently studied to the present time [3].

Coarse grained models of DPS protein and DNA fragments at various concentrations have been constructed. Structural, energy and dynamic characteristics of DPS-DPS and DPS-DNA complexes were determined during the formation of nanocrystals. It was found that the formation of certain complexes depends on the concentration of DNA and protein fragments. The obtained data made it possible to predict the formation and structure of crystals in experimental systems.

The work was supported by the Ministry of Education and Science of the Russian Federation (project # RFMEFI61616X0070). The calculations were performed on computer clusters of MSC RAS Supercomputer MVS-10P, Supercomputer Lomonosov-2.



2. Y.F.Krupyanskii et al. Biocrystallization in bacterial and fungal cells // Crystallography Reports. 2017. V. 12 (in press)

3. Minsky A. et al. Stress, order and survival // Nat. Rev. Mol. Cell Biol. 2002. V. 3. P. 50.

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