Location of DNA in complexes with DNA stabilizing proteins DPS and SASP

Tereshkin E.V., Loiko N.G.1, Tereshkina K.B., Kovalenko V.V., Zuykova A.A.2, Popelkovskaya A.I.2, Krupyanskii Y.F.

Semenov Institute of Chemical Physics of Russian Academy of Sciences, Russia, 119991, Moscow, ul. Kosygina, 4, +7 (495) 9397300,

1Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Russia, 119071, Moscow, Leninskiy prospekt, 33, b.2

2D.Mendeleev University of Chemical Technology of Russia, Russia, 125047, Miusskaya pl., 9

A comparative study of the structural features of in vivo crystals of bacterial cultures containing crystals of DNA-stabilizing proteins DPS and SASP and the corresponding molecular systems was carried out. Both proteins are involved in the in vivo or biocrystallization of a nucleoid, which occurs directly in a living cell and is aimed at preserving its genetic material under stress. The main protein involved in the biocrystallization process in a bacterial cell is the DPS protein (DNA-binding protein from starved cells). In bacterial spores, the biocrystallization of a nucleoid occurs with the help of another class of protein, SASP (small acid-soluble proteins).

The cells of the bacteria Escherichia coli strain K12 were studied. In these cells it was initiated the production of DPS protein, the molecules of which formed crystals with DNA [3]. The bacterial spores of Bacillus cereus, whose nucleoid crystallizes with the participation of the SASP protein, were also studied. Comparison of diffraction patterns, scattering curves of these systems and the dynamics of protein nanocrystals with short palindromic DNA regions 5'- GGGGGGGGGGA-3 'were studied. The dynamics of the complexes was studied by the classical molecular dynamics method using the Gromacs 5.1 software package using specially developed protocols [4].

Peculiarities in the structural, dynamic and energy characteristics of DPS and SASP proteins with DNA were determined.

The research was carried out using supercomputers at Joint Supercomputer Center of the Russian Academy of Sciences (JSCC RAS), project #CHPH2. The work was carried out within the framework of the state assignment of the Ministry of Education and Science, project #0082-2014-0001, #AAAA-A17-117040610310-6.

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