Pecularities of DNA binding to two-dimensional crystals of bacterial protein Dps from Escherichia coli based on molecular dynamics data

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Abstract

In this work, using coarse-grained molecular modeling methods, the interactions of DNA-binding protein from starved cells (Dps) of the bacterium Escherichia coli with DNA sections of various lengths and composition were investigated. The binding features in two-dimensional crystals of the Dps protein were studied. Using free energy search methods – thermodynamic integration and linear interaction energy – the most favorable conditions for the binding of DNA and Dps were determined.

About the authors

E. V. Tereshkin

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

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

К. B. Tereshkina

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

Email: ramm@mail.ru
Russian Federation, Moscow

N. G. Loiko

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: ramm@mail.ru
Russian Federation, Moscow

V. V. Kovalenko

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

Email: ramm@mail.ru
Russian Federation, Moscow

Y. F. Krupyanskii

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

Email: ramm@mail.ru
Russian Federation, Moscow

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