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.

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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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Supplementary files

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2. Fig. 1. Two-dimensional single-layer crystal of Dps protein with DNA molecules adsorbed on it (the trajectory of motion is calculated on a time interval of 0.6 μs): a, b – top view of the layer with different orientation of DNA molecules, c – side view. DNA molecules are shown as blue strands, N-terminal lysine residues – as red beads. Arrows indicate the sites of DNA binding by the N-termini of the protein. Water molecules are not shown.

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3. Fig. 2. a – Root-mean-square fluctuations of atoms in four identical 165 bp DNA molecules M165 (each molecule corresponds to one of the curves) during adsorption onto different regions of a 2D Dps crystal. The abscissa axis shows the numbers of nucleotide pairs, starting from the 5′ end of DNA; b – the average number of contacts between DNA atoms (per 100 bp of DNA) and lysine residues. The numbers are the numbers of lysine residues in the primary sequence of the Dps protein.

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4. Fig. 3. Left – structure of nanocrystals consisting of seven Dps protein molecules; from top to bottom: without DNA, in the presence of 24 bp (L24), 165 bp (M165), and 330 bp (YHIS330) DNA. Top right – dependence of the change in the average DNA-Dps interaction energy on time for DNA L24 (1), M165 (2), and YHIS330 (3), calculated per 1 bp. Below on the right – probability distributions for the average number of contacts between DNA atoms and N-terminal lysine residues (4), and other lysine residues (5), calculated per 100 bp of DNA, corresponding to the structures on the left.

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5. Fig. 4. Changes in the radii of DNA gyration depending on time in water and on a two-dimensional protein support for DNA molecules DPS26 (26 bp), ATCG24 (24 bp) and YHIS24 (24 bp). The arrow at the top indicates the time of transition from the aqueous environment to the protein support.

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