Peculiarities of DNA Binding to Two-Dimensional Crystals of Bacterial Protein DPS from Escherichia coli Based on Molecular Dynamics Data

IF 1.4 4区化学 Q4 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL

Russian Journal of Physical Chemistry B Pub Date : 2025-01-15 DOI:10.1134/S199079312470146X

E. V. Tereshkin, K. B. Tereshkina, N. G. Loiko, V. V. Kovalenko, Y. F. Krupyanskii

引用次数: 0

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 are investigated. The binding features in two-dimensional crystals of the Dps protein are studied. Using free energy search methods—thermodynamic integration and linear interaction energy—the most favorable conditions for the binding of DNA and Dps are determined.

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基于分子动力学数据的大肠杆菌细菌蛋白DPS二维晶体DNA结合特性研究

在这项工作中，使用粗粒度的分子建模方法，研究了大肠杆菌饥饿细胞（Dps）的DNA结合蛋白与不同长度和组成的DNA片段的相互作用。研究了Dps蛋白在二维晶体中的结合特性。利用自由能搜索法——热力学积分法和线性相互作用能法，确定了DNA与Dps结合的最有利条件。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Russian Journal of Physical Chemistry B 化学-物理：原子、分子和化学物理

CiteScore

2.20

自引率

71.40%

发文量

106

审稿时长

4-8 weeks

期刊介绍： Russian Journal of Physical Chemistry B: Focus on Physics is a journal that publishes studies in the following areas: elementary physical and chemical processes; structure of chemical compounds, reactivity, effect of external field and environment on chemical transformations; molecular dynamics and molecular organization; dynamics and kinetics of photoand radiation-induced processes; mechanism of chemical reactions in gas and condensed phases and at interfaces; chain and thermal processes of ignition, combustion and detonation in gases, two-phase and condensed systems; shock waves; new physical methods of examining chemical reactions; and biological processes in chemical physics.