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