Paper
In this paper, the molecular mechanisms of interaction between the antibiotic ciprofloxacin and the main protein of the stationary phase of bacterial culture development (Dps, DNA-binding protein from starved cells) studied to solve problems of increasing antibiotic resistance. Unfavorable environmental conditions lead to inhibition of bacterial cell division and transfer cells to the states of internal resource conservation. The main task for the survival of bacteria in difficult external conditions is the preservation of DNA. DNA protection under a number of stresses (starvation, oxidative, etc.) is carried out by its condensation by the DNA-binding protein Dps. In the exponential phase, the content of Dps is 60, in the stationary phase ~200 molecules per cell. The paper considers the effect of the antibiotic ciprofloxacin on this protein. The methods of modern molecular modeling were used: docking, umbrella sampling, molecular dynamics. The energy characteristics of antibiotic binding to the protein were found. The spatial distribution of small molecules relative to the protein at 28oC and 55oC was shown. It was found that the antibiotic can migrate into the protein molecules.