In silico Molecular dynamics of lead nitrate interaction with replication compounds of E.coli

The spread of pollutants, including heavy metals such as pb۲+, in water resources, has negatively affectedmany marine and freshwater ecosystems and, consequently, their habitats, especially fish. Lead is a majorused extensively in industry. Most heavy metals can be soluble in water and this is a big threat. The mainmechanism of toxicity involves the production of free radicals. Which causes damage to biologicalmolecules. Escherichia coli is a Gram-negative, facultative anaerobic bacterium. It is bacteria normally livein the intestines of healthy people and animals. Bacterial replication enzymes have vital functions, disruptionof each of which can cause serious damage to the bacterial genome. The replication process of DNA is carriedout with high efficiency and precision by DNA polymerases. The replicative enzyme in E. coli is DNA PolIII, which is a complex of ۱۰ subunits that coordinates replication strands. Computational simulations havebeen applied to investigate various facets of DNA polymerase structure and function. The identified in theDNA Pol III, the two divalent Mg۲+ ions that are essential for catalysis. In this work, the binding propertiesof pb۲+ on DNA Pol III holoenzyme complex have been studied based on molecular dynamics. GROMACSa molecular dynamics simulation software, version ۵.۰.۱ has been used to derive dynamic andthermodynamic properties.The results obtained in the study revealed the possible attachment sites of lead ions and their interactionswith domains that have metal bonding properties and examining the obtained parameters, we found that thebinding of lead to enzymes is very stable and causes a change the configuration second structure.