1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
In silico Molecular dynamics of lead nitrate interaction with replication compounds of E. coli
Paper ID : 1188-ICB10
Authors:
najmeh نجمه shadfar *1, Mahboobeh Zarrabi2
1تهران -نارمک -خیابان شهید ثانی-۶۴متری غربی -کوچه برادران صادقی
2گروه بیوفیزیک، دانشکده علوم زیستی، دانشگاه الزهرا، تهران، ایران
Abstract:
The spread of pollutants, including heavy metals such as pb2+, in water resources, has negatively affected many marine and freshwater ecosystems and, consequently, their habitats, especially fish. Lead is a major used extensively in industry. Most heavy metals can be soluble in water and this is a big threat. The main mechanism of toxicity involves the production of free radicals [1].Which causes damage to biological molecules. Escherichia coli is a Gram-negative, facultative anaerobic bacterium. It is bacteria normally live in the intestines of healthy people and animals. Bacterial replication enzymes have vital functions, disruption of each of which can cause serious damage to the bacterial genome [2]. The replication process of DNA is carried out with high efficiency and precision by DNA polymerases. The replicative enzyme in E. coli is DNA Pol III, which is a complex of 10 subunits that coordinates replication strands. Computational simulations have been applied to investigate various facets of DNA polymerase structure and function. The identified in the DNA Pol III, the two divalent Mg2+ ions that are essential for catalysis [3]. In this work, the binding properties of Pb2+ on DNA Pol III holoenzyme complex have been studied based on molecular dynamics. GROMACS a molecular dynamics simulation software, version 5.0.1 has been used to derive dynamic and thermodynamic properties.
The results obtained in the study revealed the possible attachment sites of lead ions and their interactions with domains that have metal bonding properties and examining the obtained parameters, we found that the binding of lead to enzymes is very stable and causes a change the configuration second structure.
Keywords:
Heavy Metal Poisoning; Simulations; Molecular Dynamics; Docking; Lead
Status : Paper Accepted (Poster Presentation)