1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Molecular docking and molecular dynamic simulation of the effect of Pseudomonas phenol hydroxylase enzyme on polycyclic aromatic hydrocarbons (PAHs)
Paper ID : 1209-ICB10
Authors:
Javad Saffari-Chaleshtori *1, Gashtasb Mardani2, Majid Validi2
1مرکز تحقیقات بیوشیمی بالینی، پژوهشکده علوم پایه سلامت، دانشگاه علوم پزشکی شهرکرد، شهرکرد، ایران
2مرکز تحقیقات گیاهان دارویی، پژوهشکده علوم پایه سلامت، دانشگاه علوم پزشکی شهرکرد، شهرکرد، ایران
Abstract:
Polycyclic aromatic hydrocarbons (PAHs) are hydrocarbon compounds that are composed of multiple aromatic rings. PAHs are found in coal and oil deposits and are also produced by the combustion of organic matter for example, in engines and incinerators or when biomass burns in forest fires. PAHs are one of the most significant toxins in carcinogenesis and it is important to find the best way to remove these compounds from the environment. This study investigated the effect of pseudomonas phenol hydroxylase enzyme on PAHs by molecular dynamic and simulation study. The FASTA file sequencing of phenol hydroxylase was obtained from the Uniprot server and its PDB file was performed from the i-tasser server. Then Ramachandran plot was performed from Ramachandran Plot Server. Also, the structure of PAH compounds were obtained from the PubChem server and converted to PDB files by Avogadro V1.2 software. The molecular docking of PAH compounds on phenol hydroxylase was done by Autodock v.4.2 software and the Gromacs 2021 software was used for molecular dynamics studies. The results of this study showed that the PAH compounds have a high affinity to interact with phenol hydroxylase by hydrogen and hydrophobic bonds. Among them, the Dibenzo Anthracene, Benzo Fluoranthene, and Indeno Pyrene were more potent to interact with phenol hydroxylase. Binding of Dibenzo Anthracene, Benzo Fluoranthene, and Indeno Pyrene to phenol hydroxylase binding side can induce the conformational changes on enzyme structure and induce the change on RMSD, RMSF, RG, and other molecular dynamic parameters. According to this simulation study, phenol hydroxylase enzyme can affect PAH compounds so the bacteria with enzymes such as Pseudomonas can be used in contaminated environments by PAH compounds.
Keywords:
Docking, Phenol Hydroxylase, Phenolic compounds, Simulation
Status : Paper Accepted (Poster Presentation)