Molecular docking and molecular dynamic simulation of the effect of Pseudomonas phenol hydroxylase enzyme on polycyclic aromatic hydrocarbons (PAHs)

Polycyclic aromatic hydrocarbons (PAHs) are hydrocarbon compounds that are composed of multiplearomatic rings. PAHs are found in coal and oil deposits and are also produced by the combustion of organicmatter for example, in engines and incinerators or when biomass burns in forest fires. PAHs are one of themost significant toxins in carcinogenesis and it is important to find the best way to remove these compoundsfrom the environment. This study investigated the effect of pseudomonas phenol hydroxylase enzyme onPAHs by molecular dynamic and simulation study. The FASTA file sequencing of phenol hydroxylase wasobtained from the Uniprot server and its PDB file was performed from the i-tasser server. ThenRamachandran plot was performed from Ramachandran Plot Server. Also, the structure of PAH compoundswere obtained from the PubChem server and converted to PDB files by Avogadro V۱.۲ software. Themolecular docking of PAH compounds on phenol hydroxylase was done by Autodock v.۴.۲ software and theGromacs ۲۰۲۱ software was used for molecular dynamics studies. The results of this study showed that thePAH compounds have a high affinity to interact with phenol hydroxylase by hydrogen and hydrophobicbonds. Among them, the Dibenzo Anthracene, Benzo Fluoranthene, and Indeno Pyrene were more potent tointeract with phenol hydroxylase. Binding of Dibenzo Anthracene, Benzo Fluoranthene, and Indeno Pyreneto phenol hydroxylase binding side can induce the conformational changes on enzyme structure and inducethe change on RMSD, RMSF, RG, and other molecular dynamic parameters. According to this simulationstudy, phenol hydroxylase enzyme can affect PAH compounds so the bacteria with enzymes such asPseudomonas can be used in contaminated environments by PAH compounds.

کلیدواژه ها:

Docking ، Phenol Hydroxylase ، Phenolic compounds ، Simulation