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In silico Evaluation of Substrate Binding Site and Rare Codons in the Structure of CYP152A1

[ Vol. 17 , Issue. 1 ]

Author(s):

Mojtaba Mortazavi, Navid Nezafat, Manica Negahdaripour, Mohammad J. Raee, Masoud Torkzadeh-Mahani, Ali Riahi-Madvar and Younes Ghasemi*   Pages 10 - 22 ( 13 )

Abstract:


The Cytochromes P450 (CYPs) have an essential role in the oxidation of endogenous and exogenous molecules. The CYPs are identified in all domains of life, but the CYP152A1 from Bacillus subtilis is specially considered for clinical and industrial applications. The molecular cloning of a new type of CYP from Bacillus subtilis was reported, previously. Here, we describe the hidden layer of biological information of the CYP152A1 enzyme, which can help researchers for better understanding of enzyme application. In this study, four rare codons of enzyme, including Arg63, Arg187, Arg276, and Arg338 were identified and evaluated using the bioinformatics web servers.

Methods: Through in silico modeling of CYP152A1 via the I-TASSER server, the above-mentioned rare codons were studied in the structure of enzyme that may have an important role in the proper folding of CYP152A1. In the following, the substrate binding site of CYP152A1 was studied by AutoDock Vina, and the heme and palmitic acid were considered as the substrates.

Results: The results of docking study elucidated the Arg242 in the active site is closely related to the substrate binding site of CYP152A1, which help us to further clarify the mechanism of the enzyme reaction.

Conclusion: Studies of these hidden information’s can enhance our understanding of CYP152A1 folding and protein expression challenges. Moreover, identification of rare codons can help in the rational design of new and effective drugs.

Keywords:

CYP152A1, Rare codon, AutoDock Vina, substrate docking, bioinformatics, kinetics.

Affiliation:

Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz



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