Current Proteomics ( IF 0.8 ) Pub Date : 2020-01-31 , DOI: 10.2174/1570164616666190220143131 Mojtaba Mortazavi 1 , Navid Nezafat 2 , Manica Negahdaripour 2 , Mohammad J. Raee 2 , Masoud Torkzadeh-Mahani 1 , Ali Riahi-Madvar 1 , Younes Ghasemi 2
Background: 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.中文翻译：
CYP152A1结构中底物结合位点和稀有密码子的计算机分析
背景：细胞色素P450（CYP）在内源性和外源性分子的氧化中起着至关重要的作用。CYPs在生活的所有领域都得到了鉴定，但是枯草芽孢杆菌的CYP152A1特别考虑用于临床和工业应用。先前已经报道了从枯草芽孢杆菌中克隆一种新型CYP的分子。在这里，我们描述了CYP152A1酶的生物学信息的隐藏层，这可以帮助研究人员更好地了解酶的应用。在这项研究中，使用生物信息学网络服务器识别并评估了四个罕见的酶密码子，包括Arg63，Arg187，Arg276和Arg338。
方法：通过I-TASSER服务器对CYP152A1进行计算机模拟，研究了上述稀有密码子在酶结构中的可能对CYP152A1的正确折叠起重要作用。以下，通过AutoDock Vina研究了CYP152A1的底物结合位点，将血红素和棕榈酸视为底物。 结果：对接研究的结果阐明了在活性位点上的Arg242与CYP152A1的底物结合位点密切相关，这有助于我们进一步阐明酶反应的机理。 结论：对这些隐藏信息的研究可以增强我们对CYP152A1折叠和蛋白质表达挑战的理解。而且，鉴定稀有密码子可以帮助合理设计新的有效药物。
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