Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA.
Sci Rep. 2020 Dec 17;10(1):22267. doi: 10.1038/s41598-020-79284-0.
Cytochrome P450 2J2 (CYP2J2) is responsible for the epoxidation of endogenous arachidonic acid, and is involved in the metabolism of exogenous drugs. To date, no crystal structure of CYP2J2 is available, and the proposed structural basis for the substrate recognition and specificity in CYP2J2 varies with the structural models developed using different computational protocols. In this study, we developed a new structural model of CYP2J2, and explored its sensitivity to substrate binding by molecular dynamics simulations of the interactions with chemically similar fluorescent probes. Our results showed that the induced-fit binding of these probes led to the preferred active poses ready for the catalysis by CYP2J2. Divergent conformational dynamics of CYP2J2 due to the binding of each probe were observed. However, a stable hydrophobic clamp composed of residues I127, F310, A311, V380, and I487 was identified to restrict any substrate access to the active site of CYP2J2. Molecular docking of a series of compounds including amiodarone, astemizole, danazol, ebastine, ketoconazole, terfenadine, terfenadone, and arachidonic acid to CYP2J2 confirmed the role of those residues in determining substrate binding and specificity of CYP2J2. In addition to the flexibility of CYP2J2, the present work also identified other factors such as electrostatic potential in the vicinity of the active site, and substrate strain energy and property that have implications for the interpretation of CYP2J2 metabolism.
细胞色素 P450 2J2（CYP2J2）负责内源性花生四烯酸的环氧化，参与外源性药物的代谢。迄今为止，尚无 CYP2J2 的晶体结构，并且对于 CYP2J2 中底物识别和特异性的提议结构基础因使用不同计算协议开发的结构模型而有所不同。在这项研究中，我们开发了 CYP2J2 的新结构模型，并通过与化学相似的荧光探针相互作用的分子动力学模拟探索了其对底物结合的敏感性。我们的结果表明，这些探针的诱导契合结合导致了 CYP2J2 进行催化的优选活性构象。观察到由于每个探针的结合而导致 CYP2J2 的分歧构象动力学。然而，鉴定了一个稳定的疏水性夹，由残基 I127、F310、A311、V380 和 I487 组成，以限制任何底物进入 CYP2J2 的活性部位。一系列化合物（包括胺碘酮、阿司咪唑、丹那唑、依巴斯汀、酮康唑、特非那定、特非那定酮和花生四烯酸）与 CYP2J2 的分子对接证实了这些残基在确定 CYP2J2 的底物结合和特异性中的作用。除了 CYP2J2 的灵活性外，本工作还确定了其他因素，如活性部位附近的静电势以及底物应变能和特性，这些因素对 CYP2J2 代谢的解释具有重要意义。
