Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
J Chem Inf Model. 2020 Oct 26;60(10):5026-5035. doi: 10.1021/acs.jcim.0c00482. Epub 2020 Aug 31.
The plasticity of cytochromes P450 (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protein plasticity and dynamics in different environments. CYP2B4 is featured by a high degree of plasticity, which exhibits open, closed, and intermediate states. By analyzing the CYP2B4 crystal structures, we identified the structural features for the closed, open, and intermediate states. Interestingly, formation of the dimer structure was found in the open and intermediate states. The subsequent molecular dynamics (MD) simulations of the open structure in water confirmed the importance of the dimer form in stabilizing the open conformations. MD simulations of the closed and open structures in the membrane environment and the free energies for opening the F-G cassette obtained from the umbrella sampling calculations indicate that the membrane environment is important for stabilizing the F-G cassette. The dynamical network analysis indicates that Asp105 on the B-C loop plays an important role in transiting the structure from the open to the intermediate state. Our results thus unveil the mechanisms of dimer formation and open-to-intermediate transition for CYP2B4 in the water and membrane environments.
细胞色素 P450（P450s）的可塑性被认为对其代谢各种底物的催化能力有重要贡献。尽管已经进行了许多研究，但仍不完全了解影响 P450 可塑性和动力学的因素。在这项研究中，我们以 CYP2B4 为例，剖析了不同环境下的蛋白质可塑性和动力学。CYP2B4 具有高度的可塑性，表现出开放、关闭和中间状态。通过分析 CYP2B4 的晶体结构，我们确定了封闭、开放和中间状态的结构特征。有趣的是，在开放和中间状态下发现了二聚体结构的形成。随后在水环境中对开放结构的分子动力学（MD）模拟证实了二聚体形式在稳定开放构象中的重要性。在膜环境中对封闭和开放结构的 MD 模拟以及从伞状采样计算中获得的打开 F-G 盒的自由能表明，膜环境对于稳定 F-G 盒很重要。动态网络分析表明，B-C 环上的天冬氨酸 105 在将结构从开放状态过渡到中间状态中起着重要作用。因此，我们的结果揭示了 CYP2B4 在水相和膜相环境中二聚体形成和从开放到中间状态转变的机制。
