Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland.
Sci Rep. 2017 Aug 10;7(1):7736. doi: 10.1038/s41598-017-07993-0.
Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.
了解配体与酶结合的机制对于设计新药物至关重要。在这里，我们报告了一种新的有偏差的分子动力学 (MD) 方法在研究樟脑与细胞色素 P450cam 结合机制中的应用。微秒级长的 MD 模拟使我们能够观察到反应坐标，这些反应坐标描述了配体通过三条出口途径从细胞色素 P450cam 的活性位点扩散到溶剂中的过程。这些原子模拟用于沿反应坐标估计热力学量，并指示不同的结合构象。结果表明，樟脑沿着靠近底物识别位点 (SRS) 的路径扩散在热力学上是有利的。此外，我们表明，SRS 附近的扩散是由从异构的封闭配体结合构象集合到包含细胞色素 P450cam 开放构象的盆地的转变引发的。伴随这种转变的构象变化的特征是 F 和 G 螺旋的缩回和 B' 螺旋的无序。这些结果得到了实验研究的证实，并为配体结合和细胞色素家族的构象行为提供了详细的见解。所提出的方法具有普遍性，可以应用于其他配体-蛋白质系统。
