Department of Molecular and Cell Biology , University of Connecticut , Storrs , Connecticut 06269 , United States.
J Phys Chem B. 2019 Jan 31;123(4):825-835. doi: 10.1021/acs.jpcb.8b11370. Epub 2019 Jan 22.
The enzyme phosphodiesterase 6 (PDE6) is a critical component of the visual signaling pathway and functions to convert cGMP to GMP. The ability of PDE6 to affect cellular cGMP levels leads to deactivation of cGMP-gated ion channels in both rod and cone cells. PDE6 has been difficult to structurally characterize experimentally, though the structures of the closely related PDE5 and a PDE5/6 chimera have been determined by X-ray crystallography. In this work, we employ a computational approach to study the dynamics of the catalytic domains of PDE6, PDE5, and the PDE5/6 chimera. Through equilibrium molecular dynamics (MD) simulations, we identify a region of PDE6 (α12) to be correlated to distal regions of the enzyme (H- and M-loops), which surround the catalytic center. These correlations are not observed for PDE5, and we speculate that these unique motions in PDE6 may relate to the high catalytic efficiency of PDE6 and the requirement for an endogenous inhibitory subunit (Pγ). We further investigate the ligand binding pathways and energetics by enhanced sampling simulations (metadynamics) using the inhibitor sildenafil and GMP. The energetics and pathways of ligand binding are consistent with the high efficiency of PDE6 and further implicate the α12 region as an important regulatory element for PDE6 functional dynamics.
磷酸二酯酶 6（PDE6）是视觉信号通路的关键组成部分，其功能是将 cGMP 转化为 GMP。PDE6 影响细胞 cGMP 水平的能力导致视杆和视锥细胞中 cGMP 门控离子通道失活。尽管 X 射线晶体学已经确定了密切相关的 PDE5 和 PDE5/6 嵌合体的结构，但 PDE6 的结构仍难以通过实验进行结构表征。在这项工作中，我们采用计算方法研究 PDE6、PDE5 和 PDE5/6 嵌合体的催化结构域的动力学。通过平衡分子动力学（MD）模拟，我们确定了 PDE6（α12）的一个区域与酶的远端区域（H 和 M 环）相关，这些区域环绕催化中心。这些相关性在 PDE5 中观察不到，我们推测 PDE6 中的这些独特运动可能与 PDE6 的高催化效率以及对内源性抑制亚基（Pγ）的需求有关。我们进一步通过使用抑制剂西地那非和 GMP 进行增强采样模拟（元动力学）研究配体结合途径和能量。配体结合的能量学和途径与 PDE6 的高效率一致，并进一步表明 α12 区域是 PDE6 功能动力学的重要调节元件。
