Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan.
Biochemistry. 2012 Jul 31;51(30):5958-66. doi: 10.1021/bi300696b. Epub 2012 Jul 16.
The complex of sensory rhodopsin II (SRII) and its cognate transducer HtrII (2:2 SRII-HtrII complex) consists of a photoreceptor and its signal transducer, respectively, associated with negative phototaxis in extreme halophiles. In this study to investigate how photoexcitation in SRII affects the structures of the complex, we conducted two series of molecular dynamics simulations of the complex of SRII and truncated HtrII (residues 1-136) of Natronomonas pharaonis linked with a modeled HAMP domain in the lipid bilayer using the two crystal structures of the ground state and the M-intermediate state as the starting structures. The simulation results showed significant enhancements of the structural differences observed between the two crystal structures. Helix F of SRII showed an outward motion, and the C-terminal end of transmembrane domain 2 (TM2) in HtrII rotated by ∼10°. The most significant structural changes were observed in the overall orientations of the two SRII molecules, closed in the ground state and open in the M-state. This change was attributed to substantial differences in the structure of the four-helix bundle of the HtrII dimer causing the apparent rotation of TM2. These simulation results established the structural basis for the various experimental observations explaining the structural differences between the ground state and the M-intermediate state.
视紫红质 II 复合物（SRII）及其同源转导蛋白 HtrII（2:2 SRII-HtrII 复合物）分别由光受体和其信号转导蛋白组成，与极端嗜盐生物的负趋光性有关。在这项研究中，为了研究光激发 SRII 如何影响复合物的结构，我们使用两种晶体结构（基态和 M 中间态）作为起始结构，对来自嗜盐古菌 Natronomonas pharaonis 的 SRII 和截断的 HtrII（残基 1-136）与模型化的 HAMP 结构域相连的复合物进行了两个系列的分子动力学模拟。模拟结果显示，两种晶体结构之间观察到的结构差异明显增强。SRII 的螺旋 F 向外运动，HtrII 的跨膜域 2（TM2）的 C 末端旋转约 10°。最显著的结构变化发生在两个 SRII 分子的整体取向中，在基态下关闭，在 M 态下打开。这种变化归因于 HtrII 二聚体的四螺旋束结构的显著差异，导致 TM2 的明显旋转。这些模拟结果为各种实验观察结果建立了结构基础，这些结果解释了基态和 M 中间态之间的结构差异。
