Department of Physics, University of Trento, Via Sommarive 14, 38123 Trento, Italy.
Cineca, Via Magnanelli 6/3, Casalecchio di Reno, 40033 Bologna, Italy.
Int J Mol Sci. 2021 Aug 2;22(15):8318. doi: 10.3390/ijms22158318.
The mammalian protein prestin is expressed in the lateral membrane wall of the cochlear hair outer cells and is responsible for the electromotile response of the basolateral membrane, following hyperpolarisation or depolarisation of the cells. Its impairment marks the onset of severe diseases, like non-syndromic deafness. Several studies have pointed out possible key roles of residues located in the Transmembrane Domain (TMD) that differentiate mammalian prestins as incomplete transporters from the other proteins belonging to the same solute-carrier (SLC) superfamily, which are classified as complete transporters. Here, we exploit the homology of a prototypical incomplete transporter (rat prestin, rPres) and a complete transporter (zebrafish prestin, zPres) with target structures in the outward open and inward open conformations. The resulting models are then embedded in a model membrane and investigated via a rigorous molecular dynamics simulation protocol. The resulting trajectories are analyzed to obtain quantitative descriptors of the equilibration phase and to assess a structural comparison between proteins in different states, and between different proteins in the same state. Our study clearly identifies a network of key residues at the interface between the gate and the core domains of prestin that might be responsible for the conformational change observed in complete transporters and hindered in incomplete transporters. In addition, we study the pathway of Cl- ions in the presence of an applied electric field towards their putative binding site in the gate domain. Based on our simulations, we propose a tilt and shift mechanism of the helices surrounding the ion binding cavity as the working principle of the reported conformational changes in complete transporters.
哺乳动物蛋白 prestin 表达在外毛细胞的侧膜壁上，负责基底外侧膜的电致运动反应，随后细胞去极化或超极化。其损伤标志着严重疾病的开始，如非综合征性耳聋。几项研究指出，位于跨膜域（TMD）中的残基可能具有关键作用，这些残基将哺乳动物 prestin 与属于同一溶质载体（SLC）超家族的其他蛋白区分开来，后者被归类为完整转运体。在这里，我们利用一个典型的不完全转运体（大鼠 prestin，rPres）和一个完整转运体（斑马鱼 prestin，zPres）与外向开放和内向开放构象的靶结构的同源性。然后将得到的模型嵌入到模型膜中，并通过严格的分子动力学模拟方案进行研究。对得到的轨迹进行分析，以获得平衡相的定量描述，并评估不同状态下蛋白之间以及同一状态下不同蛋白之间的结构比较。我们的研究清楚地确定了 prestin 门和核心结构域之间界面上的关键残基网络，这些残基可能负责完全转运体中观察到的构象变化，并阻碍不完全转运体的构象变化。此外，我们研究了在施加电场的情况下，Cl-离子在门域中其潜在结合位点的路径。基于我们的模拟，我们提出了一个围绕离子结合腔的螺旋倾斜和移动机制，作为报道的完整转运体中构象变化的工作原理。
