Computational Biophysics Research Team , RIKEN Center for Computational Science , 6-7-1 minatojima-Minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan.
Graduate School of Life Science , University of Hyogo , 3-2-1 Kouto, Kamigori , Ako , Hyogo 678-1297 , Japan.
J Phys Chem B. 2019 Aug 29;123(34):7270-7281. doi: 10.1021/acs.jpcb.9b04356. Epub 2019 Aug 16.
The heme importer from pathogenic bacteria is a member of the ATP-binding cassette (ABC) transporter family, which uses the energy of ATP-binding and hydrolysis for extensive conformational changes. Previous studies have indicated that conformational changes after heme translocation are triggered by ATP-binding to nucleotide binding domains (NBDs) and then, in turn, induce conformational transitions of the transmembrane domains (TMDs). In this study, we applied a template-based iterative all-atom molecular dynamics (MD) simulation to predict the ATP-bound outward-facing conformation of the heme importer BhuUV-T. The resulting model showed a stable conformation of the TMD with the cytoplasmic gate in the closed state and the periplasmic gate in the open state. Furthermore, targeted MD simulation predicted the intermediate structure of an occluded form (Occ) with bound ATP, in which both ends of the heme translocation channel are closed. The MD simulation of the predicted Occ revealed that Ser147 on the ABC signature motifs (LSGG[Q/E]) of NBDs occasionally flips and loses the active conformation required for ATP-hydrolysis. The flipping motion was found to be coupled to the inter-NBD distance. Our results highlight the functional significance of the signature motif of ABC transporters in regulation of ATPase and chemo-mechanical coupling mechanism.
致病细菌的血红素转运蛋白是 ATP 结合盒（ABC）转运蛋白家族的成员，它利用 ATP 结合和解离的能量进行广泛的构象变化。先前的研究表明，血红素转运后构象的变化是由核苷酸结合域（NBD）与 ATP 结合触发的，然后依次诱导跨膜域（TMD）的构象转变。在这项研究中，我们应用基于模板的迭代全原子分子动力学（MD）模拟来预测血红素转运蛋白 BhuUV-T 的 ATP 结合外向构象。所得模型显示了 TMD 的稳定构象，细胞质门处于关闭状态，周质门处于打开状态。此外，靶向 MD 模拟预测了结合 ATP 的闭塞形式（Occ）的中间结构，其中血红素转运通道的两端都关闭。预测的 Occ 的 MD 模拟表明，NBD 的 ABC 特征基序（LSGG[Q/E]）上的 Ser147 偶尔翻转并失去 ATP 水解所需的活性构象。发现翻转运动与 NBD 之间的距离有关。我们的结果强调了 ABC 转运蛋白特征基序在调节 ATP 酶和化学机械偶联机制中的功能意义。
