Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus
Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus
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DOI：
10.1021/acs.jpcb.1c03982
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发表时间：
2021-08-23
影响因子：
3.3
通讯作者：
Moradi, Mahmoud
中科院分区：
文献类型：
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作者：
Immadisetty, Kalyan;Moradi, Mahmoud
质子偶联寡肽转运蛋白（POTs）利用质子电化学梯度将肽转运穿过细胞膜。尽管这些蛋白质的重要的生物和生物医学的相关性，一个详细的机械图片化学机械耦合参与基板/质子运输和蛋白质结构的变化是失踪。因此，我们进行了微秒级的分子动力学模拟的细菌POT PepT（ST），它与人类POT，PepT 1，在底物结合区的序列相似性为80%。模拟了PepTSt的三种不同构象状态，包括（i）封闭的，apo，（ii）面向内的，apo，和（iii）面向内的（封闭的），Leu-Ala结合。我们提出R33与E299和E300的相互作用充当构象开关（即，以触发从面向内到面向外状态的构象变化）。此外，我们建议，E299和E400脱离与基板的相互作用，通过质子化或通过与阳离子的基板得到运输协调。这项研究提供了线索，以了解POTs的化学机械耦合，并铺平了道路，以破译在这个重要的转运蛋白家族的结构-功能关系的分子水平的基础。
Proton-coupled oligopeptide transporters (POTs) use the proton electrochemical gradient to transport peptides across the cell membrane. Despite the significant biological and biomedical relevance of these proteins, a detailed mechanistic picture for chemomechanical couplings involved in substrate/proton transport and protein structural changes is missing. Therefore, we performed microsecond-level molecular dynamics simulations of bacterial POT PepT(St), which shares similar to 80% sequence identity with the human POT, PepT1, in the substrate-binding region. Three different conformational states of PepTSt were simulated, including (i) occluded, apo, (ii) inward-facing, apo, and (iii) inward-facing(occluded), Leu-Ala bound. We propose that the interaction of R33 with E299 and E300 acts as a conformational switch (i.e., to trigger the conformational change from an inward- to outward-facing state) in the substrate transport. Additionally, we propose that E299 and E400 disengage from interacting with the substrate either through protonation or through coordination with a cation for the substrate to get transported. This study provides clues to understand the chemomechanical couplings in POTs and paves the way to decipher the molecular-level underpinnings of the structure-function relationship in this important family of transporters.