Proton-coupled peptide transporters (POTs) are crucial for the uptake of di- and tripeptides as well as drug and prodrug molecules in prokaryotes and eukaryotic cells. We illustrate from multiscale modeling how transmembrane proton flux couples within a POT protein to drive essential steps of the full functional cycle: 1) protonation of a glutamate on transmembrane helix 7 (TM7) opens the extracellular gate, allowing ligand entry; 2) inward proton flow induces the cytosolic release of ligand by varying the protonation state of a second conserved glutamate on TM10; 3) proton movement between TM7 and TM10 is thermodynamically driven and kinetically permissible via water proton shuttling without the participation of ligand. Our results, for the first time, give direct computational confirmation for the alternating access model of POTs, and point to a quantitative multiscale kinetic picture of the functioning protein mechanism.

质子偶联肽转运蛋白 (POT) 对于原核生物和真核细胞中二肽和三肽以及药物和前药分子的摄取至关重要。我们通过多尺度模型说明跨膜质子通量如何在 POT 蛋白内耦合以驱动整个功能循环的基本步骤：1）跨膜螺旋 7（TM7）上谷氨酸的质子化打开细胞外大门，允许配体进入；2) 向内质子流通过改变TM10上第二个保守谷氨酸的质子化状态来诱导配体的胞质释放；3) TM7和TM10之间的质子运动是热力学驱动的，并且在动力学上允许通过水质子穿梭而无需配体的参与。我们的结果首次为 POT 的交替访问模型提供了直接的计算确认，