Periplasmic binding proteins (PBPs) are ubiquitous receptors in gram-negative bacteria. They sense solutes and play key roles in nutrient uptake. Escherichia coli's putrescine receptor PotF has been reported to bind putrescine and spermidine. We reveal that several similar biogenic polyamines are recognized by PotF. Using isothermal titration calorimetry paired with X-ray crystallography of the different complexes, we unveil PotF's binding modes in detail. The binding site for PBPs is located between two lobes that undergo a large conformational change upon ligand recognition. Hence, analyzing the influence of ligands on complex formation is crucial. Therefore, we solved crystal structures of an open and closed apo state and used them as a basis for molecular dynamics simulations. In addition, we accessed structural behavior in solution for all complexes by ¹H-¹⁵N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering.

周质结合蛋白 (PBP) 是革兰氏阴性菌中普遍存在的受体。它们感知溶质并在营养吸收中发挥关键作用。大肠杆菌据报道，腐胺受体 PotF 可结合腐胺和亚精胺。我们揭示了几种类似的生物多胺被 PotF 识别。使用等温滴定量热法与不同复合物的 X 射线晶体学配对，我们详细揭示了 PotF 的结合模式。PBP 的结合位点位于两个叶之间，在配体识别时会发生巨大的构象变化。因此，分析配体对复合物形成的影响至关重要。因此，我们解决了开放和封闭的 apo 状态的晶体结构，并将它们用作分子动力学模拟的基础。此外，我们通过¹ H- ¹⁵N HSQC NMR光谱。这种组合分析为理解配体结合以促进药物设计和蛋白质工程的未来发展提供了一个强大的框架。