A profound understanding of the molecular interactions between receptors and ligands is important throughout diverse research, such as protein design, drug discovery, or neuroscience. What determines specificity and how do proteins discriminate against similar ligands? In this study, we analyzed factors that determine binding in two homologs belonging to the well-known superfamily of periplasmic binding proteins, PotF and PotD. Building on a previously designed construct, modes of polyamine binding were swapped. This change of specificity was approached by analyzing local differences in the binding pocket as well as overall conformational changes in the protein. Throughout the study, protein variants were generated and characterized structurally and thermodynamically, leading to a specificity swap and improvement in affinity. This dataset not only enriches our knowledge applicable to rational protein design but also our results can further lay groundwork for engineering of specific biosensors as well as help to explain the adaptability of pathogenic bacteria.

中文翻译：

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微调腐胺结合蛋白 PotF 中的亚精胺结合模式。

在蛋白质设计、药物发现或神经科学等各种研究中，深入了解受体和配体之间的分子相互作用非常重要。什么决定了特异性以及蛋白质如何区分相似的配体？在这项研究中，我们分析了决定两个同源物结合的因素，这些同源物属于众所周知的周质结合蛋白超家族 PotF 和 PotD。在先前设计的结构的基础上，交换了多胺结合模式。通过分析结合袋的局部差异以及蛋白质的整体构象变化来处理这种特异性变化。在整个研究过程中，产生了蛋白质变体，并在结构和热力学上对其进行了表征，从而导致了特异性交换和亲和力的提高。