Department for Biochemistry, University of Bayreuth, Bayreuth, Germany.
Department for Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany.
J Biol Chem. 2021 Dec;297(6):101419. doi: 10.1016/j.jbc.2021.101419. Epub 2021 Nov 19.
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.
深入了解受体和配体之间的分子相互作用对于蛋白质设计、药物发现或神经科学等各个领域的研究都非常重要。那么，特异性是由什么决定的，蛋白质又是如何区分相似的配体的呢？在这项研究中，我们分析了属于众所周知的周质结合蛋白超家族的两个同源物（PotF 和 PotD）中决定结合的因素。基于之前设计的构建体，我们交换了多胺结合的模式。通过分析结合口袋中的局部差异以及蛋白质的整体构象变化，我们研究了这种特异性的变化。在整个研究过程中，我们生成并从结构和热力学方面对蛋白质变体进行了表征，从而实现了特异性的转换和亲和力的提高。该数据集不仅丰富了我们适用于理性蛋白质设计的知识，而且我们的研究结果还可以进一步为特定生物传感器的工程设计奠定基础，并有助于解释致病菌的适应性。
