Looger Loren L, Dwyer Mary A, Smith James J, Hellinga Homme W
Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
Nature. 2003 May 8;423(6936):185-90. doi: 10.1038/nature01556.
The formation of complexes between proteins and ligands is fundamental to biological processes at the molecular level. Manipulation of molecular recognition between ligands and proteins is therefore important for basic biological studies and has many biotechnological applications, including the construction of enzymes, biosensors, genetic circuits, signal transduction pathways and chiral separations. The systematic manipulation of binding sites remains a major challenge. Computational design offers enormous generality for engineering protein structure and function. Here we present a structure-based computational method that can drastically redesign protein ligand-binding specificities. This method was used to construct soluble receptors that bind trinitrotoluene, l-lactate or serotonin with high selectivity and affinity. These engineered receptors can function as biosensors for their new ligands; we also incorporated them into synthetic bacterial signal transduction pathways, regulating gene expression in response to extracellular trinitrotoluene or l-lactate. The use of various ligands and proteins shows that a high degree of control over biomolecular recognition has been established computationally. The biological and biosensing activities of the designed receptors illustrate potential applications of computational design.
蛋白质与配体之间复合物的形成是分子水平生物过程的基础。因此，操纵配体与蛋白质之间的分子识别对于基础生物学研究很重要，并且有许多生物技术应用，包括酶、生物传感器、基因电路、信号转导途径和手性分离的构建。对结合位点进行系统性操纵仍然是一项重大挑战。计算设计为工程化蛋白质结构和功能提供了极大的通用性。在此，我们提出一种基于结构的计算方法，该方法能够大幅重新设计蛋白质配体结合特异性。此方法被用于构建对三硝基甲苯、L-乳酸或血清素具有高选择性和亲和力的可溶性受体。这些工程化受体可作为其新配体的生物传感器；我们还将它们整合到合成细菌信号转导途径中，以响应细胞外三硝基甲苯或L-乳酸来调节基因表达。对各种配体和蛋白质的使用表明，通过计算已实现对生物分子识别的高度控制。所设计受体的生物学和生物传感活性说明了计算设计的潜在应用。
