The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight on allosteric transcription factors (aTFs). Here we studied the aTF UxuR in the free form and bound to the inducer D-fructuronate or the analog D-glucuronate. We employed molecular dynamics simulations, principal component analysis and electrostatic potential surface calculations. We furthermore constructed a sensor plasmid for Dfructuronate in E. coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function and that when the inducer is bound, UxuR acquires an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein acquires closed conformations, with a more positive character at the surface of the DNA binding regions. These processes can be more general than anticipated and harnessed for biological systems engineering.

中文翻译：

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通过与锌的底物配位的转录因子变构调节。

用于生物技术和医学的新的合成生物学电路的发展需要对变构转录因子（aTFs）的更深入的机械研究。在这里，我们研究了游离形式的aTF UxuR，并与诱导剂D-果糖醛酸酯或类似物D-葡萄糖醛酸酯结合。我们采用了分子动力学模拟，主成分分析和静电势面计算。我们进一步构建了果糖醛酸在大肠杆菌中的传感器质粒，并进行了定点诱变。我们的结果表明锌配位对于UxuR功能是必需的，并且当结合诱导物时，UxuR获得一个开放的构象，在N端DNA结合结构域的表面带有更明显的负电荷。相反，蛋白质以自由和D-葡萄糖醛酸酯键形式形成封闭构象，在DNA结合区域的表面具有更积极的特征。这些过程可能比预期的更普遍，并可以用于生物系统工程。