Ding Yuan, Kathiresan Venkatesan, Zhang Xiaojun, Haworth Ian S, Qin Peter Z
Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States.
Department of Pharmacology and Pharmaceutical Sciences , University of Southern California , Los Angeles , California 90089 , United States.
J Phys Chem A. 2019 Apr 25;123(16):3592-3598. doi: 10.1021/acs.jpca.9b01027. Epub 2019 Apr 12.
Measurement of distances between spectroscopic labels (e.g., spin labels, fluorophores) attached to specific sites of biomolecules is an important method for studying biomolecular complexes. ALLNOX (Addition of Labels and Linkers) has been developed as a program to model interlabel distances based on an input macromolecule structure. Here, we report validation of ALLNOX using measured distances between nitroxide spin labels attached to specific sites of a protein-DNA complex. The results demonstrate that ALLNOX predicts average interspin distances that matched with values measured with pairs of labels attached at the protein and/or DNA. This establishes a solid foundation for using spin labeling in conjunction with ALLNOX to investigate complexes without high-resolution structures. With its high degree of flexibility for the label or the target biomolecule, ALLNOX provides a useful tool for investigating the structure-function relationship in a large variety of biological molecules.
测量附着于生物分子特定位点的光谱标记物（如自旋标记物、荧光团）之间的距离是研究生物分子复合物的重要方法。ALLNOX（标记物和连接子添加）程序已被开发出来，用于根据输入的大分子结构对标记物间距离进行建模。在此，我们报告了使用附着于蛋白质-DNA复合物特定位点的氮氧化物自旋标记物之间的测量距离对ALLNOX进行的验证。结果表明，ALLNOX预测的平均自旋间距离与在蛋白质和/或DNA上附着的标记物对测量的值相匹配。这为结合使用自旋标记和ALLNOX来研究无高分辨率结构的复合物奠定了坚实基础。由于ALLNOX对标记物或目标生物分子具有高度灵活性，它为研究多种生物分子的结构-功能关系提供了一个有用的工具。
