Larivière Damien, Galindo-Murillo Rodrigo, Fourmentin Eric, Hornus Samuel, Lévy Bruno, Papillon Julie, Ménétret Jean-François, Lamour Valérie
Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France.
Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
Methods Mol Biol. 2017;1624:193-210. doi: 10.1007/978-1-4939-7098-8_15.
The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.
大分子机器的结构建模就像一种“乐高”方法，当要将从蛋白质数据库导入的蛋白质等“积木块”与采用蛇形的元素（如DNA模板）组装在一起时，这种方法就会面临挑战。届时，DNA必须从头构建，但建模方法要么不便于用户使用，要么非常耗时且繁琐。在本章方法中，我们展示了如何使用GraphiteLifeExplorer软件，它具有简单的图形用户界面，能够在原子尺度上快速绘制任意长度的自由形式的DNA，就像在纸上画一条线一样容易。我们以DNA旋转酶的核蛋白复合物为例，DNA旋转酶是一种细菌拓扑异构酶，其结构已通过冷冻电子显微镜（Cryo-EM）确定。使用GraphiteLifeExplorer，我们能够一次性对在冷冻电镜图谱中围绕DNA旋转酶的155个碱基对长的扭曲DNA双链进行建模，与最初发表的数据相比，提高了最终模型的质量和解读。
