Department of Applied Physics, Stanford University, Stanford, California, USA.
Nat Struct Mol Biol. 2012 Apr 8;19(5):538-46, S1. doi: 10.1038/nsmb.2278.
DNA gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to introduce negative supercoils into DNA. A critical step in this reaction is the formation of a chiral DNA wrap. Here we observe gyrase structural dynamics using a single-molecule assay in which gyrase drives the processive, stepwise rotation of a nanosphere attached to the side of a stretched DNA molecule. Analysis of rotational pauses and measurements of DNA contraction reveal multiple ATP-modulated structural transitions. DNA wrapping is coordinated with the ATPase cycle and proceeds by way of an unanticipated structural intermediate that dominates the kinetics of supercoiling. Our findings reveal a conformational landscape of loosely coupled transitions funneling the motor toward productive energy transduction, a feature that may be common to the reaction cycles of other DNA and protein remodeling machines.
DNA 回旋酶是一种分子马达，它利用 ATP 水解的自由能将负超螺旋引入 DNA 中。该反应的一个关键步骤是形成手性 DNA 缠绕。在这里，我们使用单分子测定法观察了回旋酶的结构动力学，其中回旋酶驱动附着在伸展 DNA 分子侧面的纳米球进行连续的逐步旋转。对旋转暂停的分析和 DNA 收缩的测量揭示了多种 ATP 调节的结构转变。DNA 缠绕与 ATP 酶循环协调进行，通过一种出乎意料的结构中间体进行，该中间体主导超螺旋动力学。我们的发现揭示了一个松散耦合转变的构象景观，将马达引导向有效的能量转导，这一特征可能是其他 DNA 和蛋白质重塑机器的反应循环所共有的。
