IIA型DNA拓扑异构酶是复杂的分子纳米机器，在细胞中管理DNA分子的拓扑状态，并在细胞分裂和转录等细胞过程中起着关键作用。它们也是癌症化疗的靶点。我们从萨克罗米链酵母中可用的完全催化型IIA同源二聚体晶体结构出发，构建了三种状态的该分子马达，主要改变了DNA门结合的DNA片段的构型，并进行了微秒级的全原子分子模拟。全面的分析揭示了DNA门内的滑动运动和N门与DNA门之间的协作，这可能与允许DNA T段通过的必要分子事件有关。ATP酶双聚体相对于DNA结构域的观察到的运动在转运体域的K-环与结合的DNA的B-A-B形式之间表现出不同的相互作用模式。根据所获得的结果，我们将模拟的构型映射到了IIA型拓扑异构酶发挥其功能的所提出的催化循环中的结构，并讨论了可能的转变事件。这些结果扩展了我们对IIA型拓扑异构酶作用机制的理解，并对这些分子马达的一些观察特征提供了一个原子层面的解释。© 2023 作者们。

Type IIA DNA topoisomerases are complex molecular nanomachines that manage topological states of the DNA molecule in the cell and play a crucial role in cellular processes such as cell division and transcription. They are also established targets of cancer chemotherapy. Starting from the available crystal structure of a fully catalytic topoisomerase IIA homodimer from Saccharomyces cerevisiae, we constructed three states of this molecular motor primarily changing the configurations of the DNA segment bound in the DNA gate and performed μs-long all-atom molecular simulations. A comprehensive analysis revealed a sliding motion within the DNA gate and a teamwork between the N-gate and DNA gate that may be associated with the necessary molecular events that allow passage of the T-segment of DNA. The observed movement of the ATPase dimer relative to the DNA domain was reflected in different interaction patterns between the K-loops of the transducer domain and the B-A-B form of the bound DNA. Based on the obtained results, we mapped simulated configurations to the structures in the proposed catalytic cycle through which type IIA topoisomerases exert their function and discussed the possible transition events. The results extend our understanding of the mechanism of action of type IIA topoisomerases and provide an atomistic interpretation of some of the observed features of these molecular motors.© 2023 The Authors.