Dept. of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
Dept. of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
Nucleic Acids Res. 2022 Aug 26;50(15):8459-8470. doi: 10.1093/nar/gkac668.
The bacterial FtsK motor harvests energy from ATP to translocate double-stranded DNA during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA translocation in FtsK by performing long timescale simulations of its hexameric assembly and individual subunits. From these simulations we predict signaling pathways that connect the ATPase active site to DNA-gripping residues, which allows the motor to coordinate its translocation activity with its ATPase activity. Additionally, we utilize well-tempered metadynamics simulations to compute free-energy landscapes that elucidate the extended-to-compact transition involved in force generation. We show that nucleotide binding promotes a compact conformation of a motor subunit, whereas the apo subunit is flexible. Together, our results support a mechanism whereby each ATP-bound subunit of the motor conforms to the helical pitch of DNA, and ATP hydrolysis/product release causes a subunit to lose grip of DNA. By ordinally engaging and disengaging with DNA, the FtsK motor unidirectionally translocates DNA.
细菌 FtsK 马达从 ATP 中获取能量，在细胞分裂过程中转运双链 DNA。在这里，我们通过对其六聚体组装和单个亚基进行长时间尺度的模拟，探究了 FtsK 中协调 DNA 易位的分子机制。从这些模拟中，我们预测了将 ATP 酶活性位点与 DNA 抓取残基连接起来的信号通路，这使得马达能够协调其易位活性与其 ATP 酶活性。此外，我们利用经过良好调整的元动力学模拟来计算自由能景观，阐明了涉及力产生的扩展到紧凑的转变。我们表明，核苷酸结合促进了马达亚基的紧凑构象，而脱辅基亚基则具有柔韧性。总之，我们的结果支持了这样一种机制，即马达的每个 ATP 结合亚基都适应 DNA 的螺旋螺距，并且 ATP 水解/产物释放导致亚基失去对 DNA 的抓取。通过有序地与 DNA 结合和解离，FtsK 马达沿单一方向转运 DNA。
