Coordinated Motion of Dimeric Interfaces in Eukaryotic Type IIA Topoisomerases

Abstract

Type IIA Topoisomerases (Topo IIA) are enzymes that manage DNA superhelicity and disentangle chromosomes through an ATP-dependent strand passage mechanism. Topo IIAs introduce a double-stranded break in one DNA segment (the g-strand) and pass a second DNA segment (the t- strand) through this break. The topological rearrangement in Topo IIA involves the controlled opening and closing of multiple dimerization domains. However, the step by step mechanism of strand passage is not fully understood. Here, we have performed conventional and target molecular dynamics simulations in the presence and absence of the t-DNA to understand the coordinated motions in the opening and closing of the N-gate, DNA-gate, and C-gate regions. The results of our modeling indicate that the opening of the DNA-gate involves rotation of the N-domain which is necessary for the transportation of the t-DNA through the g-strand. Furthermore, the opening of the N-gate requires relatively higher energy compared to the opening of the DNA- and C-gates due to strong interactions of N-terminal residues between the two monomers. Our results also support the hypothesis that Topo IIA keeps only one gate opens at a time since there is an increased energetic cost for the opening of the DNA-gate while the C-gate is opened. The restriction of one gate open at a time may prevent the enzyme from disassembling during its reaction thereby preventing enzyme-induced genome instability.