Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases

Type II topoisomerases (TopoIIs) are essential enzymes involved in critical nuclear processes such as genome organization, chromosome segregation, and various DNA metabolic events. As large, homodimeric complexes, they undergo a complex ATPase cycle that regulates capturing and passing one DNA double-helix through a second, cleaved DNA molecule. To date, the molecular-level details of how information about the bound nucleotide state is transmitted over vast ranges in the TopoII complex, and how protein substitutions disrupt these mechanisms, remain largely unknown. Here, we conducted extensive molecular dynamics simulations of the yeast TopoII enzyme in multiple nucleotide-bound states and with various amino acid substitutions. Our results reveal remarkable flexibility in the ATPase domains on the sub-microsecond timescale, with dynamics modulated by the identity of the bound nucleotides and the presence of local and distant amino acid substitutions. We identified specific allosteric networks that transmit information as the complex progresses through the hydrolysis cycle that involve residues within the protein and the bound DNA molecule. Notably, amino acid substitutions weakened many of these pathways. Collectively, our findings provide crucial molecular-level insights into the control of the TopoII catalytic cycle through nucleotide binding and hydrolysis and shed light on how mutations may disrupt this process.