Coordinated Dynamics Orchestrating the DNA Re-Ligation by De-Poisoned Topoisomerase II

Abstract

Topoisomerase II is a crucial enzyme that tightly controls the topology of DNA to facilitate the critical sub-cellular processes involving these genetic materials. It generates transient double-strand breaks (DSB) and transports another DNA duplex through to resolve their topological problems. Although topoisomerase poisons, the drugs arresting the subsequent DNA re-ligation, have been used in anticancer therapy and the recent structural characterization of the enzyme, our understanding of the re-ligation mechanism was still distressingly restricted by the transitory nature of this process. Captivated by the fluent re-ligation following the characteristic DSB by the enzyme, we selected a high-resolution crystal structure of the drug-entrapped intermediate and exploited atomistic molecular dynamics simulations of the very large systems for up to a microsecond to investigate the dynamics of this process [1]. We observed a nearly vectorial transition of the de-poisoned complex toward the resealing-compliant configuration, and the statistical analysis revealed the non-concerted maneuvers of the two different DNA strands mediated by the enzyme. Using a neighborhood-based metric, we captured the important dynamical transitions during the re-ligation from the vast amount of correlated motions and provided the visible links between previously unsettled experimental observations. With the simulations of the drug-bound complexes, we also presented the conformational population shifts of an important residue in response to the binding of different drug molecules [2]. Furthermore, by comparing the coordinated dynamics revealed by different isoforms, we are able to dissect the differential dynamics of the critical DNA re-ligation conducted by the enzymes. We believe these are useful insights for the development of new anticancer drugs with lower cardiotoxicity.