title: Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.
abstract: Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.
authors.affiliation: Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan.
authors.forename: Nan-Lan
authors.initials: NL
authors.lastname: Huang
authors.affiliation: Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan Institute of Biomedical Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan School of Pharmacy, National Taiwan University, Taipei 10050, Taiwan jhlin@gate.sinica.edu.tw jlin@ntu.edu.tw.
authors.forename: Jung-Hsin
authors.initials: JH
authors.lastname: Lin
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D053837:DNA Cleavage; D004250:DNA Topoisomerases, Type II / Q000737:chemistry* / Q000378:metabolism; D005047:Etoposide / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009038:Motion; D017434:Protein Structure, Tertiary; D059005:Topoisomerase II Inhibitors / Q000737:chemistry
chemical_list: D059005:Topoisomerase II Inhibitors; D005047:Etoposide; D004247:DNA; D004250:DNA Topoisomerases, Type II