title: Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site.
abstract: Human topoisomerase 1B has been simulated covalently bound to a negatively supercoiled DNA minicircle, and its behavior compared to the enzyme bound to a simple linear DNA duplex. The presence of the more realistic supercoiled substrate facilitates the formation of larger number of protein-DNA interactions when compared to a simple linear duplex fragment. The number of protein-DNA hydrogen bonds doubles in proximity to the active site, affecting all of the residues in the catalytic pentad. The clamp over the DNA, characterized by the salt bridge between Lys369 and Glu497, undergoes reduced fluctuations when bound to the supercoiled minicircle. The linker domain of the enzyme, which is implicated in the controlled relaxation of superhelical stress, also displays an increased number of contacts with the minicircle compared to linear DNA. Finally, the more complex topology of the supercoiled DNA minicircle gives rise to a secondary DNA binding site involving four residues located on subdomain III. The simulation trajectories reveal significant changes in the interactions between the enzyme and the DNA for the more complex DNA topology, which are consistent with the experimental observation that the protein has a preference for binding to supercoiled DNA.
authors: Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy.
authors: Ilda
authors: I
authors: D'Annessa
authors: Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy.
authors: Andrea
authors: A
authors: Coletta
authors: School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
authors: Thana
authors: T
authors: Sutthibutpong
authors: Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, SM2 5NG, UK.
authors: Jonathan
authors: J
authors: Mitchell
authors: Cineca, via dei Tizii 3, 00166 Roma, Italy.
authors: Giovanni
authors: G
authors: Chillemi
authors: School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
authors: Sarah
authors: S
authors: Harris
authors: Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy desideri@uniroma2.it.
authors: Alessandro
authors: A
authors: Desideri
mesh_terms: D001665:Binding Sites; D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011485:Protein Binding
chemical_list: D004278:DNA, Superhelical; D004264:DNA Topoisomerases, Type I; C528909:TOP1 protein, human