| Autor: |
Larivière D; Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France. damien@fourmentinguilbert.org., Galindo-Murillo R; Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA., Fourmentin E; Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France., Hornus S; Equipe Alice, Inria Nancy - Grand Est, Villers-lès-Nancy, France., Lévy B; Equipe Alice, Inria Nancy - Grand Est, Villers-lès-Nancy, France., Papillon J; IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France., Ménétret JF; IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France., Lamour V; IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France. lamourv@igbmc.fr.; Hôpitaux Universitaires de Strasbourg, Strasbourg, France. lamourv@igbmc.fr. |
| Abstrakt: |
The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data. |
