A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data.
Fiche publication
Date publication
janvier 2017
Journal
Methods in molecular biology (Clifton, N.J.)
Auteurs
Membres identifiés du Cancéropôle Est :
Dr LAMOUR Valérie
Tous les auteurs :
Larivière D, Galindo-Murillo R, Fourmentin E, Hornus S, Lévy B, Papillon J, Ménétret JF, Lamour V
Lien Pubmed
Résumé
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.
Référence
Methods Mol. Biol.. 2017 ;1624:193-210