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.
CITATION STYLE
Larivière, D., Galindo-Murillo, R., Fourmentin, E., Hornus, S., Lévy, B., Papillon, J., … Lamour, V. (2017). A user-friendly DNA modeling software for the interpretation of cryo-electron microscopy data. In Methods in Molecular Biology (Vol. 1624, pp. 193–210). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7098-8_15
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