Chapter title |
A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data
|
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Chapter number | 15 |
Book title |
The Bacterial Nucleoid
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-7098-8_15 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7097-1, 978-1-4939-7098-8
|
Authors |
Damien Larivière, Rodrigo Galindo-Murillo, Eric Fourmentin, Samuel Hornus, Bruno Lévy, Julie Papillon, Jean-François Ménétret, Valérie Lamour, Larivière, Damien, Galindo-Murillo, Rodrigo, Fourmentin, Eric, Hornus, Samuel, Lévy, Bruno, Papillon, Julie, Ménétret, Jean-François, Lamour, Valérie |
Abstract |
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. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 3 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Professor | 1 | 33% |
Student > Ph. D. Student | 1 | 33% |
Student > Bachelor | 1 | 33% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 1 | 33% |
Agricultural and Biological Sciences | 1 | 33% |
Chemistry | 1 | 33% |