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.
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References
Glaeser RM (2016) How good can cryo-EM become. Nat Methods 13:28–32
Kühlbrandt W (2014) Microscopy: cryo-EM enters a new era. elife 3:e03678
Merk A, Bartesaghi A, Banerjee S, Falconieri S, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JLS, Subramaniam S (2016) Breaking Cryo-EM resolution barriers to facilitate drug discovery. Cell 165:1698–1707
Jolley CC, Wells SA, Fromme P, Thorpe MF (2008) Fitting low-resolution Cryo-EM maps of proteins using constrained geometric simulations. Biophys J 94:1613–1621
Raposo AN, Gomes AJP (2016) Computational 3D assembling methods for DNA: a survey. IEEE/ACM Trans Comput Biol Bioinform. 13:1068–1085. doi:10.1109/TCBB.2015.2510008
Colasanti A, Lu XJ, Olson WK (2013) Analyzing and building nucleic acid structures with 3DNA. J Vis Exp 74:e4401
Macke TA, Case DA (1998) Modeling unusual nucleic acid structures. In: Leontes NB, Jr SLJ (eds) Molecular modeling of nucleic acids. American Chemical Society, Washington, DC
Hornus S, Lévy B, Larivière D, Fourmentin E (2013) Easy DNA modeling and more with GraphiteLifeExplorer. PLoS One 8(1):e53609
Papillon J, Ménétret J-F, Batisse C, Hélye R, Schultz P, Potier N, Lamour V (2013) Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase. Nucleic Acids Res 41:7815–7827
Fisher LM, Mizuuchi K, O’Dea MH, Ohmori H, Gellert M (1981) Site-specific interaction of DNA gyrase with DNA. Proc Natl Acad Sci U S A 78:4165–4169
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
Goddard TD, Huang CC, Ferrin TE (2007) Visualizing density maps with UCSF Chimera. J Struct Biol 157:281–287
Cheatham TE III, Case DA (2013) Twenty-five years of nucleic acid simulations. Biopolymers 12:969–977
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Larivière, D. et al. (2017). A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data. In: Espéli, O. (eds) The Bacterial Nucleoid. Methods in Molecular Biology, vol 1624. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7098-8_15
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DOI: https://doi.org/10.1007/978-1-4939-7098-8_15
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Publisher Name: Humana Press, New York, NY
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