Advertisement

A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data

  • Damien LarivièreEmail author
  • Rodrigo Galindo-Murillo
  • Eric Fourmentin
  • Samuel Hornus
  • Bruno Lévy
  • Julie Papillon
  • Jean-François Ménétret
  • Valérie LamourEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1624)

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.

Key words

DNA modeling software Cryo-electron microscopy Molecular dynamics Protein Data Bank Macromolecular complex 

Supplementary material

Video 1

(MP4 28,413 kb)

References

  1. 1.
    Glaeser RM (2016) How good can cryo-EM become. Nat Methods 13:28–32CrossRefPubMedGoogle Scholar
  2. 2.
    Kühlbrandt W (2014) Microscopy: cryo-EM enters a new era. elife 3:e03678CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    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 165:1698–1707CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Jolley CC, Wells SA, Fromme P, Thorpe MF (2008) Fitting low-resolution Cryo-EM maps of proteins using constrained geometric simulations. Biophys J 94:1613–1621CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    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 CrossRefPubMedGoogle Scholar
  6. 6.
    Colasanti A, Lu XJ, Olson WK (2013) Analyzing and building nucleic acid structures with 3DNA. J Vis Exp 74:e4401Google Scholar
  7. 7.
    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, DCGoogle Scholar
  8. 8.
    Hornus S, Lévy B, Larivière D, Fourmentin E (2013) Easy DNA modeling and more with GraphiteLifeExplorer. PLoS One 8(1):e53609CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    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 41:7815–7827CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    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 78:4165–4169CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    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 25:1605–1612CrossRefPubMedGoogle Scholar
  12. 12.
    Goddard TD, Huang CC, Ferrin TE (2007) Visualizing density maps with UCSF Chimera. J Struct Biol 157:281–287CrossRefPubMedGoogle Scholar
  13. 13.
    Cheatham TE III, Case DA (2013) Twenty-five years of nucleic acid simulations. Biopolymers 12:969–977Google Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Damien Larivière
    • 1
    Email author
  • Rodrigo Galindo-Murillo
    • 2
  • Eric Fourmentin
    • 1
  • Samuel Hornus
    • 3
  • Bruno Lévy
    • 3
  • Julie Papillon
    • 4
  • Jean-François Ménétret
    • 4
  • Valérie Lamour
    • 4
    • 5
    Email author
  1. 1.Fourmentin-Guilbert Scientific FoundationNoisy-le-GrandFrance
  2. 2.Department of Medicinal Chemistry, College of PharmacyUniversity of UtahSalt Lake CityUSA
  3. 3.Equipe Alice, Inria Nancy – Grand EstVillers-lès-NancyFrance
  4. 4.IGBMC, Integrated Structural Biology DepartmentUMR7104 CNRS, U964 Inserm, Université de StrasbourgIllkirchFrance
  5. 5.Hôpitaux Universitaires de StrasbourgStrasbourgFrance

Personalised recommendations