Advertisement

Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level

  • Pablo D. Dans
  • Leonardo Darré
  • Matías R. Machado
  • Ari Zeida
  • Astrid F. Brandner
  • Sergio Pantano
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8213)

Abstract

We present a comparison between atomistic and coarse grain models for DNA developed in our group, which we introduce here with the name SIRAH. Molecular dynamics of DNA fragments performed using implicit and explicit solvation approaches show good agreement in structural and dynamical features with published state of the art atomistic simulations of double stranded DNA (using Amber and Charmm force fields). The study of the multi-microsecond timescale results in counterion condensation on DNA, in coincidence with high-resolution X-ray crystals. This result indicates that our model for solvation is able to correctly reproduce ionic strength effects, which are very difficult to capture by CG schemes.

Keywords

Molecular dynamics nucleic acids simulations WT4 flexibility counterions narrowing 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Karplus, M., McCammon, J.A.: Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9, 646–652 (2002)CrossRefGoogle Scholar
  2. 2.
    Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O., Eastwood, M.P., Bank, J.A., Jumper, J.M., Salmon, J.K., Shan, Y., Wriggers, W.: Atomic-level characterization of the structural dynamics of proteins. Science 330, 341–346 (2010)CrossRefGoogle Scholar
  3. 3.
    Arkhipov, A., Yin, Y., Schulten, K.: Four-scale description of membrane sculpting by BAR domains. Biophys. J. 95, 2806–2821 (2008)CrossRefGoogle Scholar
  4. 4.
    Yin, Y., Arkhipov, A., Schulten, K.: Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains. Structure 17, 882–892 (2009)CrossRefGoogle Scholar
  5. 5.
    Voth, G.A.: Coarse-Graining of Condensed Phase and Biomolecular Systems. Taylor & Francis Group, New-York (2009)Google Scholar
  6. 6.
    Potoyan, D., Savelyev, A., Papoian, G.: Recent successes in coarse-grained modeling of DNA. WIREs Comput. Mol. Sci. 3, 69–83 (2013)CrossRefGoogle Scholar
  7. 7.
    Dans, P.D., Zeida, A., Machado, M.R., Pantano, S.: A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. J. Chem. Theory Comput. 6, 1711–1725 (2010)CrossRefGoogle Scholar
  8. 8.
    Darré, L., Machado, M.R., Dans, P.D., Herrera, F.E., Pantano, S.: Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? J. Chem. Theory Comput. 6, 3793–3807 (2010)CrossRefGoogle Scholar
  9. 9.
    Machado, M.R., Dans, P.D., Pantano, S.: A hybrid all-atom/coarse grain model for multiscale simulations of DNA. Phys. Chem. Chem. Phys. 13, 18134–18144 (2011)CrossRefGoogle Scholar
  10. 10.
    Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaka, S., Itakura, K., Dickerson, R.E.: Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. U. S. A. 78, 2179–2183 (1981)CrossRefGoogle Scholar
  11. 11.
    Shui, X., McFail-Isom, L., Hu, G.G., Williams, L.D.: The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37, 8341–8355 (1998)CrossRefGoogle Scholar
  12. 12.
    Hawkins, G.D., Cramer, C.J., Truhlar, D.G.: Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100, 19839 (1996)CrossRefGoogle Scholar
  13. 13.
    Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham III, T.E., Laughton, C.A., Orozco, M.: Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J. 92, 3817–3829 (2007)CrossRefGoogle Scholar
  14. 14.
    Pastor, R.W., Brooks, B.R., Szabo, A.: An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol. Phys. 65, 1409–1419 (1988)CrossRefGoogle Scholar
  15. 15.
    Wu, X., Brooks, B.R.: Self-guided Langevin dynamics simulation method. Chem. Phys. Lett. 381, 512–518 (2003)CrossRefGoogle Scholar
  16. 16.
    Hess, B., Kutzner, C., van de Spoel, D., Lindahl, E.: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theo. Comp. 4, 435–447 (2008)CrossRefGoogle Scholar
  17. 17.
    Essmann, U., Perera, L., Berkowitz, M.L., Darden, T.A., Lee, H., Pedersen, L.: A smooth particle mesh ewald potential. J. Chem. Phys. 103, 8577–8592 (1995)CrossRefGoogle Scholar
  18. 18.
    Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., Haak, J.R.: Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3691 (1984)CrossRefGoogle Scholar
  19. 19.
    Pérez, A., Luque, F.J., Orozco, M.: Dynamics of B-DNA on the Microsecond Time Scale. J. Am. Chem. Soc. 129, 14739–14745 (2007)CrossRefGoogle Scholar
  20. 20.
    Perez, A., Lankas, F., Luque, F.J., Orozco, M.: Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res. 36, 2379–2394 (2008)CrossRefGoogle Scholar
  21. 21.
    Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D., Zakrzewska, K.: Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res. 37, 5917–5929 (2009)CrossRefGoogle Scholar
  22. 22.
    Humphrey, W., Dalke, A., Schulten, K.: VMD - Visual Molecular Dynamics. J. Molec. Graphics 14, 33–38 (1996)CrossRefGoogle Scholar
  23. 23.
    Zeida, A., Machado, M.R., Dans, P.D., Pantano, S.: Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations. Phys. Rev. E Stat. Nonlin. Soft. Matter Phys. 86, 021903 (2012)Google Scholar
  24. 24.
    Hamelberg, D., Williams, L.D., Wilson, W.D.: Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects. J. Am. Chem. Soc. 123, 7745–7755 (2001)CrossRefGoogle Scholar
  25. 25.
    Hamelberg, D., Williams, L.D., Wilson, W.D.: Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies. Nucleic Acids Res. 30, 3615–3623 (2002)CrossRefGoogle Scholar
  26. 26.
    Shui, X., Sines, C.C., McFail-Isom, L., VanDerveer, D., Williams, L.D.: Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 37, 16877–16887 (1998)CrossRefGoogle Scholar
  27. 27.
    Spiriti, J., Kamberaj, H., de Graff, A., Thorpe, M.F., van der Vaart, A.: DNA Bending through Large Angles Is Aided by Ionic Screening. J. Chem. Theo. Comp. 8, 2145–2156 (2012)CrossRefGoogle Scholar
  28. 28.
    Norambuena, T., Melo, F.: The Protein-DNA Interface database. BMC Bioinformatics 11, 262 (2010)CrossRefGoogle Scholar
  29. 29.
    Dans, P.D., Perez, A., Faustino, I., Lavery, R., Orozco, M.: Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res. 40, 10668–10678 (2012)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  • Pablo D. Dans
    • 1
    • 2
  • Leonardo Darré
    • 1
    • 3
  • Matías R. Machado
    • 1
  • Ari Zeida
    • 1
    • 4
  • Astrid F. Brandner
    • 1
  • Sergio Pantano
    • 1
  1. 1.Institut Pasteur de MontevideoUruguay
  2. 2.Institute for Research in Biomedicine (IRB Barcelona)BarcelonaSpain
  3. 3.Department of ChemistryKing’s College LondonLondonUnited Kingdom
  4. 4.Deptartamento de Qca. Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina

Personalised recommendations