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Modeling Nucleic Acids at the Residue–Level Resolution

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Part of the book series: Springer Series on Bio- and Neurosystems ((SSBN,volume 8))

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Abstract

Coarse–grained models and force fields have become useful in the studies of the dynamics and physicochemical properties of nucleic acids. Reduced representations of DNA or RNA allow saving computational cost of a few orders of magnitude in comparison with full–atomistic simulations. In this chapter we describe a few selected coarse–grained models of nucleic acids in which one nucleotide is represented as either one, two or three beads. We present the examples of the models designed to investigate the internal dynamics and temperature-dependent denaturation of nucleic acids, as well as created to predict the tertiary structure of RNA or used for large ribonucleoprotein complexes. We describe how the purpose of the model affects the design of the potential energy function and the choice of the simulation method. We also address the limitations of these models.

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Notes

  1. 1.

    In this chapter we ignore the \(\frac{1}{2}\) factor because the harmonic potentials in CG FFs are presented differently (either with or without the \(\frac{1}{2}\) factor). Including this factor affects only the numerical value of a force constant but does not change its general form.

  2. 2.

    There is an earlier version of the model [104] in a four collinear beads variant, with separate beads for base repulsion site and base hydrogen–bonding site.

  3. 3.

    Some of one–bead models, e.g., Trovato et al. [135], assign a mass consistent with the base type in MD simulations but it has a limited effect on the interactions.

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Acknowledgements

The authors acknowledge support from the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw (G31-4, GA65-16, GA65-17, GB65-28 to JT), National Science Centre, Poland (2011/03/N/NZ2/02482 to FL, DEC-2014/12/W/ST5/00589 Symfonia to JT, 2016/23/B/NZ1/03198 Opus to JT).

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  1. Faculty of Chemistry, Centre of New Technologies, University of Warsaw, Warsaw, Poland

    Filip Leonarski

  2. Centre of New Technologies, University of Warsaw, Warsaw, Poland

    Joanna Trylska

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    Adam Liwo

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Leonarski, F., Trylska, J. (2019). Modeling Nucleic Acids at the Residue–Level Resolution. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_5

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