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Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids

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Handbook of Computational Chemistry

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Abstract

Molecular dynamics (MD) simulations based on a classical force field are increasingly being used to study the structure and dynamics of nucleic acids. Simulation studies are limited by the accuracy of the force field description and by the time scale accessible by current MD approaches. In case of specific conformational transitions, it is often possible to improve the sampling of possible states by adding a biasing or umbrella potential along some coordinate describing the conformational transition. It is also possible to extract the associated free energy change along the reaction coordinate. The development of advanced sampling methods such as the replica-exchange MD (REMD) approach allows significant enhancement of conformational sampling of nucleic acids. Recent applications of umbrella sampling and REMD simulation as well as combinations of both methodologies on nucleic acids will be presented. These approaches have the potential to tackle many open questions in structural biology such as the role of nucleic acid structure during recognition and packing and the function of nucleic acid fine structure and dynamics.

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Acknowledgments

This work was supported by grants from DFG (Deutsche Forschungsgemeinschaft) to MZ.

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Authors and Affiliations

  1. Mathematics Department, Swiss Federal Institute of Technology, Lausanne (EPFL), Switzerland

    Jeremy Curuksu

  2. Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore, Singapore

    Srinivasaraghavan Kannan

  3. Physik-Department T38, Technische Universität München, James Franck Str. 1, D-85748, Garching, Germany

    Martin Zacharias

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  1. Jeremy Curuksu
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  2. Srinivasaraghavan Kannan
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  3. Martin Zacharias
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Correspondence to Jeremy Curuksu .

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Editors and Affiliations

  1. Department of Chemistry and Biochemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi, USA

    Jerzy Leszczynski

  2. Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland

    Anna Kaczmarek-Kedziera

  3. Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Tomasz Puzyn

  4. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Manthos G. Papadopoulos

  5. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Heribert Reis

  6. US Army Engineer Research and Development Center, Vicksburg, Mississippi, USA

    Manoj K. Shukla

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Curuksu, J., Kannan, S., Zacharias, M. (2017). Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids. In: Leszczynski, J., Kaczmarek-Kedziera, A., Puzyn, T., G. Papadopoulos, M., Reis, H., K. Shukla, M. (eds) Handbook of Computational Chemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-27282-5_32

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