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Adaptive resolution simulations of biomolecular systems

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Abstract

In this review article, we discuss and analyze some recently developed hybrid atomistic–mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping—i.e., one coarse-grained bead represents one water molecule—for development of a multiscale salt solution model. In order to make use of coarse-grained molecular models that are compatible with the MARTINI force field, one has to resort to a supramolecular mapping, in particular to a 4-to-1 mapping, where four water molecules are represented with one coarse-grained bead. To this end, bundled atomistic water models are employed, i.e., the relative movement of water molecules that are mapped to the same coarse-grained bead is restricted by employing harmonic springs. Supramolecular coupling has recently also been extended to polarizable coarse-grained water models with explicit charges. Since these coarse-grained models consist of several interaction sites, orientational degrees of freedom of the atomistic and coarse-grained representations are coupled via a harmonic energy penalty term. The latter aligns the dipole moments of both representations. The reviewed multiscale solvent models are ready to be used in biomolecular simulations, as illustrated in a few examples.

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Fig. 1

Adapted with permission from (Zavadlav et al. 2015b). Copyright 2015 American Chemical Society

Fig. 2

Adapted with permission from Zavadlav et al. (2015b). Copyright 2015 American Chemical Society

Fig. 3

Figure reprinted from Zavadlav (2015)

Fig. 4

Figure adapted from Zavadlav et al. (2014a)

Fig. 5

Figure adapted from Zavadlav et al. (2014a)

Fig. 6

Reprinted from Zavadlav et al. (2015a) with the permission of AIP Publishing

Fig. 7

Adapted from Zavadlav et al. (2015a) with the permission of AIP Publishing

Fig. 8

Adapted from Zavadlav et al. (2015a) with the permission of AIP Publishing

Fig. 9

Figure reprinted from Zavadlav et al. (2014b)

Fig. 10

Figure adapted from Zavadlav et al. (2014b)

Fig. 11

Reprinted with permission from Zavadlav et al. (2015b). Copyright 2015 American Chemical Society

Fig. 12

Adapted with permission from Zavadlav et al. (2015b). Copyright 2015 American Chemical Society

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Acknowledgements

We would like to thank S. J. Marrink and M. N. Melo for a fruitful collaboration on coupling atomistic and MARTINI molecular models for biomolecular simulations. We are grateful to C. Junghans and K. Kremer for collaboration on the salt solution. We would also like to thank R. Podgornik for collaborating with us on the DNA simulations and J. Sablić for careful reading of the manuscript. We acknowledge financial support through grants P1-0002 and J1-7135 from the Slovenian Research Agency.

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Authors and Affiliations

  1. Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia

    Julija Zavadlav, Staš Bevc & Matej Praprotnik

  2. Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000, Ljubljana, Slovenia

    Julija Zavadlav & Matej Praprotnik

  3. Chair of Computational Science, ETH Zurich, Clausiusstrasse 33, 8092, Zurich, Switzerland

    Julija Zavadlav

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  1. Julija Zavadlav
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  2. Staš Bevc
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Correspondence to Matej Praprotnik.

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Special Issue: Regional Biophysics Conference 2016.

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Zavadlav, J., Bevc, S. & Praprotnik, M. Adaptive resolution simulations of biomolecular systems. Eur Biophys J 46, 821–835 (2017). https://doi.org/10.1007/s00249-017-1248-0

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