---
_id: '804'
abstract:
- lang: eng
  text: Polysaccharides (carbohydrates) are key regulators of a large number of cell
    biological processes. However, precise biochemical or genetic manipulation of
    these often complex structures is laborious and hampers experimental structure–function
    studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool
    to generate and test hypotheses on saccharide function. Yet, currently used MD
    force fields often overestimate the aggregation propensity of polysaccharides,
    affecting the usability of those simulations. Here we tested MARTINI, a popular
    coarse-grained (CG) force field for biological macromolecules, for its ability
    to accurately represent molecular forces between saccharides. To this end, we
    calculated a thermodynamic solution property, the second virial coefficient of
    the osmotic pressure (B22). Comparison with light scattering experiments revealed
    a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing
    at an imbalance of the nonbonded solute–solute, solute–water, and water–water
    interactions. This finding also applies to smaller oligosaccharides which were
    all found to aggregate in simulations even at moderate concentrations, well below
    their solubility limit. Finally, we explored the influence of the Lennard-Jones
    (LJ) interaction between saccharide molecules and propose a simple scaling of
    the LJ interaction strength that makes MARTINI more reliable for the simulation
    of saccharides.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German
  Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF
  187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and
  Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje
  Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions
  and the IST Austria Scientific Computing Facility for support.
article_processing_charge: No
author:
- first_name: Philipp S
  full_name: Schmalhorst, Philipp S
  id: 309D50DA-F248-11E8-B48F-1D18A9856A87
  last_name: Schmalhorst
  orcid: 0000-0002-5795-0133
- first_name: Felix
  full_name: Deluweit, Felix
  last_name: Deluweit
- first_name: Roger
  full_name: Scherrers, Roger
  last_name: Scherrers
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
- first_name: Mateusz K
  full_name: Sikora, Mateusz K
  id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
  last_name: Sikora
citation:
  ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming
    the limitations of the MARTINI force field in simulations of polysaccharides.
    <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a
    href="https://doi.org/10.1021/acs.jctc.7b00374">10.1021/acs.jctc.7b00374</a>
  apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38;
    Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in
    simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>.
    American Chemical Society. <a href="https://doi.org/10.1021/acs.jctc.7b00374">https://doi.org/10.1021/acs.jctc.7b00374</a>
  chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J
    Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force
    Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>.
    American Chemical Society, 2017. <a href="https://doi.org/10.1021/acs.jctc.7b00374">https://doi.org/10.1021/acs.jctc.7b00374</a>.
  ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M.
    K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations
    of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13,
    no. 10. American Chemical Society, pp. 5039–5053, 2017.
  ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017.
    Overcoming the limitations of the MARTINI force field in simulations of polysaccharides.
    Journal of Chemical Theory and Computation. 13(10), 5039–5053.
  mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI
    Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory
    and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53,
    doi:<a href="https://doi.org/10.1021/acs.jctc.7b00374">10.1021/acs.jctc.7b00374</a>.
  short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora,
    Journal of Chemical Theory and Computation 13 (2017) 5039–5053.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2023-09-27T10:58:45Z
day: '10'
department:
- _id: CaHe
doi: 10.1021/acs.jctc.7b00374
external_id:
  isi:
  - '000412965700036'
intvolume: '        13'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1704.03773
month: '10'
oa: 1
oa_version: Submitted Version
page: 5039 - 5053
publication: Journal of Chemical Theory and Computation
publication_identifier:
  issn:
  - '15499618'
publication_status: published
publisher: American Chemical Society
publist_id: '6847'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2017'
...