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Cited by 116Advanced Physical and Chemical Molecular InteractionsProtein Structure and DynamicsAdvanced Chemical Physics Studies

Martini 3 Coarse-Grained Force Field for Carbohydrates

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Grünewald, Fabian, Punt, Mats H., Jefferys, Elizabeth E., Vainikka, Petteri A., König, Melanie, Virtanen, Valtteri, Meyer, Travis A., Pezeshkian, Weria +5 more·2022·Journal of Chemical Theory and Computation
DOI 10.1021/acs.jctc.2c00757PMC PMC9753587
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Abstract

The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.

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  • Polyply has successfully been applied to model dense polymer melts and simple ssDNA viral chromosomes.

    “This tool of the Martini ecosystem has successfully been applied to model dense polymer melts and simple ssDNA viral chromosomes.”

    From Molecular dynamics simulation of an entire cell (2023) · cites this paper as Grünewald et al., 2022

    The Methods and Validation sections describe using polyply to build dextran systems, including a mixed dextran–PEO system. They do not report its application to dense polymer melts or simple ssDNA viral chromosomes; those specific examples are unsupported by this source. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Grünewald, F., Punt, M. H., Jefferys, E. E., Vainikka, P. A., König, M., Virtanen, V., Meyer, T. A., Pezeshkian, W., Gormley, A. J., Karonen, M., Sansom, M. S. P., Souza, P. C. T., & Marrink, S. J.
Affiliations
  • University of Groningen (NL)
  • University of Oxford (GB)
  • University of Turku (FI)
  • Rutgers, The State University of New Jersey (US)
  • University of Copenhagen (DK)
  • Centre National de la Recherche Scientifique (FR)
Corresponding author
  • Souza, Paulo C. T.
  • Marrink, Siewert J.
ORCID
Venue
Journal of Chemical Theory and Computation
Publisher
American Chemical Society (ACS)
Published
2022-11-07
Volume
18
Issue
12
Pages
7555-7569
ISSN
  • 1549-9618 (ISSN-L)
  • 1549-9626
DOI
10.1021/acs.jctc.2c00757
PMC
PMC9753587
OpenAlex
W4308364841
Cited by
116
References
2
Citations by year
2026: 43 · 2025: 31 · 2024: 24 · 2023: 18
FWCI
10.88
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Chemical Theory and Computation (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
  • arXiv (Cornell University) (submittedVersion)
  • HAL (submittedVersion, other-oa)
  • UTUPub (University of Turku) (submittedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
  • UTUPub (University of Turku) (submittedVersion, cc-by)
  • arXiv (Cornell University)
Funders
  • Novo Nordisk Fonden (NNF18SA0035142)
  • H2020 Marie Sklodowska-Curie Actions (847523)
  • Wellcome Trust (203815/Z/16/Z)
  • Centre National de la Recherche Scientifique
  • National Institutes of Health (K12GM093854)
  • H2020 European Research Council
  • National Science Foundation (DMREF-2118860)
  • PharmCADD
Topics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords
Martini 3 force field, coarse-grained force field, carbohydrate conformation, osmotic pressure, dextran, cellulose, glycolipids, membrane properties, ionic liquids
MeSH terms
Carbohydrate Conformation, Cellulose, Thermodynamics, Water

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