The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index.
Martini Coarse-Grained Force Field: Extension to Carbohydrates
Abstract
We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The carbohydrate building blocks considered are the monosaccharides glucose and fructose and the disaccharides sucrose, trehalose, maltose, cellobiose, nigerose, laminarabiose, kojibiose, and sophorose. Bonded parameters for these saccharides are optimized by comparison to conformations sampled with an atomistic force field, in particular with respect to the representation of the most populated rotameric state for the glycosidic bond. Application of the new coarse-grained carbohydrate model to the oligosaccharides amylose and Curdlan shows a preservation of the main structural properties with 3 orders of magnitude more efficient sampling than the atomistic counterpart. Finally, we investigate the cryo- and anhydro-protective effect of glucose and trehalose on a lipid bilayer and find a strong decrease of the melting temperature, in good agreement with both experimental findings and atomistic simulation studies.
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Cites
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The MARTINI Coarse-Grained Force Field: Extension to Proteins
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Self-citationCoarse Grained Model for Semiquantitative Lipid Simulations
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Cited by
Martini 3: A general purpose force field for coarse-grained molecular dynamics
Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01098-3 · Cited by 1,551
‘Improved parameters for the Martini coarse-grained protein force field’
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Coarse-Grained Protein Models and Their Applications
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Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 599
Metadata
- Authors
- López, C. A., Rzepiela, A. J., de Vries, A. H., Dijkhuizen, L., Hünenberger, P. H., & Marrink, S. J.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-10-30
- Volume
- 5
- Issue
- 12
- Pages
- 3195-3210
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2119806687
- Cited by
- 411
- References
- 50
- FWCI
- 6.60
- Type
- journal article
- Language
- en
- Open access
- closed
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