Cited by 259Protein Structure and DynamicsRNA and protein synthesis mechanismsAdvanced Physical and Chemical Molecular Interactions

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Martini Coarse-Grained Force Field: Extension to RNA

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Uusitalo, Jaakko J., Ingólfsson, Helgi I., Marrink, Siewert J., Faustino, Ignacio·2017·Biophysical Journal

DOI 10.1016/j.bpj.2017.05.043PMC PMC5529176

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Abstract

RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding but rather offers a stable RNA structure for studying RNA interactions with other (bio)molecules. The RNA model is compatible with all other Martini models and opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.

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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
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“196 In addition to lipids, Martini has been extended to the most important classes of biomolecules (proteins, 197,198 carbohydrates, 199 nucleotides 200,201 ), as well as a large variety of polymers 202 and nanoparticles.”
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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 606
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Authors: Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I.
Affiliations: University of Groningen (NL)
Corresponding author: Marrink, Siewert J.
ORCID: Uusitalo, Jaakko J.
Ingólfsson, Helgi I.
Marrink, Siewert J.
Faustino, Ignacio
Venue: Biophysical Journal
Publisher: Elsevier BV
Published: 2017-07
Volume: 113
Issue: 2
Pages: 246-256
ISSN: 0006-3495 (ISSN-L)
DOI: 10.1016/j.bpj.2017.05.043
PMC: PMC5529176
OpenAlex: W2401568999
Cited by: 259
References: 151
Citations by year: 2026: 15 · 2025: 22 · 2024: 31 · 2023: 36 · 2022: 31 · 2021: 34 · 2020: 24 · 2019: 21 · 2018: 20 · 2017: 15
FWCI: 8.94
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 389 d)
Locations: Biophysical Journal (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
Funders: Emil Aaltonen Foundation
Netherlands Scientific Organisation
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords: Martini force field, coarse-grained force field, RNA tertiary structure, elastic networks, RNA-DNA interactions, RNA-protein interactions, explicit solvent molecular dynamics
MeSH terms: Elasticity, Humans, Hydrogen Bonding, Ions, Nucleic Acid Conformation, Ribosomes, RNA, Solvents, Water, Thermus thermophilus, RNA Stability, Static Electricity, Molecular Dynamics Simulation, Methanocaldococcus

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Martini Coarse-Grained Force Field: Extension to RNA

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