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Martini Coarse-Grained Force Field: Extension to RNA
Open accessAbstract
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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“These studies have benefitted from the availability of simplified CG models, particularly variants of the widely used Martini general force field (Marrink et al., 2007; Monticelli et al., 2008; Uusitalo et al., 2015).”
MethodpSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model
Miyazaki, Y., Okazaki, S., & Shinoda, W. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00946 · Cited by 31
Coarse-grained (hybrid) integrative modeling of biomolecular interactions
Roel‐Touris, J., & Bonvin, A. M. J. J. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.05.002 · Cited by 31
“The current ‘‘MARTINIdome” includes: lipids [28], proteins [29], polymers [30,31], carbohydrate [32], water [33], glycolipids [34], nucleotides [35,36] and nanoparticles [37].”
BackgroundKhan, P. M., Kaushik, R. K., & Jayaraj, A. (2022) · ACS Omega · doi:10.1021/acsomega.2c06248 · Cited by 34
Assessing the Martini 3 protein model: A review of its path and potential
Borges-Araújo, L., Pereira, G. P., Valério, M., & Souza, P. C. T. (2024) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2024.141014 · Cited by 29
Structure and conformational dynamics of scaffolded DNA origami nanoparticles
Pan, K., Bricker, W. P., Ratanalert, S., & Bathe, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx378 · Cited by 31
Martinize2 and Vermouth: Unified Framework for Topology GenerationPreprint
Kroon, P., Grunewald, F., Barnoud, J., van Tilburg, M., Souza, P., Wassenaar, T. A., & Marrink, . J. (2024) · eLife · doi:10.7554/elife.90627.2 · Cited by 31
Naskar, S., & Maiti, P. K. (2021) · Journal of Materials Chemistry B · doi:10.1039/d0tb02970j · Cited by 29
Computational Nanoscopy of Tight Junctions at the Blood–Brain Barrier Interface
Rajagopal, N., Irudayanathan, F. J., & Nangia, S. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20225583 · Cited by 30
Systematic Selection of High‐Affinity ssDNA Sequences to Carbon Nanotubes
Lee, D., Lee, J. Y., Kim, W., Suh, Y., Park, J., Kim, S., Kim, Y., Kwon, S., & Jeong, S. (2024) · Advanced Science · doi:10.1002/advs.202308915 · Cited by 27
Martini 3 Building Blocks for Lipid Nanoparticle Design
Kjølbye, L. R., Valério, M., Paloncýová, M., Borges-Araújo, L., Pestana-Nobles, R., Grünewald, F., Bruininks, B. M. H., Araya‐Osorio, R., Šrejber, M., Mera‐Adasme, R., et al. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01207 · Cited by 28
Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V., & Howorka, S. (2023) · Nature Communications · doi:10.1038/s41467-023-38681-5 · Cited by 26
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
Wei, Z., & Luijten, E. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4937384 · Cited by 26
cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA
de Bruin, L., & Maddocks, J. H. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky351 · Cited by 26
ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field
Zhang, X., Sundram, S., Oppelstrup, T., Kokkila-Schumacher, S. I. L., Carpenter, T. S., Ingólfsson, H. I., Streitz, F. H., Lightstone, F. C., & Glosli, J. N. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0014500 · Cited by 25
Self-citationPaissoni, C., Jussupow, A., & Camilloni, C. (2019) · Journal of Applied Crystallography · doi:10.1107/s1600576719002450 · Cited by 25
Atomistic and coarse-grained simulations of membrane proteins: A practical guide
Jefferies, D. F., & Khalid, S. (2020) · Methods · doi:10.1016/j.ymeth.2020.02.007 · Cited by 25
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments
Wang, W., Nocka, L. M., Wiemann, B. Z., Hinckley, D. M., Mukerji, I., & Starr, F. W. (2016) · Scientific Reports · doi:10.1038/srep22863 · Cited by 23
Development of transferable coarse-grained models of amino acids
Conway, O., An, Y., Bejagam, K. K., & Deshmukh, S. A. (2020) · Molecular Systems Design & Engineering · doi:10.1039/c9me00173e · Cited by 23
Driving forces of RNA condensation revealed through coarse-grained modeling with explicit Mg 2+
Li, S., & Chen, J. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2504583122 · Cited by 22
“Each ribonucleotide is represented by six or seven CG beads in iConRNA, similar to what is adopted in Martini - RNA (63).”
Adaptive resolution simulations of biomolecular systems
Zavadlav, J., Bevc, S., & Praprotnik, M. (2017) · European Biophysics Journal · doi:10.1007/s00249-017-1248-0 · Cited by 22
Wang, R., Zhang, Y., Zhong, H., Zang, J., Wang, W., Cheng, H., Chen, Y., & Ouyang, D. (2024) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2024.125114 · Cited by 21
Computer Aided Development of Nucleic Acid Applications in Nanotechnologies
Paloncýová, M., Pykal, M., Kührová, P., Banáš, P., Šponer, J., & Otyepka, M. (2022) · Small · doi:10.1002/smll.202204408 · Cited by 21
Elahi, A., Bidault, X., & Chaudhuri, S. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c06318 · Cited by 21
Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding
Mu, Z.-C., Tan, Y.-L., Liu, J., Zhang, B., & Shi, Y.-Z. (2023) · Molecules · doi:10.3390/molecules28124833 · Cited by 21
Soni, J., Gupta, S., & Mandal, T. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00645 · Cited by 19
Dynamics of chromosome organization in a minimal bacterial cell
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19
Self-citation
Metadata
- Authors
- Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I.
- Affiliations
- University of Groningen (NL)
- Corresponding author
- Marrink, Siewert J.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2017-07
- Volume
- 113
- Issue
- 2
- Pages
- 246-256
- ISSN
- 0006-3495 (ISSN-L)
- 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
- 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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