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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Method
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Muratov, A. D., Markina, A., Pergushov, D. V., & Аветисов, В. А. (2021) · Physics of Fluids · doi:10.1063/5.0058510 · Cited by 5
Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide
Glass, W. G., Essex, J. W., Fraternali, F., Gebbie-Rayet, J. T., Marzuoli, I., Samways, M. L., Biggin, P. C., & Khalid, S. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1394-8_14 · Cited by 5
Computer Simulation and Modeling Techniques in the Study of Nanoparticle-Membrane Interactions
Zhou, G., & Wang, Y. (2016) · Annual reports in computational chemistry · doi:10.1016/bs.arcc.2016.05.001 · Cited by 5
Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1
Das, T., & Mukhopadhyay, C. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c02286 · Cited by 4
RNA Multiscale Simulations as an Interplay of Electrostatic, Mechanical Properties, and Structures Inside Viruses
Cruz-León, S., Assenza, S., Poblete, S., & Guzman, H. V. (2023) · Springer series in biophysics · doi:10.1007/978-3-031-36815-8_2 · Cited by 4
Many-body dissipative particle dynamics with the MARTINI “Lego” approach
Carnevale, L. H., & Theodorakis, P. E. (2024) · The European Physical Journal Plus · doi:10.1140/epjp/s13360-024-05362-1 · Cited by 4
Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery
Lunt, G., Hashemi, N., Mahajan, S., & Tang, T. (2025) · Scientific Reports · doi:10.1038/s41598-025-88848-x · Cited by 4
“In the literature, Martini-based CG models have been successfully applied to study a wide range of biomolecular processes such as protein-ligand binding 97–99 , protein folding 61 and aggregation 100 , protein-protein 100,101 and DNA/RNA 76,94 interactions.”
Representations of protein structure for exploring the conformational space: A speed–accuracy trade-off
Postic, G., Janel, N., & Moroy, G. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.04.049 · Cited by 4
“Although the required experimental data might be currently too scarce for a deep learning approach, the simpler methods presented here are not specific to proteins and could be transposed to the RNA folding problem—which includes coarse-grained modeling, as the MARTINI force field has been recently extended to RNA mac…”
Method
Aggregation of Lysozyme in the Presence of a Mixed Bilayer of POPC and POPG
Islam, S., & Mukhopadhyay, C. (2021) · ACS Omega · doi:10.1021/acsomega.1c01145 · Cited by 4
The Proliferating Cell Nuclear Antigen (PCNA) Transcript Variants as Potential Relapse Markers in B-Cell Acute Lymphoblastic Leukemia
Villegas-Ruíz, V., Romo‐Mancillas, A., Vera, I., Castro-López, K. A., Ramírez‐Chiquito, J. C., Fonseca-Montaño, M. A., García‐Cruz, M. E., Rivera‐Luna, R., Mendoza‐Torreblanca, J. G., & Juárez‐Méndez, S. (2022) · Cells · doi:10.3390/cells11203205 · Cited by 4
A Guide to Titratable Martini Simulations
Sami, S., Grünewald, F., Souza, P. C. T., & Marrink, ‪. J. (2023) · doi:10.1063/9780735425279_004 · Cited by 4
Molecular dynamics simulation of siRNA loading into a nanoemulsion as a potential carrier
Pirhadi, S., & Amani, A. (2020) · Journal of Molecular Modeling · doi:10.1007/s00894-020-04471-9 · Cited by 4
“TheMartini force field for siRNAwas generated using martinize-nucleotide python script [15].”
Method
In Silico Engineering of Stable siRNA Lipid Nanoparticles: Exploring the Impact of Ionizable Lipid Concentrations for Enhanced Formulation StabilityPreprint
Biswal, M. R., Roy, S., & Singh, J. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.25.614899 · Cited by 4
“48 For DOPE and cholesterol (CHOL), the CG structures were obtained from Marrink et, al .”
Method
Comparative Analysis of Lipid Nanoparticles in Pfizer-BioNTech and Moderna COVID-19 Vaccines: Insights from Molecular Dynamics SimulationsPreprint
Biswal, M. R., Roy, S. K., & Singh, J. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.04.616619 · Cited by 4
“32 To construct vesicles mimicking these LNPs, bilayers were ﬁrst generated using PACK-MOL.”
Method
Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation
Nguyen, H. V., Nguyen, H. L., & Li, M. S. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c01391 · Cited by 3
Meeting Proceedings from 4th Minimal Cell Workshop: Exploring JCVI Minimal Cell Fundamental Insights and Integrative Applications
Peksaglam, Z., Kumar, R., de Araújo, M. E. G., Glass, S. A., Rodriguez, R., Goshia, T., & Glass, J. I. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00159 · Cited by 3
Coarse-Grained Simulations of RNA-Loaded Lipid Nanoparticles: Implications on RNA Stability and Antigenic Protein Expression in mRNA Vaccines
Pastre, A., Brass, O., Terreux, R., & Mégy, S. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c04980 · Cited by 4
Aptamers Meet Structural Bioinformatics, Computational Chemistry, and Artificial Intelligence
da Rosa, G., de Castro, M., García-Velásquez, V. M., Pintos, S., Benedetto, J., Grille, L., Valla, S., Álvarez-Salas, L. M., Calzada, V., & Dans, P. D. (2025) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.70050 · Cited by 4
“…in AIMS_ RNA_B5 [171], IsRNA2 [172], SimRNA [135, 173, 174] and Ren's model [175, 176], as well as higher-resolution models employing six or seven beads per nucleotide such as IsRNA [177], Sugar-cg [178], Martini RNA/DNA [179, 180], UNRES-like DNA [181], HiRE-RNA/DNA [182, 183], and SIRAH [184].”
Coarse-Grained Simulations Reveal Salt- and Length-Dependent Condensation of G4C2 RNA Repeats
Zhang, Q., Valério, M., Grünewald, L., Borges-Araújo, L., Grünewald, F., Wang, S., Marrink, ‪. J., Gong, Y., & Souza, P. C. T. (2026) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.6c00916 · Cited by 4
Martini 3D-OZ: A Theoretical Investigation of Solvation Shell Structures and Solvation Free Energies of Martini Coarse-Grained Proteins
Ishizuka, R. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c03897 · Cited by 3
Dispersion of Hydrophilic Nanoparticles in Natural Rubber with Phospholipids
Kitjanon, J., Nisoh, N., Phongphanphanee, S., Chattham, N., Karttunen, M., & Wong-ekkabut, J. (2024) · Polymers · doi:10.3390/polym16202901 · Cited by 3
Temperature-dependent ion migration underlies sequence-specific collapse of unstructured RNA
Zhang, H., Maity, H., & Nguyen, H. T. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.05.026 · Cited by 2
Transposition of polymer-encapsulated small interfering RNA through lung surfactant models at the air-water interface
Souza, L. M. P., Lima, M. C., Bezerra, L. F. S., & Pimentel, A. S. (2022) · Chemical Physics · doi:10.1016/j.chemphys.2022.111704 · Cited by 3
Kinetic Mechanism of Surfactant-Based Molecular Recognition: Selective Permeability across an Oil–Water Interface Regulated by Supramolecular Aggregates
Zhou, H., Shiel, E. A., Bell, T. N., Lin, S., & Lenhert, S. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c05017 · Cited by 3
Current Advancement and Future Prospects: Biomedical Nanoengineering
Singh, S. K., & Sahani, H. (2023) · Current Radiopharmaceuticals · doi:10.2174/0118744710274376231123063135 · Cited by 3

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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