Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA
The response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and des...
| Autores: | , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Universidad Autónoma de Madrid |
| Repositorio: | Biblos-e Archivo. Repositorio Institucional de la UAM |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.uam.es:10486/711598 |
| Acceso en línea: | http://hdl.handle.net/10486/711598 https://dx.doi.org/10.1021/acs.jctc.3c01089 |
| Access Level: | acceso abierto |
| Palabra clave: | Elasticity Molecular Conformation Molecular Dynamics Simulation Nucleic Acid Conformation Stress Mechanical Física |
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Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNARoldán Piñero, CarlosLuengo Márquez, JuanAssenza, SalvatorePérez Pérez, RubénElasticityMolecular ConformationMolecular Dynamics SimulationNucleic Acid ConformationStressMechanicalFísicaThe response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy of the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most popular force fields within the AMBER family, bcs1 and OL15, as well as with CHARMM36. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields and suggests a roadmap to test their performance against experiments. In the case of the stretch modulus, we reconcile these differences, showing that a single mapping between sequence-dependent conformation and elasticity via the crookedness parameter captures simultaneously the results of all force fields, supporting the key role of crookedness in the mechanical response of double-stranded DNAThe project that gave rise to these results received the support of a fellowship from the “la Caixa” Foundation (ID 100010434) and from the European Union’s Horizon research and innovation programme under Marie Skłodowska-Curie grant agreement no. 847648. The fellowship code is LCF/BQ/ PI20/11760019. S.A. acknowledges support from MCIN/AEI/ 10.13039/501100011033 and FSE + through a Ramón y Cajal Fellowship (ref. RYC2022-037744-I). We acknowledge support from the Ministerio de Ciencia e Innovación (MCIN) through the project PID2020-115864RB-I00 and the “María de Maeztu” Programme for Units of Excellence in R&D (grant no. CEX2018-000805-M)American Chemical SocietyDepartamento de Física Teórica de la Materia CondensadaFacultad de Ciencias20242024-02-27research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10486/711598https://dx.doi.org/10.1021/acs.jctc.3c01089reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengEuropean Commission http://dx.doi.org/10.13039/501100000780 Horizon 2020 Framework Programme 847648open accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:repositorio.uam.es:10486/7115982026-06-23T12:46:27Z |
| dc.title.none.fl_str_mv |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| title |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| spellingShingle |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA Roldán Piñero, Carlos Elasticity Molecular Conformation Molecular Dynamics Simulation Nucleic Acid Conformation Stress Mechanical Física |
| title_short |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| title_full |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| title_fullStr |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| title_full_unstemmed |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| title_sort |
Systematic comparison of atomistic force fields for the mechanical properties of double-stranded DNA |
| dc.creator.none.fl_str_mv |
Roldán Piñero, Carlos Luengo Márquez, Juan Assenza, Salvatore Pérez Pérez, Rubén |
| author |
Roldán Piñero, Carlos |
| author_facet |
Roldán Piñero, Carlos Luengo Márquez, Juan Assenza, Salvatore Pérez Pérez, Rubén |
| author_role |
author |
| author2 |
Luengo Márquez, Juan Assenza, Salvatore Pérez Pérez, Rubén |
| author2_role |
author author author |
| dc.contributor.none.fl_str_mv |
Departamento de Física Teórica de la Materia Condensada Facultad de Ciencias |
| dc.subject.none.fl_str_mv |
Elasticity Molecular Conformation Molecular Dynamics Simulation Nucleic Acid Conformation Stress Mechanical Física |
| topic |
Elasticity Molecular Conformation Molecular Dynamics Simulation Nucleic Acid Conformation Stress Mechanical Física |
| description |
The response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy of the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most popular force fields within the AMBER family, bcs1 and OL15, as well as with CHARMM36. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields and suggests a roadmap to test their performance against experiments. In the case of the stretch modulus, we reconcile these differences, showing that a single mapping between sequence-dependent conformation and elasticity via the crookedness parameter captures simultaneously the results of all force fields, supporting the key role of crookedness in the mechanical response of double-stranded DNA |
| publishDate |
2024 |
| dc.date.none.fl_str_mv |
2024 2024-02-27 |
| dc.type.none.fl_str_mv |
research article http://purl.org/coar/resource_type/c_2df8fbb1 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10486/711598 https://dx.doi.org/10.1021/acs.jctc.3c01089 |
| url |
http://hdl.handle.net/10486/711598 https://dx.doi.org/10.1021/acs.jctc.3c01089 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
European Commission http://dx.doi.org/10.13039/501100000780 Horizon 2020 Framework Programme 847648 |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 |
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openAccess |
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application/pdf |
| dc.publisher.none.fl_str_mv |
American Chemical Society |
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American Chemical Society |
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reponame:Biblos-e Archivo. Repositorio Institucional de la UAM instname:Universidad Autónoma de Madrid |
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Universidad Autónoma de Madrid |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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Biblos-e Archivo. Repositorio Institucional de la UAM |
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