Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/143879
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dc.contributor.authorMinhas, Vishalen_US
dc.contributor.authorSun, Tiedongen_US
dc.contributor.authorMirzoev, Alexanderen_US
dc.contributor.authorKorolev, Nikolayen_US
dc.contributor.authorLyubartsev, Alexander P.en_US
dc.contributor.authorNordenskiöld, Larsen_US
dc.date.accessioned2020-09-29T03:48:09Z-
dc.date.available2020-09-29T03:48:09Z-
dc.date.issued2020-
dc.identifier.citationMinhas, V., Sun, T., Mirzoev, A., Korolev, N., Lyubartsev, A. P., & Nordenskiöld, L. (2020). Modeling DNA flexibility : comparison of force fields from atomistic to multiscale levels. The Journal of Physical Chemistry B, 124(1), 38-49. doi:10.1021/acs.jpcb.9b09106en_US
dc.identifier.issn1520-5207en_US
dc.identifier.urihttps://hdl.handle.net/10356/143879-
dc.description.abstractAccurate parametrization of force fields (FFs) is of ultimate importance for computer simulations to be reliable and to possess a predictive power. In this work, we analyzed, in multi-microsecond simulations of a 40-base-pair DNA fragment, the performance of four force fields, namely, the two recent major updates of CHARMM and two from the AMBER family. We focused on a description of double-helix DNA flexibility and dynamics both at atomistic and at mesoscale level in coarse-grained (CG) simulations. In addition to the traditional analysis of different base-pair and base-step parameters, we extended our analysis to investigate the ability of the force field to parametrize a CG DNA model by structure-based bottom-up coarse-graining, computing DNA persistence length as a function of ionic strength. Our simulations unambiguously showed that the CHARMM36 force field is unable to preserve DNA's structural stability at over-microsecond time scale. Both versions of the AMBER FF, parmbsc0 and parmbsc1, showed good agreement with experiment, with some bias of parmbsc0 parameters for intermediate A/B form DNA structures. The CHARMM27 force field provides stable atomistic trajectories and overall (among the considered force fields) the best fit to experimentally determined DNA flexibility parameters both at atomistic and at mesoscale level.en_US
dc.description.sponsorshipMinistry of Education (MOE)en_US
dc.language.isoenen_US
dc.relation.ispartofThe Journal of Physical Chemistry Ben_US
dc.rightsThis document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry B, copyright @ American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jpcb.9b09106en_US
dc.subjectScience::Mathematics::Applied mathematics::Simulation and modeling+en_US
dc.titleModeling DNA flexibility : comparison of force fields from atomistic to multiscale levelsen_US
dc.typeJournal Articleen
dc.contributor.schoolSchool of Biological Sciencesen_US
dc.identifier.doi10.1021/acs.jpcb.9b09106-
dc.description.versionAccepted versionen_US
dc.identifier.pmid31805230-
dc.identifier.issue1en_US
dc.identifier.volume124en_US
dc.identifier.spage38en_US
dc.identifier.epage49en_US
dc.subject.keywordsDNAen_US
dc.subject.keywordsAmberen_US
dc.description.acknowledgementThis work was supported by the Singapore Ministry of Education Academic Research Fund (AcRF) Tier 2 (MOE2014-T2-1-123 (ARC51/14)) and Tier 3 (MOE2012- T3-1-001) grants (to L.N.) and by the Swedish Research Council (grant 2017-03950 to A.P.L.).en_US
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