Conformational flexibility of spermidine3+ interacting with DNA double helix

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dc.contributor.authorPerepelytsya, Sergiy
dc.contributor.authorVasiliu, Tudor
dc.contributor.authorLaaksonen, Aatto
dc.contributor.authorEngelbrecht, Leon De Villiers
dc.contributor.authorBrancato, Giuseppe
dc.contributor.authorMocci, Francesca
dc.date.accessioned2023-11-16T10:10:17Z
dc.date.available2023-11-16T10:10:17Z
dc.date.issued2023
dc.description.abstractNatural polyamines play a key role in many biological processes, particularly in the stabilization of DNA double helix structure in the cell nucleus. Among others, the conformational flexibility of polyamines, such as spermidine, is an essential property for the formation of complexes with DNA. Yet, the characterization of the conformational space of polyamines has not been fully elucidated. Using atomistic molecular dynamics (MD) simulations, we present a detailed study of the conformational space of spermidine3+ both in solution and in interaction with DNA. We have identified more than 2000 distinct conformations, which can be grouped into seven modes. Notably, the relative population of these modes is highly affected by the interaction of spermidine3+ with DNA, thus representing a fingerprint of complex formation. In particular, three of the seven dihedral angles of spermidine3+ are predominantly in trans conformation (with or without DNA), while the other four dihedral angles are observed to switch between trans, gauche+ and gauche-. The preference between the latter conformational states was analyzed in terms of the distinct energy contributions composing the potential energy. Overall, our results shed light on the conformational equilibrium and dynamics of spermidine3+, which in turn is important for understanding the nature of its interaction with DNA.en_US
dc.identifier.citationConformational flexibility of spermidine3+ interacting with DNA double helix / Sergiy Perepelytsya, Tudor Vasiliu, Aatto Laaksonen, Leon De Villiers Engelbrecht, Giuseppe Brancato, Francesca Mocci // Journal of Molecular Liquids. - 2023. - Vol. 389. - Article number 122828. - https://doi.org/10.1016/j.molliq.2023.122828en_US
dc.identifier.issn0167-7322
dc.identifier.urihttps://doi.org/10.1016/j.molliq.2023.122828
dc.identifier.urihttps://ekmair.ukma.edu.ua/handle/123456789/27091
dc.language.isoenen_US
dc.relation.sourceJournal of Molecular Liquidsen_US
dc.statusfirst publisheduk_UA
dc.subjectpolyamineen_US
dc.subjectspermidine3+en_US
dc.subjectDNA double helixen_US
dc.subjectmolecular dynamicsen_US
dc.subjectconformationen_US
dc.subjectdihedral angleen_US
dc.subjectarticleen_US
dc.titleConformational flexibility of spermidine3+ interacting with DNA double helixen_US
dc.typeArticleuk_UA
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