2019
DOI: 10.1021/acs.jpclett.9b02978
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Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi

Abstract: DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, DNA packaging is achieved by specific wellconserved proteins. Here, by means of all-atom molecular dynamics simulations, including the determination of relevant free-energy profiles, we rationalize the molecular bases for this remarkable process in bacteria, illustrating the crucial role played by positively charged a… Show more

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Cited by 21 publications
(22 citation statements)
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“…In agreement with what is observed for other DNA‐compacting proteins, [40] the main driving force for the formation of the complex is due to favorable electrostatic interactions between the negatively charged DNA backbone and the positive protein residues, mainly arginine and lysine. Interestingly, and differently from the characteristics of more globular compaction agents, such as histones or histone‐like proteins, SASP presents positively charged α helices that accommodate in the DNA minor groove, providing additional stabilization.…”
Section: Resultssupporting
confidence: 88%
“…In agreement with what is observed for other DNA‐compacting proteins, [40] the main driving force for the formation of the complex is due to favorable electrostatic interactions between the negatively charged DNA backbone and the positive protein residues, mainly arginine and lysine. Interestingly, and differently from the characteristics of more globular compaction agents, such as histones or histone‐like proteins, SASP presents positively charged α helices that accommodate in the DNA minor groove, providing additional stabilization.…”
Section: Resultssupporting
confidence: 88%
“…Indeed, from one side, we examined the specific interactions exerted between IRP1 protein and the IRE region of ferritin mRNA. Differently from other nucleic acid interacting proteins [ 41 , 57 , 58 , 59 , 60 , 61 , 62 ], IRP1 is able to develop strong and specific hydrogen bonds not only with the backbone but also with specific IRE nucleobases; in particular, the role of the mRNA hairpin region in favoring the interaction is clearly evidenced. Since the interaction with IRP1 involves different IRE structural domains, the protein should maintain an open conformation to allow for the efficient sequestration of the mRNA.…”
Section: Discussionmentioning
confidence: 93%
“…Indeed, from the one side we have examined the specific interactions exerted between IRP1 protein and the IRE region of ferritin mRNA. Differently from other nucleic acid interacting proteins [42,[58][59][60][61][62][63] IRP is able to develop strong and specific hydrogen bonds not only with the backbone but also with specific IRE nucleobases, in particular the role of the mRNA hairpin region in favoring the interaction is clearly evidenced. Since the interaction with IRP1 involves different IRE structural domains, the protein should maintain an open conformation to allow for the efficient sequestration of the mRNA.…”
Section: Discussionmentioning
confidence: 98%