Role of Mono- and Divalent Ions in Peptide Glu-Asp-Arg–DNA Interaction

Silanteva, Irina A.; Komolkin, Andrei V.; Морозова, Е. А.; Vorontsov-Vèlyaminov, P. N.; Kasyanenko, N. A.

doi:10.1021/acs.jpcb.8b10359

Cited by 4 publications

(2 citation statements)

References 34 publications

(46 reference statements)

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“…It was established that EDR can interact with the large groove of dsDNA, forming bonds with the N7 and O6 atoms of guanine. Mg 2+ ions enhance the binding of EDR to dsDNA due to their ability to screen the negatively charged phosphate groups of the dsDNA [83]. A similar mechanism of binding to dsDNA was established for AEDL, a bronchoprotective peptide [41].…”

Section: Short Peptides + Dnamentioning

confidence: 72%

Peptide Regulation of Gene Expression: A Systematic Review

et al. 2021

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Peptides are characterized by their wide range of biological activity: they regulate functions of the endocrine, nervous, and immune systems. The mechanism of such action of peptides involves their ability to regulate gene expression and protein synthesis in plants, microorganisms, insects, birds, rodents, primates, and humans. Short peptides, consisting of 2–7 amino acid residues, can penetrate into the nuclei and nucleoli of cells and interact with the nucleosome, the histone proteins, and both single- and double-stranded DNA. DNA–peptide interactions, including sequence recognition in gene promoters, are important for template-directed synthetic reactions, replication, transcription, and reparation. Peptides can regulate the status of DNA methylation, which is an epigenetic mechanism for the activation or repression of genes in both the normal condition, as well as in cases of pathology and senescence. In this context, one can assume that short peptides were evolutionarily among the first signaling molecules that regulated the reactions of template-directed syntheses. This situation enhances the prospects of developing effective and safe immunoregulatory, neuroprotective, antimicrobial, antiviral, and other drugs based on short peptides.

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Section: Short Peptides + Dnamentioning

confidence: 72%

Peptide Regulation of Gene Expression: A Systematic Review

et al. 2021

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“…Coordination of neutral peptides with metal ions may occur through the terminal amino group and/or the carbonyl oxygens of both the amide groups and the carboxylic terminus. − These structures are frequently referred to as being charge-solvated (CS), and this type of binding is common in complexes involving alkali and alkaline earth metals. − Alternatively, the amide groups of the peptide backbone may be present as iminols, which coordinate the metal ion via iminol nitrogens (described as Im-binding) with iminol OH groups assisting in delocalizing the charge in some structures by hydrogen bonding to other basic sites. , IRMPD (infrared multiple photon dissociation) studies have shown that Ni 2+ complexes with dipeptides and tripeptides prefer iminol binding. ,, …”

Section: Introductionmentioning

confidence: 99%

Structures and Dissociation Products of Ce/Peptide Complexes: Competition between Coordination and Charge Delocalization

et al. 2019

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Structures of [Ce(GGG)]3+ and [Ce(GGG – H)]2+ have been investigated by DFT calculations. The two lowest-energy structures of the triply charged metal complex have the peptide in either the iminol or conventional zwitterionic form, and these ions have almost identical energies. In the doubly charged complex, the iminol and charge-solvated structures are the best structures on the potential energy surface, but the latter is favored. In both iminol structures, the metal ion coordinates to the iminol oxygen rather than to the nitrogen, unlike in previously reported iminol-containing complexes. Triply charged [Ce(peptide)]3+ complexes are fragile and not easily isolated in a mass spectrometer, whereas the doubly charged [Ce(peptide – H)]2+ complexes are more robust. Here, we studied the fragmentations of 37 [Ce(peptide – H)]2+ and 30 [Ce(peptide)(peptide – H)]2+ complexes and the results are systematically summarized. Losses of CO and/or H2O are the most commonly observed fragmentation channels for [Ce(peptide – H)]2+ complexes and these dissociation pathways are modeled by DFT calculations. For [Ce(peptide)(peptide – H)]2+ complexes the neutral peptide plays the role of a solvent molecule but, unlike in the dissociations of [Ce(CH3CN)(peptide – H)]2+ complexes, the loss of the solvent molecule is not observed. Instead, fragmentation occurs by cleavage of the second amide bond of the solvating peptide molecule.

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Achievements and challenges in resolving molecular aspects of DNA-protein interactions

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2023

Current Opinion in Electrochemistry

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Role of Mono- and Divalent Ions in Peptide Glu-Asp-Arg–DNA Interaction

Cited by 4 publications

References 34 publications

Peptide Regulation of Gene Expression: A Systematic Review

Peptide Regulation of Gene Expression: A Systematic Review

Structures and Dissociation Products of Ce/Peptide Complexes: Competition between Coordination and Charge Delocalization

Achievements and challenges in resolving molecular aspects of DNA-protein interactions

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