Modeling of Intermolecular Interactions between Cyanine 7 and TNF-Related Amino Acid Chains
Bogdan A. Mishunin 1, Inna L. Plastun 1, Egor V. Nazariev 1, Kirill A. Laptinsky 2, Tatyana A. Dolenko 2, Ruslan Y. Yakovlev 3;1 Yuri Gagrin State Technical University of Saratov;2 Lomonosov Moscow State University; 3 LLC «Protonica», cluster «Lomonosov», Moscow
Abstract
Using density functional theory (DFT) methods, modeling and analysis were carried out of the intermolecular interactions between the amino acid chains of the tumor necrosis factor (TNF) receptor and ligand and their relationship with organic dyes. In this study, we modeled several amino acid complexes with Cyanine 7 as the dye, as well as the phenylalanine–glutamine and glutamine–glutamic acid pairs as amino acid chains. The geometries of all complexes were fully optimized at the DFT level, and the corresponding binding energies, hydrogen bond lengths, and electron density distributions were calculated. The results indicate that Cyanine 7 interacts most strongly with polar and charged amino acid residues, forming stable hydrogen bonds primarily through its sulfonate and indolium groups. At the same time, its interactions with hydrophobic residues such as phenylalanine are considerably weaker. Natural bond orbital analysis revealed that the presence of Cyanine 7 leads to a redistribution of electron density within the amino acid chains, which in turn reduces the strength of the original hydrogen bonds between the amino acid residues. Based on the modeling and calculations performed, it was concluded that Cyanine 7 weakens the hydrogen bonding of the entire complex. These findings provide important insights into how cyanine-based dyes may influence protein–protein interactions and may be useful for the rational design of fluorescent probes targeting TNF-related systems.
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Bogdan A. Mishunin
Yuri Gagrin State Technical University of Saratov
Russian Federation
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