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Context <p>Interactions between proteins and RNA, as well as between their structural fragments, are widespread in biological objects. We obtained the optimized structures of complexes of the glutathione anion with neutral molecules of uracil, thymine and cytosine. It was established that all complexes are stabilized by hydrogen bonds. The preference for various H-donors in nucleic base molecules (HN(1) or HN(3) in uracyl and thymine, N(1) or H2N in cytosine) for hydrogen bonding with the peptide has been analyzed. Chain elongation from dipeptide to tripeptide creates favorable conditions for increasing the number of hydrogen bonds in the complex. The strongest hydrogen bonds are formed with the carboxylate group of the peptide. Energy advantage of complexation with cytosine compared to other pyrimidine bases, and advantage of complexation with thymine compared to uracil have been established. The contributions of structural rearrangement of molecules, intermolecular interactions and H-bonding to the total values ​​of potential energy and Gibbs energy of the complexation process have been discussed.</p> Methods <p>The article combines the results of calculations by the DFT/ B97D/6–311 + + G(3d,3p) and QTAIM methods to model the structure of ion-molecular complexes between the tripolar anion of peptide (glutathione) and neutral nucleic bases (uracil, thymine, cytosine). The PCM was used for solvent (water). Conformational analysis of the glutathione molecule was performed by scanning the potential energy while varying the dihedral angles. Several initial structure of peptide – nucleic base complexes with different modes of coordination were created in accordance with the MEP results. Non-covalent specific interactions in the complex were highlighted by RDG analysis. The hydrogen bond energies in complexes were calculated based on the correlation with the electron density at bond critical points. Changes in the total energy and Gibbs energy during complex formation, as well as contributions ​​from intermolecular interactions and structural rearrangement of reagent molecules, were determined.</p>

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DFT-calculations and RDG analysis (topology) of complexes between glutathione and nucleic bases of pyrymidine series

  • 期刊论文

  • 发表日期：

    2025年2月26日

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  • Marina S. Kurbatova,
  • Vladimir P. Barannikov

摘要

Context

Interactions between proteins and RNA, as well as between their structural fragments, are widespread in biological objects. We obtained the optimized structures of complexes of the glutathione anion with neutral molecules of uracil, thymine and cytosine. It was established that all complexes are stabilized by hydrogen bonds. The preference for various H-donors in nucleic base molecules (HN(1) or HN(3) in uracyl and thymine, N(1) or H2N in cytosine) for hydrogen bonding with the peptide has been analyzed. Chain elongation from dipeptide to tripeptide creates favorable conditions for increasing the number of hydrogen bonds in the complex. The strongest hydrogen bonds are formed with the carboxylate group of the peptide. Energy advantage of complexation with cytosine compared to other pyrimidine bases, and advantage of complexation with thymine compared to uracil have been established. The contributions of structural rearrangement of molecules, intermolecular interactions and H-bonding to the total values ​​of potential energy and Gibbs energy of the complexation process have been discussed.

Methods

The article combines the results of calculations by the DFT/ B97D/6–311 + + G(3d,3p) and QTAIM methods to model the structure of ion-molecular complexes between the tripolar anion of peptide (glutathione) and neutral nucleic bases (uracil, thymine, cytosine). The PCM was used for solvent (water). Conformational analysis of the glutathione molecule was performed by scanning the potential energy while varying the dihedral angles. Several initial structure of peptide – nucleic base complexes with different modes of coordination were created in accordance with the MEP results. Non-covalent specific interactions in the complex were highlighted by RDG analysis. The hydrogen bond energies in complexes were calculated based on the correlation with the electron density at bond critical points. Changes in the total energy and Gibbs energy during complex formation, as well as contributions ​​from intermolecular interactions and structural rearrangement of reagent molecules, were determined.