Kurbatova Marina S, Barannikov Vladimir P
G.A.Krestov Institute of Solution Chemistry, Laboratory of Thermodynamics of Solutions of Non-Electrolytes and Biologically Active Substances, Russian Academy of Sciences, 1 Akademicheskaya Street, 153045, Ivanovo, Russia.
J Mol Model. 2025 Feb 26;31(3):98. doi: 10.1007/s00894-025-06323-w.
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.
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.
蛋白质与RNA之间以及它们的结构片段之间的相互作用在生物物体中广泛存在。我们获得了谷胱甘肽阴离子与尿嘧啶、胸腺嘧啶和胞嘧啶中性分子复合物的优化结构。已确定所有复合物均通过氢键稳定。分析了核酸碱基分子中各种氢供体（尿嘧啶和胸腺嘧啶中的HN(1)或HN(3)，胞嘧啶中的N(1)或H2N）与肽形成氢键的偏好。从二肽到三肽的链延长为增加复合物中氢键数量创造了有利条件。与肽的羧基形成最强的氢键。已确定与胞嘧啶相比与其他嘧啶碱基络合的能量优势，以及与胸腺嘧啶相比与尿嘧啶络合的优势。讨论了分子结构重排、分子间相互作用和氢键对络合过程势能和吉布斯能总值的贡献。
本文结合了DFT/B97D/6-311++G(3d,3p)计算结果和QTAIM方法，以模拟肽（谷胱甘肽）的三极阴离子与中性核酸碱基（尿嘧啶、胸腺嘧啶、胞嘧啶）之间的离子-分子复合物结构。采用PCM模拟溶剂（水）。通过扫描势能同时改变二面角对谷胱甘肽分子进行构象分析。根据MEP结果创建了具有不同配位模式的肽-核酸碱基复合物的几种初始结构。通过RDG分析突出了复合物中的非共价特异性相互作用。基于与键临界点处电子密度的相关性计算复合物中的氢键能。确定了络合过程中总能量和吉布斯能的变化，以及试剂分子间相互作用和结构重排的贡献。
