School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, Kitami 090-8507, Japan.
Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima 731-3194, Japan.
Int J Mol Sci. 2022 Aug 12;23(16):9032. doi: 10.3390/ijms23169032.
Hydrogen-bond (H-bond) energies in 3-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 3-helical conformation of total energies (whole helical model, WH model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 3-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH model, suggesting the action of H-bond cooperativity.
通过使用精确的 DFT 计算和负碎片方法（NFA），系统地研究了短丙氨酸肽 3-螺旋中的氢键（H 键）能量，这是一种基于分子剪裁方法的改进方法。从总能量的 3-螺旋构象（全螺旋模型，WH 模型）详细评估了每个氢键的贡献，并且将结果与我们之前的研究中α-螺旋中氢键的性质进行了比较。WH 模型的氢键能量表现出与α-螺旋不同的趋势，因为它们取决于相关氢键对的螺旋位置。观察到与末端氢键对相邻的氢键对被强烈去稳定化。电子结构的分析表明，结构特征导致 3-螺旋中氢键的去稳定化。我们还发现，WH 模型末端对的氢键随着螺旋长度的增加而变得更加稳定，这表明氢键协同作用的作用。
