Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
Int J Mol Sci. 2009 Jul 29;10(8):3358-3370. doi: 10.3390/ijms10083358.
Two oligomers, each containing 3 l-lysine residues, were used as model molecules for the simulation of the beta-sheet conformation of varepsilon-polylysine (varepsilon-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with alpha-l-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and alpha-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6 degrees . The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.
两个寡聚物，每个寡聚物都含有 3 个 l-赖氨酸残基，被用作 varepsilon-聚赖氨酸（varepsilon-PLL）链的β-折叠构象模拟的模型分子。它们的 C 末端分别用乙胺封端，N 末端分别用α-l-氨基丁酸封端。计算是用混合二级 ONIOM（B3LYP/6-31G:PM3）计算化学方法进行的。优化了构象，并将红外频率与实验数据进行了比较。结果表明，两条链通过分叉氢键缠绕在一起，形成了一个明显的环庚烷结构。一条链上的酰胺和α-氨腈基团以及另一条链上的羰基参与了环庚烷结构。分叉氢键的键角为 66.6 度。在 ONIOM [B3LYP/6-31G（d）:PM3]水平上的频率分析表明，主要基团的红外吸收率，如酰胺和氨腈基团，与实验数据一致。
