Abstract

The results of a molecular dynamics study of the molecular mechanism of the experimentally observed specificity of the transaminase from Desulfohalobium retbaense (Dret) to the D-isomer of leucine are presented. A full-atom 3D model of Dret is constructed based on the data on the primary sequence and the information on the crystal structures of the related enzymes. The analysis of the trajectories of the molecular dynamics demonstrates that, upon the formation of the enzyme-substrate complex with D-leucine, the α-COO^– group of the substrate forms stable hydrogen bonds with the Arg54* residue, which promotes the proper orientation of the substrate in the active site. The formation of the complex with the L-isomer of leucine leads to disraption of these hydrogen bonds and of the structure of the active site.

中文翻译：

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分子动力学模拟揭示脱脂脱卤卤虫转氨酶对D-亮氨酸立体特异性的分子机理

摘要

提出了分子动力学研究的分子机理的结果，该分子机理是通过实验观察到的从氨基苯甲酸脱硫卤虫（Dret）到亮氨酸的D-异构体的转氨酶的特异性。基于一级序列的数据和有关酶的晶体结构的信息，构建了Dret的全原子3D模型。分子动力学的轨迹的分析表明，在所述酶-底物复合物与d亮氨酸，α-COO的形成^-底物基团与Arg54 *残基形成稳定的氢键，从而促进了底物在活性位点的正确定向。具有亮氨酸的L-异构体的复合物的形成导致这些氢键和活性位点结构的分散。