Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
Biochemistry (Mosc). 2010 Aug;75(8):1017-24. doi: 10.1134/s0006297910080109.
Two models of 15-mer thrombin-binding DNA aptamer (15TGT) were comparatively analyzed by molecular dynamics simulation using the GROMACS software package. The two original models of 15TGT were obtained by NMR and X-ray analyses. The models significantly differ in the topology of loops and the direction of oligodeoxyribonucleotide chain. The evolution of the two structures in parm99 force fields and parmbsc0 optimized for nucleic acids was analyzed in our adaptation of GROMACS architecture. It is shown that the best system for description of the 15TGT structure is the model obtained by X-ray analysis in the parmbsc0 force field.
使用 GROMACS 软件包通过分子动力学模拟对两种 15 -mer 凝血酶结合 DNA 适体（15TGT）模型进行了比较分析。两种原始的 15TGT 模型是通过 NMR 和 X 射线分析获得的。这些模型在环的拓扑结构和寡脱氧核苷酸链的方向上存在显著差异。在我们对 GROMACS 架构的适应中，分析了在 parm99 力场和针对核酸优化的 parmbsc0 中这两种结构的演变。结果表明，描述 15TGT 结构的最佳系统是在 parmbsc0 力场中通过 X 射线分析获得的模型。
