Water model tuning for improved reproduction of rotational diffusion and NMR spectral density.
Water model tuning for improved reproduction of rotational diffusion and NMR spectral density.
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水模型调整可改善旋转扩散和 NMR 谱密度的再现。
DOI：
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发表时间：
2012
影响因子：
3.3
通讯作者：
A. Kitao
中科院分区：
文献类型：
--
作者：
Kazuhiro Takemura;A. Kitao
优化了分子模拟的水模型，以改善纯水和蛋白质的平移和旋转扩散的再现。 SPC/E(b)模型是在原始SPC/E模型的基础上发展而来的，其中O-H键长略微增加了1%。与实验值相比，这种调整显着改善了平移和旋转扩散，而在检查的其他热力学性质中仅观察到很小的变化。使用 SPC/E(b) 模型成功再现了泛素、蛋白 G、牛胰蛋白酶抑制剂和 barstar C42/80A 的总体翻转相关时间 (τ(p))。计算出的泛素和蛋白 G 中主链酰胺键旋转的位点特异性谱密度与核磁共振简化谱密度图得出的结果非常一致。 SPC/E(bT) 模型还开发了与温度相关的键长调节功能，以便于在室温附近重现实验 τ(p)。
A water model for molecular simulation was optimized to improve the reproduction of translational and rotational diffusion of pure water and proteins. The SPC/E(b) model was developed from the original SPC/E model with a slight increase of the O-H bond length of 1%. This tuning has significantly improved the translational and rotational diffusion when compared to the experimental values, whereas only small changes were observed in the other thermodynamic properties examined. The overall tumbling correlation times (τ(p)) from ubiquitin, protein G, bovine pancreatic trypsin inhibitor, and barstar C42/80A were successfully reproduced using the SPC/E(b) model. Calculated site-specific spectral densities of the main chain amide bond rotation in ubiquitin and protein G were in good agreement with those derived from nuclear magnetic resonance reduced spectral density mapping. The SPC/E(bT) model was also developed with temperature-dependent bond-length tuning to facilitate reproduction of the experimental τ(p) around room temperature.
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