Hayward S, Kitao A, Go N
Department of Chemistry, Faculty of Science, Kyoto University, Japan.
Protein Sci. 1994 Jun;3(6):936-43. doi: 10.1002/pro.5560030608.
A comparison is made between a 200-ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distribution of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.
为了阐明蛋白质动力学中谐波性和非谐波性的双重特性，对牛胰蛋白酶抑制剂（BPTI）在真空中进行了200皮秒的分子动力学模拟，并与正常模式分析进行了比较。使用主成分分析对分子动力学轨迹进行分析，主成分分析是一种适用于与正常模式分析结果进行比较的有效谐波分析。结果表明，第一主成分与更高阶主成分表现出质的不同行为，并且与非谐波构象能量表面上明显的势垒穿越事件相关。更高阶主成分的概率分布似乎可以用高斯分布很好地近似，表明具有谐波性。消除第一主成分的贡献后，两种方法之间显示出大量的对应关系。然而，这种对应关系涉及一个2的因子，因为更高阶主成分分布的方差平均约为正常模式分析结果的两倍。提出了一个模型来协调这些结果与先前分析的结果。
