Ichiye T, Karplus M
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Biochemistry. 1988 May 3;27(9):3487-97. doi: 10.1021/bi00409a054.
The effects of anisotropy and anharmonicity of the atomic fluctuations on the results of crystallographic refinement of proteins are examined. Atomic distribution functions from a molecular dynamics simulation for lysozyme are introduced into a real-space (electron density) refinement procedure for individual atoms. Several models for the atomic probability distributions are examined. When isotropic, harmonic motion is assumed, the largest discrepancies between the true first moments (means) and second moments (B factors) of the positions calculated from the dynamics and the fitted values occur for probability densities with multiple peaks. The refined mean is at the center of the largest peak, and the refined B factor is slightly larger than that of the largest peak, unless the distance between the peaks is small compared to the peak width. The resulting values are often significantly different from the true first and second moments of the distribution. To improve the results, alternate conformations, rather than anharmonic corrections, should be included.
研究了原子涨落的各向异性和非简谐性对蛋白质晶体学精修结果的影响。将溶菌酶分子动力学模拟得到的原子分布函数引入到单个原子的实空间（电子密度）精修过程中。研究了几种原子概率分布模型。当假设为各向同性的简谐运动时，对于具有多个峰的概率密度，由动力学计算得到的位置的真实一阶矩（均值）和二阶矩（B因子）与拟合值之间的最大差异出现。精修后的均值位于最大峰的中心，精修后的B因子略大于最大峰的B因子，除非峰之间的距离与峰宽相比很小。所得值通常与分布的真实一阶和二阶矩有显著差异。为了改善结果，应纳入交替构象，而不是非简谐校正。
