Ishima R, Yamasaki K, Saito M, Nagayama K
Nagayama Protein Array Project, ERATO, JRDC, Tsukuba Research Consortium, Pilot Laboratory, Japan.
J Biomol NMR. 1995 Sep;6(2):217-20. doi: 10.1007/BF00211786.
Spectral densities of the 15N amide in Escherichia coli ribonuclease HI, obtained from NMR relaxation experiments, were compared with those calculated using a molecular dynamics (MD) simulation. All calculations and comparisons assumed that the auto-correlation function describing the internal motions of the molecule was independent of the auto-correlation function associated with overall rotational diffusion. Comparisons were limited to those residues for which the auto-correlation function of internal motions rapidly relaxed and reached a steady state within 205 ps. The results show the importance of frequency components as well as amplitudes of internal motions in order to obtain a meaningful comparison of MD simulations with NMR data.
通过核磁共振弛豫实验获得的大肠杆菌核糖核酸酶HI中15N酰胺的光谱密度，与使用分子动力学（MD）模拟计算得到的光谱密度进行了比较。所有计算和比较都假定，描述分子内部运动的自相关函数与与整体旋转扩散相关的自相关函数无关。比较仅限于那些内部运动自相关函数快速弛豫并在205皮秒内达到稳态的残基。结果表明，为了使MD模拟与核磁共振数据进行有意义的比较，频率成分以及内部运动的幅度都很重要。
