Kundu Sibsankar, Melton Julia S, Sorensen Dan C, Phillips George N
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
Biophys J. 2002 Aug;83(2):723-32. doi: 10.1016/S0006-3495(02)75203-X.
The dynamic behavior of proteins in crystals is examined by comparing theory and experiments. The Gaussian network model (GNM) and a simplified version of the crystallographic translation libration screw (TLS) model are used to calculate mean square fluctuations of C(alpha) atoms for a set of 113 proteins whose structures have been determined by x-ray crystallography. Correlation coefficients between the theoretical estimations and experiment are calculated and compared. The GNM method gives better correlation with experimental data than the rigid-body libration model and has the added benefit of being able to calculate correlations between the fluctuations of pairs of atoms. By incorporating the effect of neighboring molecules in the crystal the correlation is further improved.
通过比较理论与实验来研究晶体中蛋白质的动态行为。使用高斯网络模型（GNM）和晶体学平移振动螺旋（TLS）模型的简化版本，来计算113种蛋白质的α碳原子的均方波动，这些蛋白质的结构已通过X射线晶体学确定。计算并比较理论估计值与实验之间的相关系数。与刚体振动模型相比，GNM方法与实验数据的相关性更好，并且具有能够计算原子对波动之间相关性的额外优势。通过纳入晶体中相邻分子的影响，相关性进一步提高。
