Harata K, Abe Y, Muraki M
National Institute of Bioscience and Human-Technology, Tsukuba, Ibaraki, Japan.
Proteins. 1998 Feb 15;30(3):232-43. doi: 10.1002/(sici)1097-0134(19980215)30:3<232::aid-prot3>3.0.co;2-m.
Crystal structures of turkey egg lysozyme (TEL) and human lysozyme (HL) were refined by full-matrix least-squares method using anisotropic temperature factors. The refinement converged at the conventional R-values of 0.104 (TEL) and 0.115 (HL) for reflections with Fo > 0 to the resolution of 1.12 A and 1.15 A, respectively. The estimated r.m.s. coordinate errors for protein atoms were 0.031 A (TEL) and 0.034 A (HL). The introduction of anisotropic temperature factors markedly reduced the R-value but did not significantly affect the main chain coordinates. The degree of anisotropy of atomic thermal motion has strong positive correlation with the square of distance from the molecular centroid. The ratio of the radial component of thermal ellipsoid to the r.m.s. magnitude of three principal components has negative correlation with the distance from the molecular centroid, suggesting the domination of libration rather than breathing motion. The TLS model was applied to elucidate the characteristics of the rigid-body motion. The TLS tensors were determined by the least-squares fit to observed temperature factors. The profile of the magnitude of reproduced temperature factors by the TLS method well fitted to that of observed B(eqv). However, considerable disagreement was observed in the shape and orientation of thermal ellipsoid for atoms with large temperature factors, indicating the large contribution of local motion. The upper estimate of the external motion, 67% (TEL) and 61% (HL) of B(eqv), was deduced from the plot of the magnitude of TLS tensors determined for main chain atoms which were grouped into shells according to the distance from the center of libration. In the external motion, the translational portion is predominant and the contribution of libration and screw motion is relatively small. The internal motion, estimated by subtracting the upper estimate of the external motion from the observed temperature factor, is very similar between TEL and HL in spite of the difference in 54 of 130 amino acid residues and in crystal packing, being suggested to reflect the intrinsic internal motion of chicken-type lysozymes.
利用各向异性温度因子，通过全矩阵最小二乘法对火鸡卵溶菌酶（TEL）和人溶菌酶（HL）的晶体结构进行了精修。对于Fo > 0的反射，精修分别在分辨率为1.12 Å和1.15 Å时收敛于传统的R值0.104（TEL）和0.115（HL）。蛋白质原子的估计均方根坐标误差分别为0.031 Å（TEL）和0.034 Å（HL）。引入各向异性温度因子显著降低了R值，但对主链坐标没有显著影响。原子热运动的各向异性程度与到分子质心距离的平方呈强正相关。热椭球径向分量与三个主分量均方根大小的比值与到分子质心的距离呈负相关，表明主要是摆动而非呼吸运动。应用TLS模型来阐明刚体运动的特征。通过对观测到的温度因子进行最小二乘拟合来确定TLS张量。TLS方法重现的温度因子大小轮廓与观测到的B(eqv)轮廓拟合良好。然而，对于温度因子较大的原子，在热椭球的形状和取向上观察到相当大的差异，表明局部运动的贡献较大。根据到摆动中心的距离将主链原子分组为壳层，从为这些主链原子确定的TLS张量大小图中推断出外部运动的上限估计值，分别为B(eqv)的67%（TEL）和61%（HL）。在外部运动中，平移部分占主导，摆动和螺旋运动贡献相对较小。通过从观测到的温度因子中减去外部运动的上限估计值来估计内部运动，尽管130个氨基酸残基中有54个不同且晶体堆积不同，但TEL和HL之间的内部运动非常相似，这表明反映了鸡型溶菌酶的固有内部运动。
