Harata K, Abe Y, Muraki M
Biomolecules Department, National Institute of Bioscience and Human-Technology, 1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
J Mol Biol. 1999 Mar 26;287(2):347-58. doi: 10.1006/jmbi.1999.2598.
The low temperature form of human alpha-lactalbumin (HAL) was crystallized from a 2H2O solution and its structure was refined to the R value of 0.119 at 1.15 A resolution by the full-matrix least-squares method. Average estimated standard deviations of atomic parameters for non-hydrogen atoms were 0.038 A for coordinates and 0.044 A2 for anisotropic temperature factors (Uij). The magnitude of equivalent isotropic temperature factors (Ueqv) was highly correlated with the distance from the molecular centroid and fitted to a quadratic equation as a function of atomic coordinates. The atomic thermal motion was rather isotropic in the core region and the anisotropy increased towards the molecular surface. The statistical analysis revealed the out-of-plane motion of main-chain oxygen atoms, indicating that peptide groups are in rotational vibration around a Calpha.Calpha axis. The TLS model, which describes the rigid-body motion in terms of translation, libration, and screw motions, was adopted for the evaluation of the molecular motion and the TLS parameters were determined by the least-squares fit to Uij. The reproduced Ueqvcal from the TLS parameters was in fair agreement with observed Ueqv, but differences were found in regions of residues, 5-22, 44-48, 70-75, and 121-123, where Ueqv was larger than Ueqvcal because of large local motions. To evaluate the internal motion of HAL, the contribution of the rigid-body motion was determined to be 42.4 % of Ueqv in magnitude, which was the highest estimation to satisfy the condition that the Uijint tensors of the internal motion have positive eigen values. The internal motion represented with atomic thermal ellipsoids clearly showed local motions different from those observed in chicken-type lysozymes which have a backbone structure very similar to HAL. The result indicates that the internal motion is closely related to biological function of proteins.
人α-乳白蛋白（HAL）的低温形式从2H2O溶液中结晶出来，其结构通过全矩阵最小二乘法在1.15 Å分辨率下精修至R值为0.119。非氢原子的原子参数平均估计标准偏差，坐标为0.038 Å，各向异性温度因子（Uij）为0.044 Å2。等效各向同性温度因子（Ueqv）的大小与距分子质心的距离高度相关，并拟合为作为原子坐标函数的二次方程。原子热运动在核心区域相当各向同性，并且各向异性朝着分子表面增加。统计分析揭示了主链氧原子的面外运动，表明肽基团围绕Cα.Cα轴进行旋转振动。采用描述刚体运动的平移、摆动和螺旋运动的TLS模型来评估分子运动，并通过对Uij的最小二乘拟合确定TLS参数。从TLS参数再现的Ueqvcal与观察到的Ueqv相当一致，但在残基5 - 22、44 - 48、70 - 75和121 - 123区域发现差异，其中由于局部运动大，Ueqv大于Ueqvcal。为了评估HAL的内部运动，确定刚体运动的贡献在大小上占Ueqv的42.4%，这是满足内部运动的Uijint张量具有正特征值条件的最高估计。用原子热椭球表示的内部运动清楚地显示出与具有与HAL非常相似的主链结构的鸡型溶菌酶中观察到的局部运动不同的局部运动。结果表明内部运动与蛋白质的生物学功能密切相关。
