Kidera A, Inaka K, Matsushima M, Go N
Protein Engineering Research Institute, Osaka, Japan.
J Mol Biol. 1992 May 20;225(2):477-86. doi: 10.1016/0022-2836(92)90933-b.
The dynamic structure of a protein, human lysozyme, is determined by the normal mode refinement of X-ray crystal structure. This method uses the normal modes of both internal and external motions to distinguish the real internal dynamics from the external terms such as lattice disorder, and gives an anisotropic and concerted picture of atomic fluctuations. The refinement is carried out with diffraction data of 5.0 to 1.8 A resolution, which are collected on an imaging plate. The results of the refinement show: (1) Debye-Waller factor consists of two parts, highly anisotropic internal fluctuations and almost isotropic external terms. The former is smaller than the latter by a factor of 0.72 in the scale of B-factor. Therefore, the internal dynamics cannot be recognized directly from the apparent electron density distribution. (2) The internal fluctuations show basically similar features as those predicted by the normal mode analysis, with almost the same amplitude and a similar level of anisotropy. (3) Correlations of fluctuations are detected between two lobes forming the active site cleft, which move simultaneously in opposite directions. This corresponds to the hinge-bending motion of lysozyme.
蛋白质人溶菌酶的动态结构是通过X射线晶体结构的正常模式精修来确定的。该方法利用内部和外部运动的正常模式，将真实的内部动力学与诸如晶格无序等外部因素区分开来，并给出原子涨落的各向异性和协同图像。精修是使用在成像板上收集的5.0至1.8埃分辨率的衍射数据进行的。精修结果表明：（1）德拜-瓦勒因子由两部分组成，高度各向异性的内部涨落和几乎各向同性的外部因素。在B因子尺度上，前者比后者小0.72倍。因此，不能直接从表观电子密度分布中识别内部动力学。（2）内部涨落显示出与正常模式分析预测的基本相似的特征，具有几乎相同的幅度和相似的各向异性水平。（3）在形成活性位点裂隙的两个叶之间检测到涨落的相关性，它们以相反方向同时移动。这对应于溶菌酶的铰链弯曲运动。
