Kidera A, Go N
Protein Engineering Research Institute, Osaka, Japan.
J Mol Biol. 1992 May 20;225(2):457-75. doi: 10.1016/0022-2836(92)90932-a.
A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In this model, the atomic fluctuations are treated as anisotropic and concerted. The normal modes of the external motion (TLS model) are also introduced to cover the factors other than the internal fluctuations, such as the lattice disorder and diffusion. A program for the normal mode refinement (NM-REF) has been developed. The method has first been tested against simulated diffraction data for human lysozyme calculated by a Monte Carlo simulation. Applications of the method have demonstrated that the normal mode refinement has: (1) improved the fitting to the diffraction data, even with fewer adjustable parameters; (2) distinguished internal fluctuations from external ones; (3) determined anisotropic thermal factors; and (4) identified concerted fluctuations in the protein molecule.
提出了一种用于X射线晶体学的动态结构精修方法，称为正常模式精修。德拜-瓦勒因子根据低频正常模式展开，其振幅和本征向量在晶体学精修过程中通过实验进行优化。在该模型中，原子涨落被视为各向异性且协同的。还引入了外部运动的正常模式（TLS模型），以涵盖除内部涨落之外的其他因素，如晶格无序和扩散。已经开发了一个用于正常模式精修的程序（NM-REF）。该方法首先针对通过蒙特卡罗模拟计算的人溶菌酶模拟衍射数据进行了测试。该方法的应用表明，正常模式精修具有：（1）即使可调参数较少，也能改善对衍射数据的拟合；（2）区分内部涨落和外部涨落；（3）确定各向异性热因子；（4）识别蛋白质分子中的协同涨落。
