A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
复制标题
对 NMR 数据的三种结构测定方法进行系统比较：对数据质量和数量的依赖。
DOI：
10.1007/bf01874815
复制
发表时间：
1992
影响因子：
2.7
通讯作者：
Jardetzky,O
中科院分区：
文献类型：
--
作者：
Liu,Y;Zhao,D;Altman,R;Jardetzky,O
我们系统地研究了NMR蛋白质结构的质量如何取决于（1）NOE距离约束的数量。(2)它们的假定精度，（3）结构计算方法和（4）蛋白质的大小。距离约束的测试集已来自于crambin（5 kDa）和葡萄球菌核酸酶（17 kDa）的晶体结构。比较了三种结构计算方法：距离几何法（DGEOM）、约束分子动力学法（XPLOR）和双迭代卡尔曼滤波法（DIKF）。这三种方法都能在所有测试条件下再现起始结构的一般特征。在许多情况下，所计算的结构的表观精度（如通过与平均值的RMS色散所测量的）大于其准确度（如通过平均结构与起始晶体结构的RMS偏差所测量的）。与参考结构的全局RMS偏差随着约束数目的增加而呈指数下降，并且在使用所有潜在约束的约30%之后，误差渐近地接近极限值。增加约束的假设精度与增加约束数量具有相同的定性效果。对于相当数量的约束/残基，无论计算方法如何，计算结构的精度对于较大的蛋白质小于较小的蛋白质。由约束分子动力学计算的平均结构的精度大于由纯几何方法（DGEOM和DIKF）获得的结构。
We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints. (2) their assumed precision, (3) the method of structure calculation and (4) the size of the protein. The test sets of distance constraints have been derived from the crystal structures of crambin (5 kDa) and staphylococcal nuclease (17 kDa). Three methods of structure calculation have been compared: Distance Geometry (DGEOM), Restrained Molecular Dynamics (XPLOR) and the Double Iterated Kalman Filter (DIKF). All three methods can reproduce the general features of the starting structure under all conditions tested. In many instances the apparent precision of the calculated structure (as measured by the RMS dispersion from the average) is greater than its accuracy (as measured by the RMS deviation of the average structure from the starting crystal structure). The global RMS deviations from the reference structures decrease exponentially as the number of constraints is increased, and after using about 30% of all potential constraints, the crrors asymptotically approach a limiting value. Increasing the assumed precision of the constraints has the same qualitative effect as increasing the number of constraints. For comparable numbers of constraints/residue, the precision of the calculated structure is less for the larger than for the smaller protein, regardless of the method of calculation. The accuracy of the average structure calculated by Restrained Molecular Dynamics is greater than that of structures obtained by purely geometric methods (DGEOM and DIKF).