REFINEMENT OF THE F-ACTIN MODEL AGAINST X-RAY FIBER DIFFRACTION DATA BY THE USE OF A DIRECTED MUTATION ALGORITHM
REFINEMENT OF THE F-ACTIN MODEL AGAINST X-RAY FIBER DIFFRACTION DATA BY THE USE OF A DIRECTED MUTATION ALGORITHM
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DOI：
10.1006/jmbi.1993.1628
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发表时间：
1993-12-05
影响因子：
5.6
通讯作者：
HOLMES, KC
中科院分区：
文献类型：
--
作者：
LORENZ, M;POPP, D;HOLMES, KC
F-肌动蛋白模型已经通过定向变异算法进行了精细化，这是一种迭代过程，它结合了在每个周期选择要精炼的子结构域的蒙特卡罗方法和非线性最小二乘例程，以获得对特定选定结构域的最佳拟合。以G-肌动蛋白晶体结构为起始模型。实验数据是由取向F-肌动蛋白凝胶的X射线纤维衍射图获得的。经过250个循环后，我们能够获得与实验衍射图几乎完美匹配的计算衍射图以及合理的立体化学，包括肌动蛋白单体与R.M.S的分子间相互作用。3·2ä的Cα位置从晶体坐标移位。用X-PLOR程序用分子动力学方法计算了亚基间堆积的立体化学。此外，还可以确定蘑菇鹅膏菌中的环状七肽--鬼伞菌素的结合部位。此外，我们能够确定F-肌动蛋白在使用和不使用鬼臼毒素的情况下的结构差异。该方法具有较强的鲁棒性和较高的收敛速度。
The F-actin model has been refined by a Directed Mutation Algorithm, a reiterative procedure which combines a Monte-Carlo method of selecting subdomains to be refined at each cycle with a non-linear least-squares routine to get the best fit for the particular selected domains. The G-actin crystal structure was used as a starting model. The experimental data were obtained by X-ray fiber diffraction patterns from oriented F-actin gels. After 250 cycles we were able to obtain an almost perfect fit of the calculated diffraction pattern to the experimental diffraction pattern as well as a reasonable stereochemistry including intermolecular interactions of the actin monomers with an r.m.s. shift in the Cα-positions of 3·2 Å from the crystal coordinates. The stereochemistry of the intersubunit packing was calculated by molecular dynamics using the program X-PLOR. In addition, the binding site of phalloidin, a cyclic heptapeptide from the mushroomAmanita phalloides, could be determined. Furthermore, we were able to determine differences in the structures of F-actin with and without phalloidin. The method proved itself robust and showed a high degree of convergence.