REFINEMENT OF THE F-ACTIN MODEL AGAINST X-RAY FIBER DIFFRACTION DATA BY THE USE OF A DIRECTED MUTATION ALGORITHM

被引:467
作者
LORENZ, M
POPP, D
HOLMES, KC
机构
[1] Max-Planck Institut für medizinisehe Forschung, Abteilung Biophysik, D-69120 Heidelberg
关键词
X-RAY FIBER DIFFRACTION; ACTIN STRUCTURE; MONTE-CARLO METHOD; PHALLOIDIN; MOLECULAR DYNAMICS;
D O I
10.1006/jmbi.1993.1628
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 mushroom Amanita 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. © 1993 Academic Press Limited.
引用
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页码:826 / 836
页数:11
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