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Refinement of the F-actin model against X-ray fiber diffraction data by the use of a directed mutation algorithm

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Lorenz,  Michael
Emeritus Group Biophysics, Max Planck Institute for Medical Research, Max Planck Society;
Department of Biomedical Optics, Max Planck Institute for Medical Research, Max Planck Society;

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Popp,  David
Max Planck Institute for Medical Research, Max Planck Society;

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Holmes,  Kenneth C.
Protein Cristallography XDS, Max Planck Institute for Medical Research, Max Planck Society;
Emeritus Group Biophysics, Max Planck Institute for Medical Research, Max Planck Society;
Muscle Research, Max Planck Institute for Medical Research, Max Planck Society;

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Citation

Lorenz, M., Popp, D., & Holmes, K. C. (1993). Refinement of the F-actin model against X-ray fiber diffraction data by the use of a directed mutation algorithm. Journal of Molecular Biology (London), 234(3), 826-836. doi:10.1006/jmbi.1993.1628.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0019-A9E9-9
Abstract
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 C alpha-positions of 3.2 A 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.